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May 8

Twin Peaks: Dual-Head Architecture for Structure-Free Prediction of Protein-Protein Binding Affinity and Mutation Effects

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.

  • 2 authors
·
Sep 26, 2025

S-MolSearch: 3D Semi-supervised Contrastive Learning for Bioactive Molecule Search

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.

  • 6 authors
·
Aug 27, 2024

Follow the Flow: On Information Flow Across Textual Tