Daily Papers

The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor generalization due to limited supervised data. In this paper, we propose to learn protein-ligand binding representation in a self-supervised learning manner. Different from existing pre-training approaches which treat proteins and ligands individually, we emphasize to discern the intricate binding patterns from fine-grained interactions. Specifically, this self-supervised learning problem is formulated as a prediction of the conclusive binding complex structure given a pocket and ligand with a Transformer based interaction module, which naturally emulates the binding process. To ensure the representation of rich binding information, we introduce two pre-training tasks, i.e.~atomic pairwise distance map prediction and mask ligand reconstruction, which comprehensively model the fine-grained interactions from both structure and feature space. Extensive experiments have demonstrated the superiority of our method across various binding tasks, including protein-ligand affinity prediction, virtual screening and protein-ligand docking.

CLIP (Contrastive Language-Image Pretraining) has become a popular choice for various downstream tasks. However, recent studies have questioned its ability to represent compositional concepts effectively. These works suggest that CLIP often acts like a bag-of-words (BoW) model, interpreting images and text as sets of individual concepts without grasping the structural relationships. In particular, CLIP struggles to correctly bind attributes to their corresponding objects when multiple objects are present in an image or text. In this work, we investigate why CLIP exhibits this BoW-like behavior. We find that the correct attribute-object binding information is already present in individual text and image modalities. Instead, the issue lies in the cross-modal alignment, which relies on cosine similarity. To address this, we propose Linear Attribute Binding CLIP or LABCLIP. It applies a linear transformation to text embeddings before computing cosine similarity. This approach significantly improves CLIP's ability to bind attributes to correct objects, thereby enhancing its compositional understanding.

To correctly use in-context information, language models (LMs) must bind entities to their attributes. For example, given a context describing a "green square" and a "blue circle", LMs must bind the shapes to their respective colors. We analyze LM representations and identify the binding ID mechanism: a general mechanism for solving the binding problem, which we observe in every sufficiently large model from the Pythia and LLaMA families. Using causal interventions, we show that LMs' internal activations represent binding information by attaching binding ID vectors to corresponding entities and attributes. We further show that binding ID vectors form a continuous subspace, in which distances between binding ID vectors reflect their discernability. Overall, our results uncover interpretable strategies in LMs for representing symbolic knowledge in-context, providing a step towards understanding general in-context reasoning in large-scale LMs.

We introduce AvatarPointillist, a novel framework for generating dynamic 4D Gaussian avatars from a single portrait image. At the core of our method is a decoder-only Transformer that autoregressively generates a point cloud for 3D Gaussian Splatting. This sequential approach allows for precise, adaptive construction, dynamically adjusting point density and the total number of points based on the subject's complexity. During point generation, the AR model also jointly predicts per-point binding information, enabling realistic animation. After generation, a dedicated Gaussian decoder converts the points into complete, renderable Gaussian attributes. We demonstrate that conditioning the decoder on the latent features from the AR generator enables effective interaction between stages and markedly improves fidelity. Extensive experiments validate that AvatarPointillist produces high-quality, photorealistic, and controllable avatars. We believe this autoregressive formulation represents a new paradigm for avatar generation, and we will release our code inspire future research.

We present a novel dual-head deep learning architecture for protein-protein interaction modeling that enables simultaneous prediction of binding affinity (ΔG) and mutation-induced affinity changes (ΔΔG) using only protein sequence information. Our approach offers a significant advancement over existing methods by employing specialized prediction heads that operate on a shared representation network, allowing direct and optimized prediction of both values. To ensure robust generalization, we integrated complementary datasets from SKEMPI v2 and PDBbind with a rigorous protein domain-based splitting strategy that prevents information leakage between training and validation sets. Our architecture combines transformer-based encoders with a novel cross-attention mechanism that processes paired protein sequences directly, without requiring any structural information. The network embeds input sequences using ESM3 representations, then employs a learnable sliced window embedding layer to manage variable-length sequences efficiently. A multi-layer transformer encoder with bidirectional self-attention captures intra-protein patterns, while cross-attention layers enable explicit modeling of interactions between protein pairs. This shared representation network feeds into separate ΔG and ΔΔG prediction heads, allowing task-specific optimization while leveraging common features. The model achieves ΔΔG validation of Pearson correlation at 0.485, while maintaining strong ΔG predictions (Pearson: 0.638). While existing approaches require protein structure data and binding interface information, our model eliminates these constraints. This provides a critical advantage for the numerous proteins with unknown structures or those challenging to crystallize, such as viral and intrinsically disordered proteins.

To advance models of multimodal context, we introduce a simple yet powerful neural architecture for data that combines vision and natural language. The "Bounding Boxes in Text Transformer" (B2T2) also leverages referential information binding words to portions of the image in a single unified architecture. B2T2 is highly effective on the Visual Commonsense Reasoning benchmark (https://visualcommonsense.com), achieving a new state-of-the-art with a 25% relative reduction in error rate compared to published baselines and obtaining the best performance to date on the public leaderboard (as of May 22, 2019). A detailed ablation analysis shows that the early integration of the visual features into the text analysis is key to the effectiveness of the new architecture. A reference implementation of our models is provided (https://github.com/google-research/language/tree/master/language/question_answering/b2t2).

Virtual Screening is an essential technique in the early phases of drug discovery, aimed at identifying promising drug candidates from vast molecular libraries. Recently, ligand-based virtual screening has garnered significant attention due to its efficacy in conducting extensive database screenings without relying on specific protein-binding site information. Obtaining binding affinity data for complexes is highly expensive, resulting in a limited amount of available data that covers a relatively small chemical space. Moreover, these datasets contain a significant amount of inconsistent noise. It is challenging to identify an inductive bias that consistently maintains the integrity of molecular activity during data augmentation. To tackle these challenges, we propose S-MolSearch, the first framework to our knowledge, that leverages molecular 3D information and affinity information in semi-supervised contrastive learning for ligand-based virtual screening. Drawing on the principles of inverse optimal transport, S-MolSearch efficiently processes both labeled and unlabeled data, training molecular structural encoders while generating soft labels for the unlabeled data. This design allows S-MolSearch to adaptively utilize unlabeled data within the learning process. Empirically, S-MolSearch demonstrates superior performance on widely-used benchmarks LIT-PCBA and DUD-E. It surpasses both structure-based and ligand-based virtual screening methods for AUROC, BEDROC and EF.

We introduce Hyperdimensional Graph Learner (HDGL), a novel method for node classification and link prediction in graphs. HDGL maps node features into a very high-dimensional space (hyperdimensional or HD space for short) using the injectivity property of node representations in a family of Graph Neural Networks (GNNs) and then uses HD operators such as bundling and binding to aggregate information from the local neighborhood of each node yielding latent node representations that can support both node classification and link prediction tasks. HDGL, unlike GNNs that rely on computationally expensive iterative optimization and hyperparameter tuning, requires only a single pass through the data set. We report results of experiments using widely used benchmark datasets which demonstrate that, on the node classification task, HDGL achieves accuracy that is competitive with that of the state-of-the-art GNN methods at substantially reduced computational cost; and on the link prediction task, HDGL matches the performance of DeepWalk and related methods, although it falls short of computationally demanding state-of-the-art GNNs.

Medical decision-making requires integrating diverse medical information, from imaging to clinical narratives. These medical modalities are often acquired in a many-to-many manner. However, current medical vision-language pretraining models (Med-VLPMs) fail to directly account for this many-to-many mapping in their model training and embeddings. To address this, we present Probabilistic Modality-Enhanced Diagnosis (ProbMED), a multimodal Med-VLPM that employs probabilistic contrastive learning to model distributions over embeddings rather than deterministic estimates. ProbMED aligns four distinct modalities -- chest X-rays, electrocardiograms, echocardiograms, and clinical text -- into a unified probabilistic embedding space. We use InfoNCE loss with Hellinger distance to integrate inter-modality distributions. We introduce a probabilistic synthetic sampling loss that captures modality-specific mean and variance to improve intra-modality binding. Extensive experiments across 13 medical datasets demonstrate that our model outperforms current Med-VLPMs in cross-modality retrieval, zero-shot, and few-shot classification. We also demonstrate the robust integration of multiple modalities for prognostication, showing improved intra- and inter-medical modality binding.

Though end-to-end neural approaches have recently been dominating NLP tasks in both performance and ease-of-use, they lack interpretability and robustness. We propose Binder, a training-free neural-symbolic framework that maps the task input to a program, which (1) allows binding a unified API of language model (LM) functionalities to a programming language (e.g., SQL, Python) to extend its grammar coverage and thus tackle more diverse questions, (2) adopts an LM as both the program parser and the underlying model called by the API during execution, and (3) requires only a few in-context exemplar annotations. Specifically, we employ GPT-3 Codex as the LM. In the parsing stage, with only a few in-context exemplars, Codex is able to identify the part of the task input that cannot be answerable by the original programming language, correctly generate API calls to prompt Codex to solve the unanswerable part, and identify where to place the API calls while being compatible with the original grammar. In the execution stage, Codex can perform versatile functionalities (e.g., commonsense QA, information extraction) given proper prompts in the API calls. Binder achieves state-of-the-art results on WikiTableQuestions and TabFact datasets, with explicit output programs that benefit human debugging. Note that previous best systems are all finetuned on tens of thousands of task-specific samples, while Binder only uses dozens of annotations as in-context exemplars without any training. Our code is available at https://github.com/HKUNLP/Binder .

Text-to-Image (T2I) models often suffer from issues such as semantic leakage, incorrect feature binding, and omissions of key concepts in the generated image. This work studies these phenomena by looking into the role of information flow between textual token representations. To this end, we generate images by applying the diffusion component on a subset of contextual token representations in a given prompt and observe several interesting phenomena. First, in many cases, a word or multiword expression is fully represented by one or two tokens, while other tokens are redundant. For example, in "San Francisco's Golden Gate Bridge", the token "gate" alone captures the full expression. We demonstrate the redundancy of these tokens by removing them after textual encoding and generating an image from the resulting representation. Surprisingly, we find that this process not only maintains image generation performance but also reduces errors by 21\% compared to standard generation. We then show that information can also flow between different expressions in a sentence, which often leads to semantic leakage. Based on this observation, we propose a simple, training-free method to mitigate semantic leakage: replacing the leaked item's representation after the textual encoding with its uncontextualized representation. Remarkably, this simple approach reduces semantic leakage by 85\%. Overall, our work provides a comprehensive analysis of information flow across textual tokens in T2I models, offering both novel insights and practical benefits.

Predicting drug-target interaction (DTI) is critical in the drug discovery process. Despite remarkable advances in recent DTI models through the integration of representations from diverse drug and target encoders, such models often struggle to capture the fine-grained interactions between drugs and protein, i.e. the binding of specific drug atoms (or substructures) and key amino acids of proteins, which is crucial for understanding the binding mechanisms and optimising drug design. To address this issue, this paper introduces a novel model, called FusionDTI, which uses a token-level Fusion module to effectively learn fine-grained information for Drug-Target Interaction. In particular, our FusionDTI model uses the SELFIES representation of drugs to mitigate sequence fragment invalidation and incorporates the structure-aware (SA) vocabulary of target proteins to address the limitation of amino acid sequences in structural information, additionally leveraging pre-trained language models extensively trained on large-scale biomedical datasets as encoders to capture the complex information of drugs and targets. Experiments on three well-known benchmark datasets show that our proposed FusionDTI model achieves the best performance in DTI prediction compared with seven existing state-of-the-art baselines. Furthermore, our case study indicates that FusionDTI could highlight the potential binding sites, enhancing the explainability of the DTI prediction.

Recent advances in vision language models (VLM) have been driven by contrastive models such as CLIP, which learn to associate visual information with their corresponding text descriptions. However, these models have limitations in understanding complex compositional scenes involving multiple objects and their spatial relationships. To address these challenges, we propose a novel approach that diverges from commonly used strategies, which rely on the design of hard-negative augmentations. Instead, our work focuses on integrating inductive biases into pre-trained CLIP-like models to improve their compositional understanding without using any additional hard-negatives. To that end, we introduce a binding module that connects a scene graph, derived from a text description, with a slot-structured image representation, facilitating a structured similarity assessment between the two modalities. We also leverage relationships as text-conditioned visual constraints, thereby capturing the intricate interactions between objects and their contextual relationships more effectively. Our resulting model not only enhances the performance of CLIP-based models in multi-object compositional understanding but also paves the way towards more accurate and sample-efficient image-text matching of complex scenes.

The economic value of inference depends on how capacity and task information are distributed across stages of AI production. We study these organizational margins using controlled workflow experiments on externally verified software-engineering tasks. In two matched resource panels, direct execution records the same success rate of 59.6 percent at logical-token ceilings of 12,000 and 24,000, while success under information-constrained planning rises from 36.2 to 51.2 percent. The planning disadvantage narrows by 15.0 percentage points (95 percent task-cluster bootstrap interval: 4.2 to 25.8). A strict read-only planning campaign varies whether the planner sees the task issue. At 12,000 tokens, issue access raises success by about 16 percentage points over issue-hidden planning. Compared with direct execution, task-informed planning is about 10 points lower at 12,000 tokens; at 24,000 tokens, it shows a 29.6-point advantage. In the resource panels, direct execution uses substantially less than either ceiling, while the planning workflow's binding rate falls from 46.2 to 0.8 percent and downstream execution accounts for 89.9 percent of the increase in total use. Scale determines the capacity available to a system; workflow and information structure shape the productive value

Multimodal learning has rapidly advanced visual understanding, largely via multimodal large language models (MLLMs) that use powerful LLMs as cognitive cores. In visual generation, however, these powerful core models are typically reduced to global text encoders for diffusion models, leaving most of their reasoning and planning ability unused. This creates a gap: current multimodal LLMs can parse complex layouts, attributes, and knowledge-intensive scenes, yet struggle to generate images or videos with equally precise and structured control. We propose MetaCanvas, a lightweight framework that lets MLLMs reason and plan directly in spatial and spatiotemporal latent spaces and interface tightly with diffusion generators. We empirically implement MetaCanvas on three different diffusion backbones and evaluate it across six tasks, including text-to-image generation, text/image-to-video generation, image/video editing, and in-context video generation, each requiring precise layouts, robust attribute binding, and reasoning-intensive control. MetaCanvas consistently outperforms global-conditioning baselines, suggesting that treating MLLMs as latent-space planners is a promising direction for narrowing the gap between multimodal understanding and generation.

Vision Language Models (VLMs) are designed to extend Large Language Models (LLMs) with visual capabilities, yet in this work we observe a surprising phenomenon: VLMs can outperform their underlying LLMs on purely text-only tasks, particularly in long-context information retrieval. To investigate this effect, we build a controlled synthetic retrieval task and find that a transformer trained only on text achieves perfect in-distribution accuracy but fails to generalize out of distribution, while subsequent training on an image-tokenized version of the same task nearly doubles text-only OOD performance. Mechanistic interpretability reveals that visual training changes the model's internal binding strategy: text-only training encourages positional shortcuts, whereas image-based training disrupts them through spatial translation invariance, forcing the model to adopt a more robust symbolic binding mechanism that persists even after text-only examples are reintroduced. We further characterize how binding strategies vary across training regimes, visual encoders, and initializations, and show that analogous shifts occur during pretrained LLM-to-VLM transitions. Our findings suggest that cross-modal training can enhance reasoning and generalization even for tasks grounded in a single modality.

Recently, human-computer interaction with various modalities has shown promising applications, like GPT-4o and Gemini. Given the foundational role of multimodal joint representation in understanding and generation pipelines, high-quality omni joint representations would be a step toward co-processing more diverse multimodal information. In this work, we present OmniBind, large-scale multimodal joint representation models ranging in scale from 7 billion to 30 billion parameters, which support 3D, audio, image, and language inputs. Due to the scarcity of data pairs across all modalities, instead of training large models from scratch, we propose remapping and binding the spaces of various pre-trained specialist models together. This approach enables "scaling up" by indirectly increasing the model parameters and the amount of seen data. To effectively integrate various spaces, we dynamically assign weights to different spaces by learning routers with two objectives: cross-modal overall alignment and language representation decoupling. Notably, since binding and routing spaces both only require lightweight networks, OmniBind is extremely training-efficient. Learning the largest 30B model requires merely unpaired unimodal data and approximately 3 days on a single 8-4090 node. Extensive experiments demonstrate the versatility and superiority of OmniBind as an omni representation model, highlighting its great potential for diverse applications, such as any-query and composable multimodal understanding.

Structure-Based Drug Design (SBDD) is a powerful strategy in computational drug discovery, utilizing three-dimensional protein structures to guide the design of molecules with improved binding affinity. However, capturing complex protein-ligand interactions across multiple scales remains challenging, as current methods often overlook the hierarchical organization and intrinsic asymmetry of these interactions. To address these limitations, we propose MSCoD, a novel Bayesian updating-based generative framework for structure-based drug design. In our MSCoD, Multi-Scale Information Bottleneck (MSIB) was developed, which enables semantic compression at multiple abstraction levels for efficient hierarchical feature extraction. Furthermore, a multi-head cooperative attention (MHCA) mechanism was developed, which employs asymmetric protein-to-ligand attention to capture diverse interaction types while addressing the dimensionality disparity between proteins and ligands. Empirical studies showed that MSCoD outperforms state-of-the-art methods on the benchmark dataset. Case studies on challenging targets such as KRAS G12D further demonstrate its applicability in real-world scenarios. The code and data underlying this article are freely available at https://github.com/xulong0826/MSCoD.

We report on an extraction of the polarized photoproduction cross-section for the proton, deuteron, neutron and ^3He, obtained by extrapolating electron scattering data to the real photon point. The data are from the Jefferson Lab E97-110 (^3He) and CLAS EG4 (proton and deuteron) experiments. Information on the neutron is extracted from the deuteron or ^3He data using the weak binding approximation. Comparing with data obtained with real photons, we find that while the proton results agree, our results on the deuteron and the neutron exhibit a larger strength in the Δ(1232) region, and are more consistent with isospin symmetry when compared with the proton results.

Electrical control of individual spins and photons in solids is key for quantum technologies, but scaling down to small, static systems remains challenging. Here, we demonstrate nanoscale electrical tuning of neutral and charged excitons in monolayer WSe2 using 1-nm carbon nanotube gates. Electrostatic simulations reveal a confinement radius below 15 nm, reaching the exciton Bohr radius limit for few-layer dielectric spacing. In situ photoluminescence spectroscopy shows gate-controlled conversion between neutral excitons, negatively charged trions, and biexcitons at 4 K. Important for quantum information processing applications, our measurements indicate gating of a local 2D electron gas in the WSe2 layer, coupled to photons via trion transitions with binding energies exceeding 20 meV. The ability to deterministically tune and address quantum emitters using nanoscale gates provides a pathway towards large-scale quantum optoelectronic circuits and spin-photon interfaces for quantum networking.

Answering spatial questions about multi-source scenes requires a model both to identify each sound and to locate it. Existing spatial audio-language models obtain spatial information from a dedicated encoder, which separates spatial and semantic processing into distinct feature spaces. We study whether a general-audio codec trained without spatial supervision can serve both purposes. A controlled layer-wise analysis shows that the frozen codec retains spatial information, with lateral cues carried by the difference between the two ear channels. This information, however, is not readily accessible: in dual-source scenes, a model trained on these features predicts left/right at chance and, on the remaining axes, assigns the detected direction to the queried and the non-queried source equally often. We attribute this failure to an audio--text information asymmetry, in which the audio contains both sources while the answer describes only the queried one. A controlled 2times2 experiment shows that either completing the scene description or exposing the inter-channel difference lifts left/right accuracy above chance, whereas binding directions to the queried source requires both. Building on these findings, AURA keeps the codec and the language model frozen and exceeds the strongest dedicated system on SpatialSoundQA by 10.31 points in dual-source direction accuracy, with about 40\% of its trainable parameters.

Large language models can generate interactive web interfaces, but reliable generative UI requires maintaining an executable artifact as user requests evolve. We introduce EvoGenUI-Bench, a benchmark for multi-turn interface maintenance comprising 150 five-turn tasks and 750 turns across three scenarios: information presentation, executable interaction, and tool-grounded external state. We execute generated artifacts in a browser and evaluate them using screenshots, source and DOM evidence, actor traces, and runtime logs. Beyond turn-level and episode-level success, we measure cross-turn retention with Adjacent Pass Retention. Across eight models, even the strongest achieves 74.9% Turn Pass while completing only 37.3% of five-turn episodes; APR further falls to 52.4% on tool-grounded tasks. Diagnostic analysis shows that presentation failures center on information architecture, interaction failures on derived-state propagation and affordance binding, and tool-grounded failures additionally involve external-state grounding and requirement decomposition. These results reframe generative UI evaluation from judging isolated outputs to testing whether interface behavior, derived state, external state, and assistant claims remain synchronized as the artifact evolves.

The growing sophistication of drug discovery calls for new advances in artificial intelligence (AI). Transformers have underpinned recent breakthroughs in AI, yet their conventional source-target attention mechanism can become a bottleneck for modeling complex interactions. Here, we introduce TopoLIA, a topology-inspired latent interaction attention mechanism that learns not only how much information should be exchanged between interaction partners, but also how that information should be transformed. Source-target-dependent attention is mediated through a compact latent interaction space, providing a structured representation of complex interactions. We further incorporate topological spectral representations to capture multiscale data geometry and extract algebraic relationships. TopoLIA thus incorporates topological principles into both data representation and neural network architecture. We demonstrate TopoLIA on protein-ligand binding, where persistent spectra encode multiscale topological and geometric patterns in 3D protein-ligand complexes, while latent interaction attention (LIA) enables structured, source-target-dependent information exchange. We pretrain TopoLIA by reconstructing masked multiscale spectral tokens from unlabeled molecular structures, yielding transferable structural representations without task-specific annotations. Across multiple scoring and docking benchmarks, TopoLIA achieves state-of-the-art performance and consistently outperforms its standard-attention counterpart. Rank analyses show that compact latent dimensions yield the best performance, supporting compact interaction spaces as an effective inductive bias for biomolecular learning. More broadly, LIA provides a general framework for structured, source-target-dependent information exchange that is applicable to diverse scientific and AI problems involving complex heterogeneous interactions.

In medicine, claims remain valid when supported by empirical evidence grounded in stable biological reality. In law, by contrast, truth is contingent, defined by jurisdiction, temporal validity, and the hierarchy of authoritative sources. The recent success of large language models (LLMs) on medical licensing examinations has encouraged an expectation of comparable legal competence. This analogy, however, obscures a critical distinction between domains. Unlike in medicine, legal performance often depends less on inference than on determining when external authority is applicable, valid, and non-contradictory. We introduce a comparative diagnostic framework evaluating legal reasoning against medical baselines along four axes (knowledge recall, grounding, confidence, and robustness), uncovering a sharp domain asymmetry when applied to a new benchmark that encodes temporal validity and normative relationships. While medical LLMs reliably benefit from verified sources, legal LLMs struggle to assess when retrieved citations are useful or misleading, exhibiting overconfidence in perturbed contexts and sensitivity to superficial formatting cues. Increased model scale amplifies this tendency, revealing that stronger instruction following can coincide with weaker resistance to authoritative perturbations. These findings show that LLMs treat law as unstructured text rather than binding precedent, while revealing a tendency to over-trust authoritative but false information when external references conflict with a model's internal knowledge.

The transformer architecture has revolutionized bioinformatics and driven progress in the understanding and prediction of the properties of biomolecules. Almost all research on large-scale biosequence transformers has focused on one domain at a time (single-omic), usually nucleotides or peptides. These models have seen incredible success in downstream tasks in each domain and have achieved particularly noteworthy breakthroughs in sequences of peptides and structural modeling. However, these single-omic models are naturally incapable of modeling multi-omic tasks, one of the most biologically critical being nucleotide-peptide interactions. We present our work training the first multi-omic nucleotide-peptide foundation models. We show that these multi-omic models (MOMs) can learn joint representations between various single-omic distributions that are emergently consistent with the Central Dogma of molecular biology, despite only being trained on unlabeled biosequences. We further demonstrate that MOMs can be fine-tuned to achieve state-of-the-art results on peptide-nucleotide interaction tasks, namely predicting the change in Gibbs free energy ({\Delta}G) of the binding interaction between a given oligonucleotide and peptide, as well as the effect on this binding interaction due to mutations in the oligonucleotide sequence ({\Delta}{\Delta}G). Remarkably, we show that multi-omic biosequence transformers emergently learn useful structural information without any prior structural training, allowing us to predict which peptide residues are most involved in the peptide-nucleotide binding interaction. Lastly, we provide evidence that multi-omic biosequence models are non-inferior to foundation models trained on single-omics distributions, suggesting a more generalized or foundational approach to building these models.

Structure-based drug design (SBDD) aims to discover drug candidates by finding molecules (ligands) that bind tightly to a disease-related protein (targets), which is the primary approach to computer-aided drug discovery. Recently, applying deep generative models for three-dimensional (3D) molecular design conditioned on protein pockets to solve SBDD has attracted much attention, but their formulation as probabilistic modeling often leads to unsatisfactory optimization performance. On the other hand, traditional combinatorial optimization methods such as genetic algorithms (GA) have demonstrated state-of-the-art performance in various molecular optimization tasks. However, they do not utilize protein target structure to inform design steps but rely on a random-walk-like exploration, which leads to unstable performance and no knowledge transfer between different tasks despite the similar binding physics. To achieve a more stable and efficient SBDD, we propose Reinforced Genetic Algorithm (RGA) that uses neural models to prioritize the profitable design steps and suppress random-walk behavior. The neural models take the 3D structure of the targets and ligands as inputs and are pre-trained using native complex structures to utilize the knowledge of the shared binding physics from different targets and then fine-tuned during optimization. We conduct thorough empirical studies on optimizing binding affinity to various disease targets and show that RGA outperforms the baselines in terms of docking scores and is more robust to random initializations. The ablation study also indicates that the training on different targets helps improve performance by leveraging the shared underlying physics of the binding processes. The code is available at https://github.com/futianfan/reinforced-genetic-algorithm.

The landscape of joint audio and video generation has been fundamentally transformed by the advent of powerful foundation models. Despite these strides, achieving cohesive multimodal customization for the simultaneous preservation of visual identities and vocal timbres across multiple interacting subjects remains largely underexplored. To bridge this gap, we present Omni-Customizer, an end-to-end framework targeted at the precise binding and seamless fusion of multimodal identity information. Specifically, we introduce an Omni-Context Fusion (OCF) module that effectively enriches the base textual prompt with dense, multimodal identity cues, along with a Masked TTS Cross-Attention (MTP-CA) mechanism explicitly designed to prevent the severe "speech leakage" problem. Within this architecture, we propose Semantic-Anchored Multimodal RoPE (SA-MRoPE) to anchor visual and audio reference tokens, along with TTS embeddings, to their corresponding semantic descriptions, enabling structured multimodal fusion and robust identity binding. Furthermore, we devise a comprehensive training strategy that incorporates interleaved audio-video scheduling to rapidly adapt the audio branch to multilingual scenarios without degrading foundational priors, and a progressive in-pair to cross-pair curriculum to facilitate the learning of high-level and robust identity features. Extensive experiments demonstrate that Omni-Customizer achieves state-of-the-art performance in dual-modal customized generation, excelling across visual identity similarity, timbre consistency, precise audio-video synchronization, and overall video-audio fidelity.

Powerful generative AI models of protein-ligand structure have recently been proposed, but few of these methods support both flexible protein-ligand docking and affinity estimation. Of those that do, none can directly model multiple binding ligands concurrently or have been rigorously benchmarked on pharmacologically relevant drug targets, hindering their widespread adoption in drug discovery efforts. In this work, we propose FlowDock, the first deep geometric generative model based on conditional flow matching that learns to directly map unbound (apo) structures to their bound (holo) counterparts for an arbitrary number of binding ligands. Furthermore, FlowDock provides predicted structural confidence scores and binding affinity values with each of its generated protein-ligand complex structures, enabling fast virtual screening of new (multi-ligand) drug targets. For the well-known PoseBusters Benchmark dataset, FlowDock outperforms single-sequence AlphaFold 3 with a 51% blind docking success rate using unbound (apo) protein input structures and without any information derived from multiple sequence alignments, and for the challenging new DockGen-E dataset, FlowDock outperforms single-sequence AlphaFold 3 and matches single-sequence Chai-1 for binding pocket generalization. Additionally, in the ligand category of the 16th community-wide Critical Assessment of Techniques for Structure Prediction (CASP16), FlowDock ranked among the top-5 methods for pharmacological binding affinity estimation across 140 protein-ligand complexes, demonstrating the efficacy of its learned representations in virtual screening. Source code, data, and pre-trained models are available at https://github.com/BioinfoMachineLearning/FlowDock.

Although text-to-image (T2I) models exhibit remarkable generation capabilities, they frequently fail to accurately bind semantically related objects or attributes in the input prompts; a challenge termed semantic binding. Previous approaches either involve intensive fine-tuning of the entire T2I model or require users or large language models to specify generation layouts, adding complexity. In this paper, we define semantic binding as the task of associating a given object with its attribute, termed attribute binding, or linking it to other related sub-objects, referred to as object binding. We introduce a novel method called Token Merging (ToMe), which enhances semantic binding by aggregating relevant tokens into a single composite token. This ensures that the object, its attributes and sub-objects all share the same cross-attention map. Additionally, to address potential confusion among main objects with complex textual prompts, we propose end token substitution as a complementary strategy. To further refine our approach in the initial stages of T2I generation, where layouts are determined, we incorporate two auxiliary losses, an entropy loss and a semantic binding loss, to iteratively update the composite token to improve the generation integrity. We conducted extensive experiments to validate the effectiveness of ToMe, comparing it against various existing methods on the T2I-CompBench and our proposed GPT-4o object binding benchmark. Our method is particularly effective in complex scenarios that involve multiple objects and attributes, which previous methods often fail to address. The code will be publicly available at https://github.com/hutaihang/ToMe.

Humans easily determine which color belongs to which shape in multi-object scenes, an ability known as concept binding. Vision-language embedding models such as CLIP struggle with binding: they recognize individual concepts but fail to represent which concepts form which objects. Although CLIP behaves like a bag-of-concepts model in cross-modal retrieval, object information is recoverable from its image and text embeddings separately. We study this tension through the binding function, which maps concepts to scene embeddings. We find that scene embeddings decompose additively into object representations, explaining why uni-modal probes can recover object information. However, CLIP's binding function is high-complexity, which likely prevents the image and text encoders from learning a shared binding mechanism that generalizes to unseen concept combinations. We then ask whether this limitation is fundamental. We show that it is not. In controlled transformer models trained from scratch, binding generalization emerges with sufficient data coverage. These models learn low-complexity binding functions characterized by multiplicative interactions between concepts, enabling systematic generalization. Code is publicly available at https://github.com/oshapio/binding-concepts-complexity.

Object binding, the brain's ability to bind the many features that collectively represent an object into a coherent whole, is central to human cognition. It groups low-level perceptual features into high-level object representations, stores those objects efficiently and compositionally in memory, and supports human reasoning about individual object instances. While prior work often imposes object-centric attention (e.g., Slot Attention) explicitly to probe these benefits, it remains unclear whether this ability naturally emerges in pre-trained Vision Transformers (ViTs). Intuitively, they could: recognizing which patches belong to the same object should be useful for downstream prediction and thus guide attention. Motivated by the quadratic nature of self-attention, we hypothesize that ViTs represent whether two patches belong to the same object, a property we term IsSameObject. We decode IsSameObject from patch embeddings across ViT layers using a similarity probe, which reaches over 90% accuracy. Crucially, this object-binding capability emerges reliably in self-supervised ViTs (DINO, MAE, CLIP), but markedly weaker in ImageNet-supervised models, suggesting that binding is not a trivial architectural artifact, but an ability acquired through specific pretraining objectives. We further discover that IsSameObject is encoded in a low-dimensional subspace on top of object features, and that this signal actively guides attention. Ablating IsSameObject from model activations degrades downstream performance and works against the learning objective, implying that emergent object binding naturally serves the pretraining objective. Our findings challenge the view that ViTs lack object binding and highlight how symbolic knowledge of "which parts belong together" emerges naturally in a connectionist system.

Emerging large-scale text-to-image generative models, e.g., Stable Diffusion (SD), have exhibited overwhelming results with high fidelity. Despite the magnificent progress, current state-of-the-art models still struggle to generate images fully adhering to the input prompt. Prior work, Attend & Excite, has introduced the concept of Generative Semantic Nursing (GSN), aiming to optimize cross-attention during inference time to better incorporate the semantics. It demonstrates promising results in generating simple prompts, e.g., ``a cat and a dog''. However, its efficacy declines when dealing with more complex prompts, and it does not explicitly address the problem of improper attribute binding. To address the challenges posed by complex prompts or scenarios involving multiple entities and to achieve improved attribute binding, we propose Divide & Bind. We introduce two novel loss objectives for GSN: a novel attendance loss and a binding loss. Our approach stands out in its ability to faithfully synthesize desired objects with improved attribute alignment from complex prompts and exhibits superior performance across multiple evaluation benchmarks. More videos and updates can be found on the project page https://sites.google.com/view/divide-and-bind.

The binding problem in human cognition, concerning how the brain represents and connects objects within a fixed network of neural connections, remains a subject of intense debate. Most machine learning efforts addressing this issue in an unsupervised setting have focused on slot-based methods, which may be limiting due to their discrete nature and difficulty to express uncertainty. Recently, the Complex AutoEncoder was proposed as an alternative that learns continuous and distributed object-centric representations. However, it is only applicable to simple toy data. In this paper, we present Rotating Features, a generalization of complex-valued features to higher dimensions, and a new evaluation procedure for extracting objects from distributed representations. Additionally, we show the applicability of our approach to pre-trained features. Together, these advancements enable us to scale distributed object-centric representations from simple toy to real-world data. We believe this work advances a new paradigm for addressing the binding problem in machine learning and has the potential to inspire further innovation in the field.

Retrieval is a fundamental task in multimodal systems: given an image or text query, the goal is to find the most relevant images or texts in a collection, often using a shared embedding space. Reliable retrieval requires these embeddings to capture not only which concepts are present, but also how they are composed. One key compositional challenge is attribute--object binding: encoding which attributes belong to which objects. Existing benchmarks provide a limited view of this capability, typically covering a subset of modality pairings, simple two-object swaps, or small attribute sets. Consequently, it remains unclear how robustly current models preserve attribute--object bindings across different modality pairings and more complex settings. We therefore introduce SABER, a controlled benchmark for evaluating attribute--object binding across all four image and text modality pairings, spanning diverse attribute types and scenes with up to ten objects. Evaluating models on SABER reveals substantial binding failures in both CLIP-style dual encoders and recent MLLM-based embedders. These findings motivate us to ask how binding can be improved efficiently. While multimodal supervision may be effective, collecting suitable images is difficult and costly. Text, on the other hand, is well suited to binding supervision: it is cheap to generate, supports a broader range of attributes and enables precisely controlled hard negatives. We thus finetune an MLLM-based embedder exclusively on synthetic attribute-binding text. Despite the absence of image supervision, the gains transfer to cross-modal and image--image retrieval while preserving general multimodal embedding performance. Our model achieves SOTA results on SABER while also improving on negation and instance-retrieval benchmarks, demonstrating broader benefits of our binding-focused supervision.

Recent diffusion-based video generation models have made significant progress in multi-reference image-conditioned video editing. However, existing methods still struggle to coordinate information from multiple visual sources accurately. We identify a critical deficiency in existing approaches. Existing editing instructions lack explicit reference relationships, and most multimodal large language models (MLLMs) cannot generate them reliably. To address this problem, we propose ReBind, a systematic framework that introduces semantic instructions with embedded reference tokens as the intermediate representation for multi-reference image-conditioned video editing. Our key insight is embedding reference tokens at semantic positions to eliminate ambiguity and establish precise bindings between visual attributes and their sources. We develop ReBind-Instruct, a specialized MLLM that learns to establish explicit bindings between visual attributes and their reference sources through a two-stage progressive scheme for precise reference relationships. We further develop ReBind-Edit, which enables lightweight adaptation of text-to-video models to coordinate multiple references by binding visual attributes to their designated sources. Extensive experiments demonstrate that ReBind substantially outperforms general-purpose MLLMs in instruction quality and achieves state-of-the-art performance among open-source methods on reference image conditioned video editing. Our project webpage: https://rebind-mrv2v.github.io/.

Protein-molecule virtual screening is increasingly cast as a problem of representation learning in a shared embedding space. Existing methods rely on dense holistic alignment, entangling invariant binding determinants with nuisance correlations and limiting transfer to new targets. It has been noted that binding in protein-molecule systems involves sparse cross-modality interactions: binding is governed by a small contact interface and a few decisive local interactions (e.g., hydrogen bonds, hydrophobic contacts, and salt bridges) rather than the global structures of the protein and molecule. We hypothesize that uncovering and leveraging sparse interaction patterns is critical for generalization beyond the training data, as these patterns are reusable and expected to improve performance across different scenarios. In this paper, we aim to identify and leverage sparse interaction patterns, and verify our hypothesis. Since the training data contain only observed binding pairs, we formalize this prior via a V-structure causal model under Heckman-style selection, and establish three theoretical results: (i) the latent concepts of interacting proteins and molecules are not identifiable without appropriate sparsity constraints; (ii) these concepts and their sparse interactions are component-wise identifiable under structural sparsity conditions; and (iii) a low-rank relaxation of these conditions yields subspace identifiability of the concepts and interactions. Inspired by these principles, we propose CausalBind with three implementation variants. Extensive experiments on DUD-E and LIT-PCBA benchmarks show that all variants consistently outperform strong retrieval baselines, with the largest gains on LIT-PCBA early enrichment, and further generalize to target- and scaffold-level out-of-distribution splits. Code is available at https://github.com/lokali/CausalBind.

We introduce Point-Bind, a 3D multi-modality model aligning point clouds with 2D image, language, audio, and video. Guided by ImageBind, we construct a joint embedding space between 3D and multi-modalities, enabling many promising applications, e.g., any-to-3D generation, 3D embedding arithmetic, and 3D open-world understanding. On top of this, we further present Point-LLM, the first 3D large language model (LLM) following 3D multi-modal instructions. By parameter-efficient fine-tuning techniques, Point-LLM injects the semantics of Point-Bind into pre-trained LLMs, e.g., LLaMA, which requires no 3D instruction data, but exhibits superior 3D and multi-modal question-answering capacity. We hope our work may cast a light on the community for extending 3D point clouds to multi-modality applications. Code is available at https://github.com/ZiyuGuo99/Point-Bind_Point-LLM.

What is it about human brains that allows us to reason symbolically whereas most other animals cannot? There is evidence that dynamic binding, the ability to combine neurons into groups on the fly, is necessary for symbolic thought, but there is also evidence that it is not sufficient. We propose that two kinds of hierarchical integration (integration of multiple role-bindings into multiplace predicates, and integration of multiple correspondences into structure mappings) are minimal requirements, on top of basic dynamic binding, to realize symbolic thought. We tested this hypothesis in a systematic collection of 17 simulations that explored the ability of cognitive architectures with and without the capacity for multi-place predicates and structure mapping to perform various kinds of tasks. The simulations were as generic as possible, in that no task could be performed based on any diagnostic features, depending instead on the capacity for multi-place predicates and structure mapping. The results are consistent with the hypothesis that, along with dynamic binding, multi-place predicates and structure mapping are minimal requirements for basic symbolic thought. These results inform our understanding of how human brains give rise to symbolic thought and speak to the differences between biological intelligence, which tends to generalize broadly from very few training examples, and modern approaches to machine learning, which typically require millions or billions of training examples. The results we report also have important implications for bio-inspired artificial intelligence.

Enterprises often own large collections of structured data in the form of large databases or an enterprise data lake. Such data collections come with limited metadata and strict access policies that could limit access to the data contents and, therefore, limit the application of classic retrieval and analysis solutions. As a result, there is a need for solutions that can effectively utilize the available metadata. In this paper, we study the problem of matching table metadata to a business glossary containing data labels and descriptions. The resulting matching enables the use of an available or curated business glossary for retrieval and analysis without or before requesting access to the data contents. One solution to this problem is to use manually-defined rules or similarity measures on column names and glossary descriptions (or their vector embeddings) to find the closest match. However, such approaches need to be tuned through manual labeling and cannot handle many business glossaries that contain a combination of simple as well as complex and long descriptions. In this work, we leverage the power of large language models (LLMs) to design generic matching methods that do not require manual tuning and can identify complex relations between column names and glossaries. We propose methods that utilize LLMs in two ways: a) by generating additional context for column names that can aid with matching b) by using LLMs to directly infer if there is a relation between column names and glossary descriptions. Our preliminary experimental results show the effectiveness of our proposed methods.

Text-conditioned image generation models often generate incorrect associations between entities and their visual attributes. This reflects an impaired mapping between linguistic binding of entities and modifiers in the prompt and visual binding of the corresponding elements in the generated image. As one notable example, a query like ``a pink sunflower and a yellow flamingo'' may incorrectly produce an image of a yellow sunflower and a pink flamingo. To remedy this issue, we propose SynGen, an approach which first syntactically analyses the prompt to identify entities and their modifiers, and then uses a novel loss function that encourages the cross-attention maps to agree with the linguistic binding reflected by the syntax. Specifically, we encourage large overlap between attention maps of entities and their modifiers, and small overlap with other entities and modifier words. The loss is optimized during inference, without retraining or fine-tuning the model. Human evaluation on three datasets, including one new and challenging set, demonstrate significant improvements of SynGen compared with current state of the art methods. This work highlights how making use of sentence structure during inference can efficiently and substantially improve the faithfulness of text-to-image generation.

Reality may establish that an outcome occurred without identifying which evolving procedure produced it or why. This distinction matters in production ML systems whose code, configuration, and artifacts change while external feedback accumulates. We examine it in a human-directed, agent-engineered quantitative trading system, using oracle to mean an external source of realized outcomes rather than a complete correctness specification. Across one year, the account gained and outperformed a broad market index, while annual alpha was not statistically distinguishable from zero under the main retrospective specification. Retrospectively selected subperiods include adverse relative performance and conditional candidate-level weakness under declared approximate references. Engineering records document changes during the episode, and complete recommendation-to-runtime binding is unavailable. The archive does not establish a common frozen instance or a unique cause. The case motivates an outcome--diagnosis gap: outcome evidence, evaluated-object identity, and causal explanation support distinct claims. We distinguish frozen instances, pre-specified adaptive procedures, and ad-hoc development; organize archive-relative claim identifiability and an evidence hierarchy; and propose a prospective production-binding protocol. An illustrative compatible-history example shows how factual binding can resolve a recommendation's referent without supplying its counterfactual effect. The protocol is proposed rather than prospectively validated. External feedback constrains outcome claims, while provenance and additional identification structure determine the resolution of diagnosis.

Unified multi-model representation spaces are the foundation of multimodal understanding and generation. However, the billions of model parameters and catastrophic forgetting problems make it challenging to further enhance pre-trained unified spaces. In this work, we propose FreeBind, an idea that treats multimodal representation spaces as basic units, and freely augments pre-trained unified space by integrating knowledge from extra expert spaces via "space bonds". Specifically, we introduce two kinds of basic space bonds: 1) Space Displacement Bond and 2) Space Combination Bond. Based on these basic bonds, we design Complex Sequential & Parallel Bonds to effectively integrate multiple spaces simultaneously. Benefiting from the modularization concept, we further propose a coarse-to-fine customized inference strategy to flexibly adjust the enhanced unified space for different purposes. Experimentally, we bind ImageBind with extra image-text and audio-text expert spaces, resulting in three main variants: ImageBind++, InternVL_IB, and InternVL_IB++. These resulting spaces outperform ImageBind on 5 audio-image-text downstream tasks across 9 datasets. Moreover, via customized inference, it even surpasses the advanced audio-text and image-text expert spaces.

Text-to-image diffusion models particularly Stable Diffusion, have revolutionized the field of computer vision. However, the synthesis quality often deteriorates when asked to generate images that faithfully represent complex prompts involving multiple attributes and objects. While previous studies suggest that blended text embeddings lead to improper attribute binding, few have explored this in depth. In this work, we critically examine the limitations of the CLIP text encoder in understanding attributes and investigate how this affects diffusion models. We discern a phenomenon of attribute bias in the text space and highlight a contextual issue in padding embeddings that entangle different concepts. We propose Magnet, a novel training-free approach to tackle the attribute binding problem. We introduce positive and negative binding vectors to enhance disentanglement, further with a neighbor strategy to increase accuracy. Extensive experiments show that Magnet significantly improves synthesis quality and binding accuracy with negligible computational cost, enabling the generation of unconventional and unnatural concepts.

Predicting how a drug-like molecule binds to a specific protein target is a core problem in drug discovery. An extremely fast computational binding method would enable key applications such as fast virtual screening or drug engineering. Existing methods are computationally expensive as they rely on heavy candidate sampling coupled with scoring, ranking, and fine-tuning steps. We challenge this paradigm with EquiBind, an SE(3)-equivariant geometric deep learning model performing direct-shot prediction of both i) the receptor binding location (blind docking) and ii) the ligand's bound pose and orientation. EquiBind achieves significant speed-ups and better quality compared to traditional and recent baselines. Further, we show extra improvements when coupling it with existing fine-tuning techniques at the cost of increased running time. Finally, we propose a novel and fast fine-tuning model that adjusts torsion angles of a ligand's rotatable bonds based on closed-form global minima of the von Mises angular distance to a given input atomic point cloud, avoiding previous expensive differential evolution strategies for energy minimization.

With most modern visualization tools, authors need to transform their data into tidy formats to create visualizations they want. Because this requires experience with programming or separate data processing tools, data transformation remains a barrier in visualization authoring. To address this challenge, we present a new visualization paradigm, concept binding, that separates high-level visualization intents and low-level data transformation steps, leveraging an AI agent. We realize this paradigm in Data Formulator, an interactive visualization authoring tool. With Data Formulator, authors first define data concepts they plan to visualize using natural languages or examples, and then bind them to visual channels. Data Formulator then dispatches its AI-agent to automatically transform the input data to surface these concepts and generate desired visualizations. When presenting the results (transformed table and output visualizations) from the AI agent, Data Formulator provides feedback to help authors inspect and understand them. A user study with 10 participants shows that participants could learn and use Data Formulator to create visualizations that involve challenging data transformations, and presents interesting future research directions.

Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary binding prediction and affinity regression. However, these evaluations provide limited evidence of whether models can localize binding sites or identify the non-covalent interactions underlying molecular recognition. To address this gap, we introduce InteractBind, a large-scale protein-ligand dataset comprising approximately 100k protein-ligand pairs, together with a benchmark for fine-grained evaluation. The core fine-grained task is that of binding-site localization, which uses protein-residue and ligand-atom interaction maps spanning six major types of non-covalent interactions to assess whether model-derived interaction maps localize binding sites. InteractBind further includes binding affinity and protein similarity-controlled splits to support realistic generalization assessment. Using InteractBind, we evaluate eight existing sequence-based and interaction-aware models, assessing binary binding prediction and binding-site localization. Results reveal limited binding-site localization despite strong binary binding prediction, with marked variation across non-covalent interaction types. Overall, InteractBind establishes a benchmark paradigm that encourages the development of more interpretable and physically grounded protein-ligand models.

Recent advances in text-to-image (T2I) generation have led to impressive visual results. However, these models still face significant challenges when handling complex prompt, particularly those involving multiple subjects with distinct attributes. Inspired by the human drawing process, which first outlines the composition and then incrementally adds details, we propose Detail++, a training-free framework that introduces a novel Progressive Detail Injection (PDI) strategy to address this limitation. Specifically, we decompose a complex prompt into a sequence of simplified sub-prompts, guiding the generation process in stages. This staged generation leverages the inherent layout-controlling capacity of self-attention to first ensure global composition, followed by precise refinement. To achieve accurate binding between attributes and corresponding subjects, we exploit cross-attention mechanisms and further introduce a Centroid Alignment Loss at test time to reduce binding noise and enhance attribute consistency. Extensive experiments on T2I-CompBench and a newly constructed style composition benchmark demonstrate that Detail++ significantly outperforms existing methods, particularly in scenarios involving multiple objects and complex stylistic conditions.

We present ImageBind-LLM, a multi-modality instruction tuning method of large language models (LLMs) via ImageBind. Existing works mainly focus on language and image instruction tuning, different from which, our ImageBind-LLM can respond to multi-modality conditions, including audio, 3D point clouds, video, and their embedding-space arithmetic by only image-text alignment training. During training, we adopt a learnable bind network to align the embedding space between LLaMA and ImageBind's image encoder. Then, the image features transformed by the bind network are added to word tokens of all layers in LLaMA, which progressively injects visual instructions via an attention-free and zero-initialized gating mechanism. Aided by the joint embedding of ImageBind, the simple image-text training enables our model to exhibit superior multi-modality instruction-following capabilities. During inference, the multi-modality inputs are fed into the corresponding ImageBind encoders, and processed by a proposed visual cache model for further cross-modal embedding enhancement. The training-free cache model retrieves from three million image features extracted by ImageBind, which effectively mitigates the training-inference modality discrepancy. Notably, with our approach, ImageBind-LLM can respond to instructions of diverse modalities and demonstrate significant language generation quality. Code is released at https://github.com/OpenGVLab/LLaMA-Adapter.

Traditional systems designed for task oriented dialog utilize knowledge present only in structured knowledge sources to generate responses. However, relevant information required to generate responses may also reside in unstructured sources, such as documents. Recent state of the art models such as HyKnow and SeKnow aimed at overcoming these challenges make limiting assumptions about the knowledge sources. For instance, these systems assume that certain types of information, such as a phone number, is always present in a structured knowledge base (KB) while information about aspects such as entrance ticket prices, would always be available in documents. In this paper, we create a modified version of the MutliWOZ-based dataset prepared by SeKnow to demonstrate how current methods have significant degradation in performance when strict assumptions about the source of information are removed. Then, in line with recent work exploiting pre-trained language models, we fine-tune a BART based model using prompts for the tasks of querying knowledge sources, as well as, for response generation, without making assumptions about the information present in each knowledge source. Through a series of experiments, we demonstrate that our model is robust to perturbations to knowledge modality (source of information), and that it can fuse information from structured as well as unstructured knowledge to generate responses.

Data selection for language models is often framed as balancing example quality and diversity. We argue that both are consequences of a more fundamental principle: selected examples should preserve the downstream query space induced by instructions, task signals, or retrieval needs. We present Greedy Information Projection (GIP), a query-aligned method that requires only candidate embeddings and a score signal from LLM judgments, metadata, or intrinsic geometry. GIP greedily selects examples whose embedding span explains the largest residual component of task/query scores, yielding a fast matching-pursuit selector. A Gaussian projection view connects this update to maximizing mutual information, equivalently minimizing the residual volume of the query subspace left unexplained by selected data; this explains how quality and diversity emerge from one objective. Empirically, GIP matches or surpasses full-data fine-tuning using small instruction and reasoning subsets, while pretraining and RAG passage-selection experiments show that the same residual principle transfers beyond supervised fine-tuning.

Humans can learn to operate the user interface (UI) of an application by reading an instruction manual or how-to guide. Along with text, these resources include visual content such as UI screenshots and images of application icons referenced in the text. We explore how to leverage this data to learn generic visio-linguistic representations of UI screens and their components. These representations are useful in many real applications, such as accessibility, voice navigation, and task automation. Prior UI representation models rely on UI metadata (UI trees and accessibility labels), which is often missing, incompletely defined, or not accessible. We avoid such a dependency, and propose Lexi, a pre-trained vision and language model designed to handle the unique features of UI screens, including their text richness and context sensitivity. To train Lexi we curate the UICaption dataset consisting of 114k UI images paired with descriptions of their functionality. We evaluate Lexi on four tasks: UI action entailment, instruction-based UI image retrieval, grounding referring expressions, and UI entity recognition.

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this challenge, with sampling-based and regression-based methods emerging as two prominent approaches. However, these methods have notable limitations. Sampling-based methods often suffer from low efficiency due to the need for generating multiple candidate structures for selection. On the other hand, regression-based methods offer fast predictions but may experience decreased accuracy. Additionally, the variation in protein sizes often requires external modules for selecting suitable binding pockets, further impacting efficiency. In this work, we propose FABind, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding. FABind incorporates a unique ligand-informed pocket prediction module, which is also leveraged for docking pose estimation. The model further enhances the docking process by incrementally integrating the predicted pocket to optimize protein-ligand binding, reducing discrepancies between training and inference. Through extensive experiments on benchmark datasets, our proposed FABind demonstrates strong advantages in terms of effectiveness and efficiency compared to existing methods. Our code is available at https://github.com/QizhiPei/FABind

We simplify space binding by focusing on two core components, a single encoder per modality and high-quality data; enabling training state-of-the-art models on a single GPU in a few hours as opposed to multiple days. We present EBind, an Easy, data-centric, and parameter-efficient method to Bind the embedding spaces of multiple contrastive models. We demonstrate that a simple 1.8B-parameter image-text-video-audio-3D model can outperform models 4 to 17x the size. The key to achieving this is a carefully curated dataset of three complementary data sources: i) 6.7M fully-automated multimodal quintuples sourced via SOTA retrieval models, ii) 1M diverse, semi-automated triples annotated by humans as negative, partial, or positive matches, and iii) 3.4M pre-existing captioned data items. We use 13 different evaluations to demonstrate the value of each data source. Due to limitations with existing benchmarks, we further introduce the first high-quality, consensus-annotated zero-shot classification benchmark between audio and PCs. In contrast to related work, we will open-source our code, model weights, and datasets.

A key component of in-context reasoning is the ability of language models (LMs) to bind entities for later retrieval. For example, an LM might represent "Ann loves pie" by binding "Ann" to "pie", allowing it to later retrieve "Ann" when asked "Who loves pie?" Prior research on short lists of bound entities found strong evidence that LMs implement such retrieval via a positional mechanism, where "Ann" is retrieved based on its position in context. In this work, we find that this mechanism generalizes poorly to more complex settings; as the number of bound entities in context increases, the positional mechanism becomes noisy and unreliable in middle positions. To compensate for this, we find that LMs supplement the positional mechanism with a lexical mechanism (retrieving "Ann" using its bound counterpart "pie") and a reflexive mechanism (retrieving "Ann" through a direct pointer). Through extensive experiments on nine models and ten binding tasks, we uncover a consistent pattern in how LMs mix these mechanisms to drive model behavior. We leverage these insights to develop a causal model combining all three mechanisms that estimates next token distributions with 95% agreement. Finally, we show that our model generalizes to substantially longer inputs of open-ended text interleaved with entity groups, further demonstrating the robustness of our findings in more natural settings. Overall, our study establishes a more complete picture of how LMs bind and retrieve entities in-context.

For an LLM to correctly respond to an instruction it must understand both the semantics and the domain (i.e., subject area) of a given task-instruction pair. However, syntax can also convey implicit information Recent work shows that syntactic templates -- frequent sequences of Part-of-Speech (PoS) tags -- are prevalent in training data and often appear in model outputs. In this work we characterize syntactic templates, domain, and semantics in task-instruction pairs. We identify cases of spurious correlations between syntax and domain, where models learn to associate a domain with syntax during training; this can sometimes override prompt semantics. Using a synthetic training dataset, we find that the syntactic-domain correlation can lower performance (mean 0.51 +/- 0.06) on entity knowledge tasks in OLMo-2 models (1B-13B). We introduce an evaluation framework to detect this phenomenon in trained models, and show that it occurs on a subset of the FlanV2 dataset in open (OLMo-2-7B; Llama-4-Maverick), and closed (GPT-4o) models. Finally, we present a case study on the implications for safety finetuning, showing that unintended syntactic-domain correlations can be used to bypass refusals in OLMo-2-7B Instruct and GPT-4o. Our findings highlight two needs: (1) to explicitly test for syntactic-domain correlations, and (2) to ensure syntactic diversity in training data, specifically within domains, to prevent such spurious correlations.

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

Retrieval augmented generation (RAG) is often used to fix hallucinations and provide up-to-date knowledge for large language models (LLMs). However, in cases when the LLM alone incorrectly answers a question, does providing the correct retrieved content always fix the error? Conversely, in cases where the retrieved content is incorrect, does the LLM know to ignore the wrong information, or does it recapitulate the error? To answer these questions, we systematically analyze the tug-of-war between a LLM's internal knowledge (i.e. its prior) and the retrieved information in settings when they disagree. We test GPT-4 and other LLMs on question-answering abilities across datasets with and without reference documents. As expected, providing the correct retrieved information fixes most model mistakes (94% accuracy). However, when the reference document is perturbed with increasing levels of wrong values, the LLM is more likely to recite the incorrect, modified information when its internal prior is weaker but is more resistant when its prior is stronger. Similarly, we also find that the more the modified information deviates from the model's prior, the less likely the model is to prefer it. These results highlight an underlying tension between a model's prior knowledge and the information presented in reference documents.

Language-model systems can separate contextual computation, persistent storage, and exact execution instead of updating all capabilities through one shared parameter system. We investigate FEM-ASM, a finite-element-method-inspired organization in which independently constructed document states and deterministic executable skills contribute typed proposals to a shared language-model state. An explicit residual operator reconciles proposals attached to common interface nodes. We evaluate this organization through controlled experiments and negative results rather than claiming a physical finite-element formulation of language. An attention-free Multi-Mesh prototype learns causal language modeling but does not establish competitive general capability. A versioned store contains 52,809 reconstructive memory elements near a 1.7-billion-floating-value budget; reconstruction is incomplete, with approximately 75\% token accuracy. Support-aware lexical indices make these elements addressable under provenance-controlled query construction. For executable arithmetic, positional result observations substantially improve neural rendering relative to a repeated global result vector, and output substitutions change the model's preferred answer. A bounded attachment demonstration further measures the effect of making selected evidence available, without establishing the utility of loading an entire multi-billion-value store. The results support a separation of storage, execution, and neural coordination, while identifying unresolved limitations in question-only retrieval, unrestricted answer generation, and end-to-end efficiency.

Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. In this paper, we present a novel generative model, BindGPT which uses a conceptually simple but powerful approach to create 3D molecules within the protein's binding site. Our model produces molecular graphs and conformations jointly, eliminating the need for an extra graph reconstruction step. We pretrain BindGPT on a large-scale dataset and fine-tune it with reinforcement learning using scores from external simulation software. We demonstrate how a single pretrained language model can serve at the same time as a 3D molecular generative model, conformer generator conditioned on the molecular graph, and a pocket-conditioned 3D molecule generator. Notably, the model does not make any representational equivariance assumptions about the domain of generation. We show how such simple conceptual approach combined with pretraining and scaling can perform on par or better than the current best specialized diffusion models, language models, and graph neural networks while being two orders of magnitude cheaper to sample.

When a user supplies a document and wants the answer drawn from it, a language model is expected to follow it even when it contradicts its parametric knowledge. Prior work has focused on making the model rely on context by steering activations, contrasting logits during decoding, or instructing it in plain language. We ask whether the document alone, with no instruction written into it and no access to the model at inference time, is enough. We optimize a document suffix by discrete token search, starting from the answer to a single question and extending the objective to a set of passages, to multi-hop questions that follow from the planted fact, and to later turns of a conversation. On counterfactual passages that contradict parametric knowledge of the model, the suffix flips nearly all items the model resists across three instruction-tuned model families, in most settings outperforms the decoding baseline and the strongest instruction we could write, and matches activation steering. Controls show that the suffix largely acts through the passage rather than injecting the answer, and a single suffix per model transfers to unseen passages. Each extended objective carries the effect to its target, so the objective, not only the document, sets how far the effect reaches.

Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, current molecular representation learning methods do not provide a comprehensive view of cell states under these perturbations and struggle to remove noise, hindering model generalization. We introduce the Information Alignment (InfoAlign) approach to learn molecular representations through the information bottleneck method in cells. We integrate molecules and cellular response data as nodes into a context graph, connecting them with weighted edges based on chemical, biological, and computational criteria. For each molecule in a training batch, InfoAlign optimizes the encoder's latent representation with a minimality objective to discard redundant structural information. A sufficiency objective decodes the representation to align with different feature spaces from the molecule's neighborhood in the context graph. We demonstrate that the proposed sufficiency objective for alignment is tighter than existing encoder-based contrastive methods. Empirically, we validate representations from InfoAlign in two downstream tasks: molecular property prediction against up to 19 baseline methods across four datasets, plus zero-shot molecule-morphology matching.

Subject-driven image generation is increasingly expected to support fine-grained control over multiple entities within a single image. In multi-reference workflows, users may provide several subject images, a background reference, and long, entity-indexed prompts to control multiple people within one scene. In this setting, a key failure mode is cross-subject attribute misbinding: attributes are preserved, edited, or transferred to the wrong subject. Existing benchmarks and metrics largely emphasize holistic fidelity or per-subject self-similarity, making such failures hard to diagnose. We introduce MultiBind, a benchmark built from real multi-person photographs. Each instance provides slot-ordered subject crops with masks and bounding boxes, canonicalized subject references, an inpainted background reference, and a dense entity-indexed prompt derived from structured annotations. We also propose a dimension-wise confusion evaluation protocol that matches generated subjects to ground-truth slots and measures slot-to-slot similarity using specialists for face identity, appearance, pose, and expression. By subtracting the corresponding ground-truth similarity matrices, our method separates self-degradation from true cross-subject interference and exposes interpretable failure patterns such as drift, swap, dominance, and blending. Experiments on modern multi-reference generators show that MultiBind reveals binding failures that conventional reconstruction metrics miss.

Large language models with instruction-following abilities have revolutionized the field of artificial intelligence. These models show exceptional generalizability to tackle various real-world tasks through their natural language interfaces. However, their performance heavily relies on high-quality exemplar data, which is often difficult to obtain. This challenge is further exacerbated when it comes to multimodal instruction following. We introduce TextBind, an almost annotation-free framework for empowering larger language models with the multi-turn interleaved multimodal instruction-following capabilities. Our approach requires only image-caption pairs and generates multi-turn multimodal instruction-response conversations from a language model. We release our dataset, model, and demo to foster future research in the area of multimodal instruction following.

Despite the critical need to align search targets with users' intention, retrievers often only prioritize query information without delving into the users' intended search context. Enhancing the capability of retrievers to understand intentions and preferences of users, akin to language model instructions, has the potential to yield more aligned search targets. Prior studies restrict the application of instructions in information retrieval to a task description format, neglecting the broader context of diverse and evolving search scenarios. Furthermore, the prevailing benchmarks utilized for evaluation lack explicit tailoring to assess instruction-following ability, thereby hindering progress in this field. In response to these limitations, we propose a novel benchmark,INSTRUCTIR, specifically designed to evaluate instruction-following ability in information retrieval tasks. Our approach focuses on user-aligned instructions tailored to each query instance, reflecting the diverse characteristics inherent in real-world search scenarios. Through experimental analysis, we observe that retrievers fine-tuned to follow task-style instructions, such as INSTRUCTOR, can underperform compared to their non-instruction-tuned counterparts. This underscores potential overfitting issues inherent in constructing retrievers trained on existing instruction-aware retrieval datasets.

Background. In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoption in bioinformatics due to their advantages for representing data in a generic graph format. For example, yummydata.org catalogs more than 60 knowledge graphs accessible through SPARQL, a technical query language. Although SPARQL allows powerful, expressive queries, even across physically distributed knowledge graphs, formulating such queries is a challenge for most users. Therefore, to guide users in retrieving the relevant data, many of these resources provide representative examples. These examples can also be an important source of information for machine learning, if a sufficiently large number of examples are provided and published in a common, machine-readable and standardized format across different resources. Findings. We introduce a large collection of human-written natural language questions and their corresponding SPARQL queries over federated bioinformatics knowledge graphs (KGs) collected for several years across different research groups at the SIB Swiss Institute of Bioinformatics. The collection comprises more than 1000 example questions and queries, including 65 federated queries. We propose a methodology to uniformly represent the examples with minimal metadata, based on existing standards. Furthermore, we introduce an extensive set of open-source applications, including query graph visualizations and smart query editors, easily reusable by KG maintainers who adopt the proposed methodology. Conclusions. We encourage the community to adopt and extend the proposed methodology, towards richer KG metadata and improved Semantic Web services.

Recent AI advances have enabled multi-modal systems to model and translate diverse information spaces. Extending beyond text and vision, we introduce OneProt, a multi-modal AI for proteins that integrates structural, sequence, alignment, and binding site data. Using the ImageBind framework, OneProt aligns the latent spaces of modality encoders along protein sequences. It demonstrates strong performance in retrieval tasks and surpasses state-of-the-art methods in various downstream tasks, including metal ion binding classification, gene-ontology annotation, and enzyme function prediction. This work expands multi-modal capabilities in protein models, paving the way for applications in drug discovery, biocatalytic reaction planning, and protein engineering.

Recently, prompt-tuning has achieved promising results for specific few-shot classification tasks. The core idea of prompt-tuning is to insert text pieces (i.e., templates) into the input and transform a classification task into a masked language modeling problem. However, for relation extraction, determining an appropriate prompt template requires domain expertise, and it is cumbersome and time-consuming to obtain a suitable label word. Furthermore, there exists abundant semantic and prior knowledge among the relation labels that cannot be ignored. To this end, we focus on incorporating knowledge among relation labels into prompt-tuning for relation extraction and propose a Knowledge-aware Prompt-tuning approach with synergistic optimization (KnowPrompt). Specifically, we inject latent knowledge contained in relation labels into prompt construction with learnable virtual type words and answer words. Then, we synergistically optimize their representation with structured constraints. Extensive experimental results on five datasets with standard and low-resource settings demonstrate the effectiveness of our approach. Our code and datasets are available in https://github.com/zjunlp/KnowPrompt for reproducibility.

Text prompting is an indirect interface for poster generation, requiring users to encode inherently two-dimensional composition intent into a one-dimensional sequence of words. We introduce a Spatial Canvas Interface that enables users to directly compose generation intent in space through four complementary binding types: semantic, identity, text, and pixel, together with Text Specifications for individual elements and global appearance. Based on this interface, we develop Compo, a poster generation model adapted from a pretrained image editing model to understand Spatial Canvas inputs and Text Specifications. Compo supports both direct inference, where users explicitly construct the canvas, and agentic mode, where a high-level request is automatically translated into a planned Spatial Canvas. To train Compo, we develop a scalable pipeline that automatically constructs supervision data for different binding types and their combinations, enabling efficient adaptation without training a specialized poster generator from scratch. We further introduce a benchmark that evaluates adherence to individual binding types and their joint composition. Experiments show that Compo achieves stronger compositional controllability than both general-purpose image generation models and dedicated poster generation systems while maintaining high visual quality. By decoupling intent specification from visual generation, our work shifts poster generation from prompting toward composing.

Task-oriented dialogue (TOD) systems are required to identify key information from conversations for the completion of given tasks. Such information is conventionally specified in terms of intents and slots contained in task-specific ontology or schemata. Since these schemata are designed by system developers, the naming convention for slots and intents is not uniform across tasks, and may not convey their semantics effectively. This can lead to models memorizing arbitrary patterns in data, resulting in suboptimal performance and generalization. In this paper, we propose that schemata should be modified by replacing names or notations entirely with natural language descriptions. We show that a language description-driven system exhibits better understanding of task specifications, higher performance on state tracking, improved data efficiency, and effective zero-shot transfer to unseen tasks. Following this paradigm, we present a simple yet effective Description-Driven Dialog State Tracking (D3ST) model, which relies purely on schema descriptions and an "index-picking" mechanism. We demonstrate the superiority in quality, data efficiency and robustness of our approach as measured on the MultiWOZ (Budzianowski et al.,2018), SGD (Rastogi et al., 2020), and the recent SGD-X (Lee et al., 2021) benchmarks.

This paper explores the relationship between the condition number of a neural network's weight tensor and the extent of information encoded by the associated processing unit, viewed through the lens of information theory. It argues that a high condition number, though not sufficient for effective knowledge encoding, may indicate that the unit has learned to selectively amplify and compress information. This intuition is formalized for linear units with Gaussian inputs, linking the condition number and the transformation's log-volume scaling factor to the characteristics of the output entropy and the geometric properties of the learned transformation. The analysis demonstrates that for a fixed weight norm, a concentrated distribution of singular values (high condition number) corresponds to reduced overall information transfer, indicating a specialized and efficient encoding strategy. Furthermore, the linear stage entropy bound provides an upper limit on post-activation information for contractive, element-wise nonlinearities, supporting the condition number as a scale-invariant proxy for encoding capacity in practical neural networks. An empirical case study applies these principles to guide selective fine-tuning of Large Language Models for both a new task and a new input modality. The experiments show that the proposed method, named KappaTune, effectively mitigates catastrophic forgetting. Unlike many existing catastrophic forgetting mitigation methods that rely on access to pre-training statistics, which are often unavailable, this selective fine-tuning approach offers a way to bypass this common requirement.

The de novo design of ligand-binding proteins with tailored functions is essential for advancing biotechnology and molecular medicine, yet existing AI approaches are limited by scarce protein-ligand complex data. To circumvent this data bottleneck, we leverage the abundant natural language descriptions characterizing protein-ligand interactions. Here, we introduce InstructPro, a family of generative models that design proteins following the guidance of natural language instructions and ligand formulas. InstructPro produces protein sequences consistent with specified function descriptions and ligand targets. To enable training and evaluation, we develop InstructProBench, a large-scale dataset of 9.6 million (function description, ligand, protein) triples. We train two model variants -- InstructPro-1B and InstructPro-3B -- that substantially outperform strong baselines. InstructPro-1B achieves an AlphaFold3 ipTM of 0.918 and a binding affinity of -8.764 on seen ligands, while maintaining robust performance in a zero-shot setting with scores of 0.869 and -6.713, respectively. These results are accompanied by novelty scores of 70.1% and 68.8%, underscoring the model's ability to generalize beyond the training set. Furthermore, the model yields a superior binding free energy of -20.9 kcal/mol and an average of 5.82 intermolecular hydrogen bonds, validating its proficiency in designing high-affinity ligand-binding proteins. Notably, scaling to InstructPro-3B further improves the zero-shot ipTM to 0.882, binding affinity to -6.797, and binding free energy to -25.8 kcal/mol, demonstrating clear performance gains associated with increased model capacity. These findings highlight the power of natural language-guided generative models to mitigate the data bottlenecks in traditional structure-based methods, significantly broadening the scope of de novo protein design.

Mathematical symbols and descriptions appear in various forms across document section boundaries without explicit markup. In this paper, we present a new large-scale dataset that emphasizes extracting symbols and descriptions in scientific documents. Symlink annotates scientific papers of 5 different domains (i.e., computer science, biology, physics, mathematics, and economics). Our experiments on Symlink demonstrate the challenges of the symbol-description linking task for existing models and call for further research effort in this area. We will publicly release Symlink to facilitate future research.

This document offers a detailed linguistic description of SNACS (Semantic Network of Adposition and Case Supersenses; Schneider et al., 2018), an inventory of 52 semantic labels ("supersenses") that characterize the use of adpositions and case markers at a somewhat coarse level of granularity, as demonstrated in the STREUSLE corpus (https://github.com/nert-nlp/streusle/ ; version 4.5 tracks guidelines version 2.6). Though the SNACS inventory aspires to be universal, this document is specific to English; documentation for other languages will be published separately. Version 2 is a revision of the supersense inventory proposed for English by Schneider et al. (2015, 2016) (henceforth "v1"), which in turn was based on previous schemes. The present inventory was developed after extensive review of the v1 corpus annotations for English, plus previously unanalyzed genitive case possessives (Blodgett and Schneider, 2018), as well as consideration of adposition and case phenomena in Hebrew, Hindi, Korean, and German. Hwang et al. (2017) present the theoretical underpinnings of the v2 scheme. Schneider et al. (2018) summarize the scheme, its application to English corpus data, and an automatic disambiguation task. Liu et al. (2021) offer an English Lexical Semantic Recognition tagger that includes SNACS labels in its output. This documentation can also be browsed alongside corpus data on the Xposition website (Gessler et al., 2022): http://www.xposition.org/

Information seeking is a fundamental requirement for humans. However, existing LLM agents rely heavily on open-web search, which exposes two fundamental weaknesses: online content is noisy and unreliable, and many real-world tasks require precise, domain-specific knowledge unavailable from the web. The emergence of the Model Context Protocol (MCP) now allows agents to interface with thousands of specialized tools, seemingly resolving this limitation. Yet it remains unclear whether agents can effectively leverage such tools -- and more importantly, whether they can integrate them with general-purpose search to solve complex tasks. Therefore, we introduce InfoMosaic-Bench, the first benchmark dedicated to multi-source information seeking in tool-augmented agents. Covering six representative domains (medicine, finance, maps, video, web, and multi-domain integration), InfoMosaic-Bench requires agents to combine general-purpose search with domain-specific tools. Tasks are synthesized with InfoMosaic-Flow, a scalable pipeline that grounds task conditions in verified tool outputs, enforces cross-source dependencies, and filters out shortcut cases solvable by trivial lookup. This design guarantees both reliability and non-triviality. Experiments with 14 state-of-the-art LLM agents reveal three findings: (i) web information alone is insufficient, with GPT-5 achieving only 38.2% accuracy and 67.5% pass rate; (ii) domain tools provide selective but inconsistent benefits, improving some domains while degrading others; and (iii) 22.4% of failures arise from incorrect tool usage or selection, highlighting that current LLMs still struggle with even basic tool handling.

We propose a simple Named Entity Linking system that can be trained from Wikidata only. This demonstrates the strengths and weaknesses of this data source for this task and provides an easily reproducible baseline to compare other systems against. Our model is lightweight to train, to run and to keep synchronous with Wikidata in real time.

The web provides a rich, open-domain environment with textual, structural, and spatial properties. We propose a new task for grounding language in this environment: given a natural language command (e.g., "click on the second article"), choose the correct element on the web page (e.g., a hyperlink or text box). We collected a dataset of over 50,000 commands that capture various phenomena such as functional references (e.g. "find who made this site"), relational reasoning (e.g. "article by john"), and visual reasoning (e.g. "top-most article"). We also implemented and analyzed three baseline models that capture different phenomena present in the dataset.

Multimodal agents use web and image tools to answer questions beyond their internal knowledge. Some search tasks use images mainly to identify an initial entity, then rely on text retrieval. These tasks offer limited insight into how agents connect information across images, objects, and search steps. We therefore focus on visual context management. This involves organizing and using visual information and linking it to other findings during search. Visually intensive tasks require agents to combine object appearance, local details, or spatial relations with external information. We introduce VisSearch-Bench, with 204 human-written tasks across 7 main domains and 25 subdomains. It covers Set-wise Visual Search, Sequential Visual Search, Hybrid Wide-Deep Search, Competitive Visual Disambiguation, and Visual-Structure-Guided Search. Each task provides a reference answer, traceable evidence, and scoring rules. Accuracy measures complete task success, while Process Score measures the correctness and completeness of individual results and subquestion answers. Across 16 multimodal models, the best system fully solves only 26.47% of tasks, even with search tools. These results highlight the challenge of linking visual evidence with search results to produce complete answers.

Entities are at the center of how we represent and aggregate knowledge. For instance, Encyclopedias such as Wikipedia are structured by entities (e.g., one per Wikipedia article). The ability to retrieve such entities given a query is fundamental for knowledge-intensive tasks such as entity linking and open-domain question answering. Current approaches can be understood as classifiers among atomic labels, one for each entity. Their weight vectors are dense entity representations produced by encoding entity meta information such as their descriptions. This approach has several shortcomings: (i) context and entity affinity is mainly captured through a vector dot product, potentially missing fine-grained interactions; (ii) a large memory footprint is needed to store dense representations when considering large entity sets; (iii) an appropriately hard set of negative data has to be subsampled at training time. In this work, we propose GENRE, the first system that retrieves entities by generating their unique names, left to right, token-by-token in an autoregressive fashion. This mitigates the aforementioned technical issues since: (i) the autoregressive formulation directly captures relations between context and entity name, effectively cross encoding both; (ii) the memory footprint is greatly reduced because the parameters of our encoder-decoder architecture scale with vocabulary size, not entity count; (iii) the softmax loss is computed without subsampling negative data. We experiment with more than 20 datasets on entity disambiguation, end-to-end entity linking and document retrieval tasks, achieving new state-of-the-art or very competitive results while using a tiny fraction of the memory footprint of competing systems. Finally, we demonstrate that new entities can be added by simply specifying their names. Code and pre-trained models at https://github.com/facebookresearch/GENRE.

We present an elegant and effective approach for addressing limitations in existing multi-label classification models by incorporating interaction matching, a concept shown to be useful for ad-hoc search result ranking. By performing soft n-gram interaction matching, we match labels with natural language descriptions (which are common to have in most multi-labeling tasks). Our approach can be used to enhance existing multi-label classification approaches, which are biased toward frequently-occurring labels. We evaluate our approach on two challenging tasks: automatic medical coding of clinical notes and automatic labeling of entities from software tutorial text. Our results show that our method can yield up to an 11% relative improvement in macro performance, with most of the gains stemming labels that appear infrequently in the training set (i.e., the long tail of labels).

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the L+M-24 dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, L+M-24 is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction.

In contrastive learning, the choice of ``view'' controls the information that the representation captures and influences the performance of the model. However, leading graph contrastive learning methods generally produce views via random corruption or learning, which could lead to the loss of essential information and alteration of semantic information. An anchor view that maintains the essential information of input graphs for contrastive learning has been hardly investigated. In this paper, based on the theory of graph information bottleneck, we deduce the definition of this anchor view; put differently, the anchor view with essential information of input graph is supposed to have the minimal structural uncertainty. Furthermore, guided by structural entropy, we implement the anchor view, termed SEGA, for graph contrastive learning. We extensively validate the proposed anchor view on various benchmarks regarding graph classification under unsupervised, semi-supervised, and transfer learning and achieve significant performance boosts compared to the state-of-the-art methods.

Natural language descriptions sometimes accompany visualizations to better communicate and contextualize their insights, and to improve their accessibility for readers with disabilities. However, it is difficult to evaluate the usefulness of these descriptions, and how effectively they improve access to meaningful information, because we have little understanding of the semantic content they convey, and how different readers receive this content. In response, we introduce a conceptual model for the semantic content conveyed by natural language descriptions of visualizations. Developed through a grounded theory analysis of 2,147 sentences, our model spans four levels of semantic content: enumerating visualization construction properties (e.g., marks and encodings); reporting statistical concepts and relations (e.g., extrema and correlations); identifying perceptual and cognitive phenomena (e.g., complex trends and patterns); and elucidating domain-specific insights (e.g., social and political context). To demonstrate how our model can be applied to evaluate the effectiveness of visualization descriptions, we conduct a mixed-methods evaluation with 30 blind and 90 sighted readers, and find that these reader groups differ significantly on which semantic content they rank as most useful. Together, our model and findings suggest that access to meaningful information is strongly reader-specific, and that research in automatic visualization captioning should orient toward descriptions that more richly communicate overall trends and statistics, sensitive to reader preferences. Our work further opens a space of research on natural language as a data interface coequal with visualization.

We propose a new method that allows an LLM to automatically pull in factual knowledge from a knowledge base during token generation. This means that (1)~factual knowledge in the LLM output can be updated without retraining the LLM, (2)~facts in the LLM output can be traced to the knowledge base for transparency and explainability, and (3)~smaller models can achieve the same factual accuracy as larger models. Our core idea is to train the model to produce special tokens that trigger a query to the knowledge base. Our experiments show that our method improves factual grounding in both short and long-form generation, and allows factual revisions to take effect through KB edits rather than parameter updates.

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein-ligand docking have recently been introduced, to date no prior works have systematically studied the behavior of the latest docking and structure prediction methods within the broadly applicable context of (1) using predicted (apo) protein structures for docking (e.g., for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (e.g., for enzyme design); and (3) having no prior knowledge of binding pockets (e.g., for generalization to unknown pockets). To enable a deeper understanding of docking methods' real-world utility, we introduce PoseBench, the first comprehensive benchmark for broadly applicable protein-ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein-ligand docking and protein-ligand structure prediction using both primary ligand and multi-ligand benchmark datasets, the latter of which we introduce for the first time to the DL community. Empirically, using PoseBench, we find that (1) DL co-folding methods generally outperform comparable conventional and DL docking baselines, yet popular methods such as AlphaFold 3 are still challenged by prediction targets with novel protein sequences; (2) certain DL co-folding methods are highly sensitive to their input multiple sequence alignments, while others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting novel or multi-ligand protein targets. Code, data, tutorials, and benchmark results are available at https://github.com/BioinfoMachineLearning/PoseBench.

Formulating selective information needs results in queries that implicitly specify set operations, such as intersection, union, and difference. For instance, one might search for "shorebirds that are not sandpipers" or "science-fiction films shot in England". To study the ability of retrieval systems to meet such information needs, we construct QUEST, a dataset of 3357 natural language queries with implicit set operations, that map to a set of entities corresponding to Wikipedia documents. The dataset challenges models to match multiple constraints mentioned in queries with corresponding evidence in documents and correctly perform various set operations. The dataset is constructed semi-automatically using Wikipedia category names. Queries are automatically composed from individual categories, then paraphrased and further validated for naturalness and fluency by crowdworkers. Crowdworkers also assess the relevance of entities based on their documents and highlight attribution of query constraints to spans of document text. We analyze several modern retrieval systems, finding that they often struggle on such queries. Queries involving negation and conjunction are particularly challenging and systems are further challenged with combinations of these operations.

As LLM agents decide on users' behalf which product to buy, which hotel to book, or which paper to cite, a preference for items from certain sources (the sites or services they come from) shapes what users receive and which sources are selected. We study source preference in end-to-end search with 12 agent models across three domains. Comparing items from different sources that satisfy the same requirements at the same position, we find that each model prefers some sources and avoids others in every domain, largely agreeing on which. This preference can outweigh how well items satisfy the request: an item satisfying one requirement fewer is selected about two-thirds of the time when it comes from a preferred source and the better one from a dispreferred source, but almost never in the reverse case. The information identifying an item's source affects selection by itself: hiding it weakens the preference, and relabeling an item with a preferred source raises its selection rate. We test two routes to this preference: training that rewards better items can make a source a shortcut for requirement satisfaction, and missing information can trigger preconceptions about the source. Supplying missing information or a prompt countering these preconceptions reduces source preference.

We demonstrate that LLMs may learn indicators of document usefulness and modulate their updates accordingly. We introduce random strings ("tags") as indicators of usefulness in a synthetic fine-tuning dataset. Fine-tuning on this dataset leads to implicit meta-learning (IML): in further fine-tuning, the model updates to make more use of text that is tagged as useful. We perform a thorough empirical investigation of this phenomenon, finding (among other things) that (i) it occurs in both pretrained LLMs and those trained from scratch, as well as on a vision task, and (ii) larger models and smaller batch sizes tend to give more IML. We also use probing to examine how IML changes the way models store knowledge in their parameters. Finally, we reflect on what our results might imply about capabilities, risks, and controllability of future AI systems. Our code can be found at https://github.com/krasheninnikov/internalization.

Recent advancements in text-to-image models, such as Stable Diffusion, have demonstrated their ability to synthesize visual images through natural language prompts. One approach of personalizing text-to-image models, exemplified by DreamBooth, fine-tunes the pre-trained model by binding unique text identifiers with a few images of a specific subject. Although existing fine-tuning methods have demonstrated competence in rendering images according to the styles of famous painters, it is still challenging to learn to produce images encapsulating distinct art styles due to abstract and broad visual perceptions of stylistic attributes such as lines, shapes, textures, and colors. In this paper, we introduce a new method, Single-StyleForge, for personalization. It fine-tunes pre-trained text-to-image diffusion models to generate diverse images in specified styles from text prompts. By using around 15-20 images of the target style, the approach establishes a foundational binding of a unique token identifier with a broad range of the target style. It also utilizes auxiliary images to strengthen this binding, resulting in offering specific guidance on representing elements such as persons in a target style-consistent manner. In addition, we present ways to improve the quality of style and text-image alignment through a method called Multi-StyleForge, which inherits the strategy used in StyleForge and learns tokens in multiple. Experimental evaluation conducted on six distinct artistic styles demonstrates substantial improvements in both the quality of generated images and the perceptual fidelity metrics, such as FID, KID, and CLIP scores.

Does semantic communication require a semantic information theory parallel to Shannon's information theory, or can Shannon's work be generalized for semantic communication? This paper advocates for the latter and introduces a semantic generalization of Shannon's information theory (G theory for short). The core idea is to replace the distortion constraint with the semantic constraint, achieved by utilizing a set of truth functions as a semantic channel. These truth functions enable the expressions of semantic distortion, semantic information measures, and semantic information loss. Notably, the maximum semantic information criterion is equivalent to the maximum likelihood criterion and similar to the Regularized Least Squares criterion. This paper shows G theory's applications to daily and electronic semantic communication, machine learning, constraint control, Bayesian confirmation, portfolio theory, and information value. The improvements in machine learning methods involve multilabel learning and classification, maximum mutual information classification, mixture models, and solving latent variables. Furthermore, insights from statistical physics are discussed: Shannon information is similar to free energy; semantic information to free energy in local equilibrium systems; and information efficiency to the efficiency of free energy in performing work. The paper also proposes refining Friston's minimum free energy principle into the maximum information efficiency principle. Lastly, it compares G theory with other semantic information theories and discusses its limitation in representing the semantics of complex data.

Information Extraction (IE) from text refers to the task of extracting structured knowledge from unstructured text. The task typically consists of a series of sub-tasks such as Named Entity Recognition and Relation Extraction. Sourcing entity and relation type specific training data is a major bottleneck in domains with limited resources such as biomedicine. In this work we present a slot filling approach to the task of biomedical IE, effectively replacing the need for entity and relation-specific training data, allowing us to deal with zero-shot settings. We follow the recently proposed paradigm of coupling a Tranformer-based bi-encoder, Dense Passage Retrieval, with a Transformer-based reading comprehension model to extract relations from biomedical text. We assemble a biomedical slot filling dataset for both retrieval and reading comprehension and conduct a series of experiments demonstrating that our approach outperforms a number of simpler baselines. We also evaluate our approach end-to-end for standard as well as zero-shot settings. Our work provides a fresh perspective on how to solve biomedical IE tasks, in the absence of relevant training data. Our code, models and datasets are available at https://github.com/ypapanik/biomedical-slot-filling.

Slot Filling (SF) is one of the sub-tasks of Spoken Language Understanding (SLU) which aims to extract semantic constituents from a given natural language utterance. It is formulated as a sequence labeling task. Recently, it has been shown that contextual information is vital for this task. However, existing models employ contextual information in a restricted manner, e.g., using self-attention. Such methods fail to distinguish the effects of the context on the word representation and the word label. To address this issue, in this paper, we propose a novel method to incorporate the contextual information in two different levels, i.e., representation level and task-specific (i.e., label) level. Our extensive experiments on three benchmark datasets on SF show the effectiveness of our model leading to new state-of-the-art results on all three benchmark datasets for the task of SF.

In many machine learning systems that jointly learn from multiple modalities, a core research question is to understand the nature of multimodal interactions: the emergence of new task-relevant information during learning from both modalities that was not present in either alone. We study this challenge of interaction quantification in a semi-supervised setting with only labeled unimodal data and naturally co-occurring multimodal data (e.g., unlabeled images and captions, video and corresponding audio) but when labeling them is time-consuming. Using a precise information-theoretic definition of interactions, our key contributions are the derivations of lower and upper bounds to quantify the amount of multimodal interactions in this semi-supervised setting. We propose two lower bounds based on the amount of shared information between modalities and the disagreement between separately trained unimodal classifiers, and derive an upper bound through connections to approximate algorithms for min-entropy couplings. We validate these estimated bounds and show how they accurately track true interactions. Finally, two semi-supervised multimodal applications are explored based on these theoretical results: (1) analyzing the relationship between multimodal performance and estimated interactions, and (2) self-supervised learning that embraces disagreement between modalities beyond agreement as is typically done.

Textual label names (descriptions) are typically semantically rich in many natural language understanding (NLU) tasks. In this paper, we incorporate the prompting methodology, which is widely used to enrich model input, into the label side for the first time. Specifically, we propose a Mask Matching method, which equips an input with a prompt and its label with another, and then makes predictions by matching their mask representations. We evaluate our method extensively on 8 NLU tasks with 14 datasets. The experimental results show that Mask Matching significantly outperforms its counterparts of fine-tuning and conventional prompt-tuning, setting up state-of-the-art performances in several datasets. Mask Matching is particularly good at handling NLU tasks with large label counts and informative label names. As pioneering efforts that investigate the label-side prompt, we also discuss open issues for future study.

In recent years, short Text Matching tasks have been widely applied in the fields ofadvertising search and recommendation. The difficulty lies in the lack of semantic information and word ambiguity caused by the short length of the text. Previous works have introduced complement sentences or knowledge bases to provide additional feature information. However, these methods have not fully interacted between the original sentence and the complement sentence, and have not considered the noise issue that may arise from the introduction of external knowledge bases. Therefore, this paper proposes a short Text Matching model that combines contrastive learning and external knowledge. The model uses a generative model to generate corresponding complement sentences and uses the contrastive learning method to guide the model to obtain more semantically meaningful encoding of the original sentence. In addition, to avoid noise, we use keywords as the main semantics of the original sentence to retrieve corresponding knowledge words in the knowledge base, and construct a knowledge graph. The graph encoding model is used to integrate the knowledge base information into the model. Our designed model achieves state-of-the-art performance on two publicly available Chinese Text Matching datasets, demonstrating the effectiveness of our model.

We provide here a dataset for tasks related to natural language understanding and natural language inference. The dataset contains logical puzzles in natural language from three domains: comparing puzzles, knighs and knaves, and zebra puzzles. Each puzzle is associated with the entire set of atomic questions that can be generated based on the relations and individuals occurring in the text. For each question we provide the correct answer: entailment, contradiction or ambiguity. The answer's correctness is verified against theorem provers. Good puzzles have two properties: (i) each piece of information is necessary and (ii) no unnecessary information is provided. These properties make puzzles interesting candidates for machine comprehension tasks.

Language model fine-tuning is essential for modern natural language processing, but is computationally expensive and time-consuming. Further, the effectiveness of fine-tuning is limited by the inclusion of training examples that negatively affect performance. Here we present a general fine-tuning method that we call information gain filtration for improving the overall training efficiency and final performance of language model fine-tuning. We define the information gain of an example as the improvement on a test metric after training on that example. A secondary learner is then trained to approximate this quantity. During fine-tuning, this learner selects informative examples and skips uninformative ones. We show that our method has consistent improvement across datasets, fine-tuning tasks, and language model architectures. For example, we achieve a median perplexity of 54.0 on a books dataset compared to 57.3 for standard fine-tuning. We present statistical evidence that offers insight into the improvements of our method over standard fine-tuning. The generality of our method leads us to propose a new paradigm for language model fine-tuning -- we encourage researchers to release pretrained secondary learners on common corpora to promote efficient and effective fine-tuning, thereby improving the performance and reducing the overall energy footprint of language model fine-tuning.

Natural language interfaces often require supervised data to translate user requests into programs, database queries, or other structured intent representations. During data collection, it can be difficult to anticipate and formalize the full range of user needs -- for example, in a system designed to handle simple requests (like find my meetings tomorrow or move my meeting with my manager to noon), users may also express more elaborate requests (like swap all my calls on Monday and Tuesday). We introduce an approach for equipping a simple language-to-code model to handle complex utterances via a process of hierarchical natural language decomposition. Our approach uses a pre-trained language model to decompose a complex utterance into a sequence of smaller natural language steps, then interprets each step using the language-to-code model. To test our approach, we collect and release DeCU -- a new NL-to-program benchmark to evaluate Decomposition of Complex Utterances. Experiments show that the proposed approach enables the interpretation of complex utterances with almost no complex training data, while outperforming standard few-shot prompting approaches.

Researchers often summarize their work in the form of posters. Posters provide a coherent and efficient way to convey core ideas from scientific papers. Generating a good scientific poster, however, is a complex and time consuming cognitive task, since such posters need to be readable, informative, and visually aesthetic. In this paper, for the first time, we study the challenging problem of learning to generate posters from scientific papers. To this end, a data-driven framework, that utilizes graphical models, is proposed. Specifically, given content to display, the key elements of a good poster, including panel layout and attributes of each panel, are learned and inferred from data. Then, given inferred layout and attributes, composition of graphical elements within each panel is synthesized. To learn and validate our model, we collect and make public a Poster-Paper dataset, which consists of scientific papers and corresponding posters with exhaustively labelled panels and attributes. Qualitative and quantitative results indicate the effectiveness of our approach.

Conditional graphic layout generation, which automatically maps user constraints to high-quality layouts, has attracted widespread attention today. Although recent works have achieved promising performance, the lack of versatility and data efficiency hinders their practical applications. In this work, we propose LayoutPrompter, which leverages large language models (LLMs) to address the above problems through in-context learning. LayoutPrompter is made up of three key components, namely input-output serialization, dynamic exemplar selection and layout ranking. Specifically, the input-output serialization component meticulously designs the input and output formats for each layout generation task. Dynamic exemplar selection is responsible for selecting the most helpful prompting exemplars for a given input. And a layout ranker is used to pick the highest quality layout from multiple outputs of LLMs. We conduct experiments on all existing layout generation tasks using four public datasets. Despite the simplicity of our approach, experimental results show that LayoutPrompter can compete with or even outperform state-of-the-art approaches on these tasks without any model training or fine-tuning. This demonstrates the effectiveness of this versatile and training-free approach. In addition, the ablation studies show that LayoutPrompter is significantly superior to the training-based baseline in a low-data regime, further indicating the data efficiency of LayoutPrompter. Our project is available at https://github.com/microsoft/LayoutGeneration/tree/main/LayoutPrompter.

This open access book provides a comprehensive overview of the state of the art in research and applications of Foundation Models and is intended for readers familiar with basic Natural Language Processing (NLP) concepts. Over the recent years, a revolutionary new paradigm has been developed for training models for NLP. These models are first pre-trained on large collections of text documents to acquire general syntactic knowledge and semantic information. Then, they are fine-tuned for specific tasks, which they can often solve with superhuman accuracy. When the models are large enough, they can be instructed by prompts to solve new tasks without any fine-tuning. Moreover, they can be applied to a wide range of different media and problem domains, ranging from image and video processing to robot control learning. Because they provide a blueprint for solving many tasks in artificial intelligence, they have been called Foundation Models. After a brief introduction to basic NLP models the main pre-trained language models BERT, GPT and sequence-to-sequence transformer are described, as well as the concepts of self-attention and context-sensitive embedding. Then, different approaches to improving these models are discussed, such as expanding the pre-training criteria, increasing the length of input texts, or including extra knowledge. An overview of the best-performing models for about twenty application areas is then presented, e.g., question answering, translation, story generation, dialog systems, generating images from text, etc. For each application area, the strengths and weaknesses of current models are discussed, and an outlook on further developments is given. In addition, links are provided to freely available program code. A concluding chapter summarizes the economic opportunities, mitigation of risks, and potential developments of AI.

Text-to-image diffusion models have shown impressive capabilities in generating realistic visuals from natural-language prompts, yet they often struggle with accurately binding attributes to corresponding objects, especially in prompts containing multiple attribute-object pairs. This challenge primarily arises from the limitations of commonly used text encoders, such as CLIP, which can fail to encode complex linguistic relationships and modifiers effectively. Existing approaches have attempted to mitigate these issues through attention map control during inference and the use of layout information or fine-tuning during training, yet they face performance drops with increased prompt complexity. In this work, we introduce a novel compositional generation method that leverages pairwise image embeddings to improve attribute-object binding. Our approach decomposes complex prompts into sub-prompts, generates corresponding images, and computes visual prototypes that fuse with text embeddings to enhance representation. By applying segmentation-based localization training, we address cross-attention misalignment, achieving improved accuracy in binding multiple attributes to objects. Our approaches outperform existing compositional text-to-image diffusion models on the benchmark T2I CompBench, achieving better image quality, evaluated by humans, and emerging robustness under scaling number of binding pairs in the prompt.

Visual Entity Linking (VEL) is a crucial task for achieving fine-grained visual understanding, matching objects within images (visual mentions) to entities in a knowledge base. Previous VEL tasks rely on textual inputs, but writing queries for complex scenes can be challenging. Visual inputs like clicks or bounding boxes offer a more convenient alternative. Therefore, we propose a new task, Pixel-Level Visual Entity Linking (PL-VEL), which uses pixel masks from visual inputs to refer to objects, supplementing reference methods for VEL. To facilitate research on this task, we have constructed the MaskOVEN-Wiki dataset through an entirely automatic reverse region-entity annotation framework. This dataset contains over 5 million annotations aligning pixel-level regions with entity-level labels, which will advance visual understanding towards fine-grained. Moreover, as pixel masks correspond to semantic regions in an image, we enhance previous patch-interacted attention with region-interacted attention by a visual semantic tokenization approach. Manual evaluation results indicate that the reverse annotation framework achieved a 94.8% annotation success rate. Experimental results show that models trained on this dataset improved accuracy by 18 points compared to zero-shot models. Additionally, the semantic tokenization method achieved a 5-point accuracy improvement over the trained baseline.

Prompting Large Language Models (LLMs), or providing context on the expected model of operation, is an effective way to steer the outputs of such models to satisfy human desiderata after they have been trained. But in rapidly evolving domains, there is often need to fine-tune LLMs to improve either the kind of knowledge in their memory or their abilities to perform open ended reasoning in new domains. When human's learn new concepts, we often do so by linking the new material that we are studying to concepts we have already learned before. To that end, we ask, "can prompting help us teach LLMs how to learn". In this work, we study a novel generalization of instruction tuning, called contextual fine-tuning, to fine-tune LLMs. Our method leverages instructional prompts designed to mimic human cognitive strategies in learning and problem-solving to guide the learning process during training, aiming to improve the model's interpretation and understanding of domain-specific knowledge. We empirically demonstrate that this simple yet effective modification improves the ability of LLMs to be fine-tuned rapidly on new datasets both within the medical and financial domains.

We study retrieval over catalogs of structured metadata, where each record is a small schema whose fields answer different kinds of query. Embedding a record with a text encoder first serializes its fields into a string, which forces a choice of field order. We show this choice, usually treated as an implementation detail, silently controls retrieval quality once the encoder is fine-tuned. A standard fine-tune loses 7.4 nDCG@10 points when the index is rebuilt under a different field order, because it reads absolute position instead of the field labels. We propose permutation-invariant fine-tuning (PI-FT), which serializes each record under a freshly sampled field order with random field dropout, so meaning binds to the labels rather than to position. The change is about two lines in the data loader; it costs negligible in-distribution accuracy and cuts the order-change penalty to 0.2 points. We study this in the discovery of development statistics, a catalog of nearly 10,000 indicators that should be searchable in many languages by a model small enough to self-host. As AI assistants and agents increasingly mediate access to public data and statistics, this retrieval step decides whether an answer is grounded in the right indicator or series, making discoverability a precondition for disseminating data through AI. Because usage logs cannot provide training signal for indicators no one has searched, we generate the queries instead. DevDataBench is a fully LLM-generated benchmark of grounded, facet-targeted queries across 15 languages, covering every indicator for both training and evaluation. A fine-tuned 118M-parameter CPU encoder outperforms every zero-shot baseline, including text-embedding-3-large (0.707 vs.\ 0.556 nDCG@10), with the largest gains in low-resource languages. We release the benchmark, pipeline, models, and a reusable PI-FT framework.

Information elicitation is an open-ended information-seeking problem in which an interaction can unfold in many potentially valuable directions, requiring an elicitor to continually determine which information to pursue as new information emerges. In agentic elicitation, these decisions may be delegated to a foundation model, yet how model choice shapes the resulting information-seeking behavior remains understudied. We study how judgments about information value vary across LLMs and how these differences shape sequential information seeking. We first examine these judgments across 11 LLMs spanning multiple model families and parameter scales, using a shared set of information and elicitation objectives. We then develop a controlled elicitation simulation in which different models encounter the same information space and use the same selection rule, isolating these judgments from question generation and respondent behavior. Using this setting, we characterize the breadth-depth behavior that emerges from model-specific information-seeking preferences over the course of elicitation. We further examine how interaction history changes the evaluation and subsequent selection of prospective information. We test the robustness and boundaries of these findings through sensitivity analyses and ablations over the opportunities available to the elicitor, the response labels used to operationalize information-seeking preferences, the presence of interaction history, and whether redundancy is explicitly relevant to the assessment. The project code, data, and trajectory files are available at https://github.com/infosenselab/open-elicitation.

This article presents the Cogni-CISMeF project, which aims at improving medical information search in the CISMeF system (Catalog and Index of French-language health resources) by including a conversational agent to interact with the user in natural language. To study the cognitive processes involved during the information search, a bottom-up methodology was adopted. Experimentation has been set up to obtain human dialogs between a user (playing the role of patient) dealing with medical information search and a CISMeF expert refining the request. The analysis of these dialogs underlined the use of discursive evidence: vocabulary, reformulation, implicit or explicit expression of user intentions, conversational sequences, etc. A model of artificial agent is proposed. It leads the user in its information search by proposing to him examples, assistance and choices. This model was implemented and integrated in the CISMeF system. ---- Cet article d\'ecrit le projet Cogni-CISMeF qui propose un module de dialogue Homme-Machine \`a int\'egrer dans le syst\`eme d'indexation de connaissances m\'edicales CISMeF (Catalogue et Index des Sites M\'edicaux Francophones). Nous avons adopt\'e une d\'emarche de mod\'elisation cognitive en proc\'edant \`a un recueil de corpus de dialogues entre un utilisateur (jouant le r\^ole d'un patient) d\'esirant une information m\'edicale et un expert CISMeF af inant cette demande pour construire la requ\^ete. Nous avons analys\'e la structure des dialogues ainsi obtenus et avons \'etudi\'e un certain nombre d'indices discursifs : vocabulaire employ\'e, marques de reformulation, commentaires m\'eta et \'epilinguistiques, expression implicite ou explicite des intentions de l'utilisateur, encha\^inement conversationnel, etc. De cette analyse, nous avons construit un mod\`ele d'agent artificiel dot\'e de capacit\'es cognitives capables d'aider l'utilisateur dans sa t\^ache de recherche d'information. Ce mod\`ele a \'et\'e impl\'ement\'e et int\'egr\'e dans le syst\`eme CISMeF.

Background: Large language models (LLMs) are trained to follow directions, but this introduces a vulnerability to blindly comply with user requests even if they generate wrong information. In medicine, this could accelerate the generation of misinformation that impacts human well-being. Objectives/Methods: We analyzed compliance to requests to generate misleading content about medications in settings where models know the request is illogical. We investigated whether in-context directions and instruction-tuning of LLMs to prioritize logical reasoning over compliance reduced misinformation risk. Results: While all frontier LLMs complied with misinformation requests, both prompt-based and parameter-based approaches can improve the detection of logic flaws in requests and prevent the dissemination of medical misinformation. Conclusion: Shifting LLMs to prioritize logic over compliance could reduce risks of exploitation for medical misinformation.

We introduce Kosmos-2, a Multimodal Large Language Model (MLLM), enabling new capabilities of perceiving object descriptions (e.g., bounding boxes) and grounding text to the visual world. Specifically, we represent refer expressions as links in Markdown, i.e., ``[text span](bounding boxes)'', where object descriptions are sequences of location tokens. Together with multimodal corpora, we construct large-scale data of grounded image-text pairs (called GrIT) to train the model. In addition to the existing capabilities of MLLMs (e.g., perceiving general modalities, following instructions, and performing in-context learning), Kosmos-2 integrates the grounding capability into downstream applications. We evaluate Kosmos-2 on a wide range of tasks, including (i) multimodal grounding, such as referring expression comprehension, and phrase grounding, (ii) multimodal referring, such as referring expression generation, (iii) perception-language tasks, and (iv) language understanding and generation. This work lays out the foundation for the development of Embodiment AI and sheds light on the big convergence of language, multimodal perception, action, and world modeling, which is a key step toward artificial general intelligence. Data, demo, and pretrained models are available at https://aka.ms/kosmos-2.

When re-finding items, users who forget or are uncertain about identifying details often rely on creative strategies for expressing their information needs -- complex queries that describe content elements (e.g., book characters or events), information beyond the document text (e.g., descriptions of book covers), or personal context (e.g., when they read a book). This retrieval setting, called tip of the tongue (TOT), is especially challenging for models heavily reliant on lexical and semantic overlap between query and document text. In this work, we introduce a simple yet effective framework for handling such complex queries by decomposing the query into individual clues, routing those as sub-queries to specialized retrievers, and ensembling the results. This approach allows us to take advantage of off-the-shelf retrievers (e.g., CLIP for retrieving images of book covers) or incorporate retriever-specific logic (e.g., date constraints). We show that our framework incorportating query decompositions into retrievers can improve gold book recall up to 7% relative again for Recall@5 on a new collection of 14,441 real-world query-book pairs from an online community for resolving TOT inquiries.

Pre-training techniques have been verified successfully in a variety of NLP tasks in recent years. Despite the widespread use of pre-training models for NLP applications, they almost exclusively focus on text-level manipulation, while neglecting layout and style information that is vital for document image understanding. In this paper, we propose the LayoutLM to jointly model interactions between text and layout information across scanned document images, which is beneficial for a great number of real-world document image understanding tasks such as information extraction from scanned documents. Furthermore, we also leverage image features to incorporate words' visual information into LayoutLM. To the best of our knowledge, this is the first time that text and layout are jointly learned in a single framework for document-level pre-training. It achieves new state-of-the-art results in several downstream tasks, including form understanding (from 70.72 to 79.27), receipt understanding (from 94.02 to 95.24) and document image classification (from 93.07 to 94.42). The code and pre-trained LayoutLM models are publicly available at https://aka.ms/layoutlm.

Language models can store vast amounts of factual knowledge, but their ability to use this knowledge for logical reasoning remains questionable. This paper explores a language model's ability to manipulate its stored knowledge during inference. We focus on four manipulation types: retrieval (e.g., "What is person A's attribute X"), classification (e.g., "Is A's attribute X even or odd?"), comparison (e.g., "Is A greater than B in attribute X?") and inverse search (e.g., "Which person's attribute X equals T?") We observe that pre-trained language models like GPT2/3/4 excel in knowledge retrieval but struggle with simple classification or comparison tasks unless Chain of Thoughts (CoTs) are employed during both training and inference. They also perform poorly in inverse knowledge search, irrespective of the prompts. Our primary contribution is a synthetic dataset for a controlled experiment that confirms these inherent weaknesses: a language model cannot efficiently manipulate knowledge from pre-training data, even when such knowledge is perfectly stored and fully extractable in the models, and despite adequate instruct fine-tuning.

Mediated by today's visual displays, information space allows users to discover, access and interact with a wide range of digital and physical information. The information presented in this space may be digital, physical or a blend of both, and appear across different dimensions - such as texts, images, 3D content and physical objects embedded within real-world environment. Navigating within the information space often involves interacting with mixed-dimensional entities, visually represented in both 2D and 3D. At times, interactions also involve transitioning among entities represented in different dimensions. We introduce the concept of mixed-dimensional information space, encompassing entities represented in both 2D and 3D. Interactions within the mixed-dimensional information space should be seamless and efficient: users should be able to focus on their primary tasks without being distracted by interactions with or transitions between entities. While incorporating 3D representations into the mixed-dimensional information space offers intuitive and immersive ways to interact with complex information, it is important to address potential seams and inefficiencies that arise while interacting with both 2D and 3D entities. This dissertation introduces new interactive techniques and systems to realize seamless and efficient interactions within the mixed-dimensional information space. This dissertation introduces three interactive systems: MemoVis which aims to use emergent generative AI to help users create reference images for 3D design feedback; PaperToPlace which demonstrates how paper-based instruction documents can be transformed and spatialized into a context-aware MR experience; and VRContour which explores how contour delineation workflow can be brought into VR.

Textual Large Language Models (LLMs) provide a simple and familiar interface: a string of text is used for both input and output. However, the information conveyed to an LLM often has a richer structure and semantics, which is not conveyed in a string. For example, most prompts contain both instructions ("Summarize this paper into a paragraph") and data (the paper to summarize), but these are usually not distinguished when passed to the model. This can lead to model confusion and security risks, such as prompt injection attacks. This work addresses this shortcoming by introducing an LLM-native mark-up language, LLMON (LLM Object Notation, pronounced "Lemon"), that enables the structure and semantic metadata of the text to be communicated in a natural way to an LLM. This information can then be used during model training, model prompting, and inference implementation, leading to improvements in model accuracy, safety, and security. This is analogous to how programming language types can be used for many purposes, such as static checking, code generation, dynamic checking, and IDE highlighting. We discuss the general design requirements of an LLM-native markup language, introduce the LLMON markup language and show how it meets these design requirements, describe how the information contained in a LLMON artifact can benefit model training and inference implementation, and provide some preliminary empirical evidence of its value for both of these use cases. We also discuss broader issues and research opportunities that are enabled with an LLM-native approach.

Tool-augmented language-model agents execute multi-step workflows over external systems, resolving an entity once and then acting on it across subsequent steps. Prior work shows that in single-step actions, agents select the correct tool but bind it to the wrong entity 24-26% of the time. We study what happens to entity bindings over time: do they stay correct, silently drift to a different entity, or, if wrong from the start, propagate and compound? We formalize binding drift (correct at step 1, wrong later) as distinct from error propagation (wrong at step 1, carried forward), and score them on disjoint workflow sets so the two cannot be conflated. In a controlled multi-step testbed (200 workflows, 580 entity-binding-scored steps, four enterprise domains, eight model backends spanning small to frontier), we find: (1) under controlled error injection, an entity lock (the intuitive "persist the first binding" fix) amplifies wrong actions from 907 to 2,746 (3.0x; bootstrap 95% CI [2.8, 3.3]), because it faithfully carries the seeded wrong entity into every later step; (2) the amplification reaches 8.5x on the most affected model (Claude Opus 4.5); (3) a practical LLM-based re-verifier (a single cheap second model call re-reading the original instruction) reduces wrong actions by 79% (0.21x; CI [0.18, 0.25]), closing the gap to within 1 percentage point of an oracle upper-bound (0.20x); and (4) in the natural (non-injected) setting, baseline agents drift on 18% of eligible workflows, with the per-step error rate rising across steps. Persistence and re-verification are not interchangeable: a defense that eliminates drift can worsen propagation, and a practical re-verifier nearly matches oracle recovery.

Molecular knowledge resides within three different modalities of information sources: molecular structures, biomedical documents, and knowledge bases. Effective incorporation of molecular knowledge from these modalities holds paramount significance in facilitating biomedical research. However, existing multimodal molecular foundation models exhibit limitations in capturing intricate connections between molecular structures and texts, and more importantly, none of them attempt to leverage a wealth of molecular expertise derived from knowledge graphs. In this study, we introduce MolFM, a multimodal molecular foundation model designed to facilitate joint representation learning from molecular structures, biomedical texts, and knowledge graphs. We propose cross-modal attention between atoms of molecular structures, neighbors of molecule entities and semantically related texts to facilitate cross-modal comprehension. We provide theoretical analysis that our cross-modal pre-training captures local and global molecular knowledge by minimizing the distance in the feature space between different modalities of the same molecule, as well as molecules sharing similar structures or functions. MolFM achieves state-of-the-art performance on various downstream tasks. On cross-modal retrieval, MolFM outperforms existing models with 12.13% and 5.04% absolute gains under the zero-shot and fine-tuning settings, respectively. Furthermore, qualitative analysis showcases MolFM's implicit ability to provide grounding from molecular substructures and knowledge graphs. Code and models are available on https://github.com/BioFM/OpenBioMed.

Visual document retrieval aims to retrieve a set of document pages relevant to a query from visually rich collections. Existing methods often employ Vision-Language Models (VLMs) to encode queries and visual pages into a shared embedding space, which is then optimized via contrastive training. However, during visual document representation, localized evidence is usually scattered across complex document layouts, making it difficult for retrieval models to capture crucial cues for effective embedding learning. In this paper, we propose Reasoning-Guided Alignment (ReAlign), a method that enhances visual document retrieval by leveraging the reasoning capability of VLMs to provide fine-grained visual document descriptions as supervision signals for training. Specifically, ReAlign employs a superior VLM to identify query-related regions on a page and then generates a query-aware description grounding the cropped visual regions. The retriever is then trained using these region-focused descriptions to align the semantics between queries and visual documents by encouraging the document ranking distribution induced by the region-focused descriptions to match that induced by the original query. Experiments on diverse visually rich document retrieval benchmarks demonstrate that ReAlign consistently improves visual document retrieval performance on both in-domain and out-of-domain datasets, achieving up to 2% relative improvements. Moreover, the advantages of ReAlign generalize across different VLM backbones by guiding models to better focus their attention on critical visual cues for document representation. All code and datasets are available at https://github.com/NEUIR/ReAlign.

The video-language (VL) pretraining has achieved remarkable improvement in multiple downstream tasks. However, the current VL pretraining framework is hard to extend to multiple modalities (N modalities, N>=3) beyond vision and language. We thus propose LanguageBind, taking the language as the bind across different modalities because the language modality is well-explored and contains rich semantics. Specifically, we freeze the language encoder acquired by VL pretraining, then train encoders for other modalities with contrastive learning. As a result, all modalities are mapped to a shared feature space, implementing multi-modal semantic alignment. While LanguageBind ensures that we can extend VL modalities to N modalities, we also need a high-quality dataset with alignment data pairs centered on language. We thus propose VIDAL-10M with Video, Infrared, Depth, Audio and their corresponding Language, naming as VIDAL-10M. In our VIDAL-10M, all videos are from short video platforms with complete semantics rather than truncated segments from long videos, and all the video, depth, infrared, and audio modalities are aligned to their textual descriptions. After pretraining on VIDAL-10M, we outperform ImageBind by 1.2% R@1 on the MSR-VTT dataset with only 15% of the parameters in the zero-shot video-text retrieval, validating the high quality of our dataset. Beyond this, our LanguageBind has achieved great improvement in the zero-shot video, audio, depth, and infrared understanding tasks. For instance, on the LLVIP and NYU-D datasets, LanguageBind outperforms ImageBind-huge with 23.8% and 11.1% top-1 accuracy. Code address: https://github.com/PKU-YuanGroup/LanguageBind.

Multimodal knowledge editing (MKE) aims to correct the internal knowledge of large vision-language models after deployment, yet the behavioral patterns of post-edit models remain underexplored. In this paper, we identify a systemic failure mode in edited models, termed Entity Identity Confusion (EIC): edited models exhibit an absurd behavior where text-only queries about the original entity's identity unexpectedly return information about the new entity. To rigorously investigate EIC, we construct EC-Bench, a diagnostic benchmark that directly probes how image-entity bindings shift before and after editing. Our analysis reveals that EIC stems from existing methods failing to distinguish between Image-Entity (I-E) binding and Entity-Entity (E-E) relational knowledge in the model, causing models to overfit E-E associations as a shortcut: the image is still perceived as the original entity, with the new entity's name serving only as a spurious identity label. We further explore potential mitigation strategies, showing that constraining edits to the model's I-E processing stage encourages edits to act more faithfully on I-E binding, thereby substantially reducing EIC. Based on these findings, we discuss principled desiderata for faithful MKE and provide methodological guidance for future research.

We investigate a relatively under-explored class of hybrid neurosymbolic models that integrate symbolic learning with neural reasoning to construct data generators meeting formal correctness criteria. In Symbolic Neural Generators (SNGs), symbolic learners examine logical specifications of feasible data from a small set of instances -- sometimes just one. Each specification in turn constrains the conditional information supplied to a neural-based generator, which rejects any instance violating the symbolic specification. Like other neurosymbolic approaches, SNG exploits the complementary strengths of symbolic and neural methods. The outcome of an SNG is a pair (H, X), where H is a symbolic description of feasible instances constructed from data, and X a set of generated new instances that satisfy the description. We introduce a semantics for such systems, based on the construction of appropriate base and fibre partially-ordered sets combined into an overall partial order. We implement an SNG combining a restricted form of Inductive Logic Programming (ILP) with a large language model (LLM) and evaluate it on early-stage drug design. Our main interest is the description and the set of potential inhibitor molecules generated by the SNG. On benchmark problems -- where drug targets are well understood -- SNG performance is statistically comparable to state-of-the-art methods. On exploratory problems with poorly understood targets, generated molecules exhibit binding affinities on par with leading clinical candidates. Experts further find the symbolic specifications useful as preliminary filters, with several generated molecules identified as viable for synthesis and wet-lab testing.

Accurate prediction of protein-ligand binding affinities is crucial in drug discovery, particularly during hit-to-lead and lead optimization phases, however, limitations in ligand force fields continue to impact prediction accuracy. In this work, we validate relative binding free energy (RBFE) accuracy using neural network potentials (NNPs) for the ligands. We utilize a novel NNP model, AceForce 1.0, based on the TensorNet architecture for small molecules that broadens the applicability to diverse drug-like compounds, including all important chemical elements and supporting charged molecules. Using established benchmarks, we show overall improved accuracy and correlation in binding affinity predictions compared with GAFF2 for molecular mechanics and ANI2-x for NNPs. Slightly less accuracy but comparable correlations with OPLS4. We also show that we can run the NNP simulations at 2 fs timestep, at least two times larger than previous NNP models, providing significant speed gains. The results show promise for further evolutions of free energy calculations using NNPs while demonstrating its practical use already with the current generation. The code and NNP model are publicly available for research use.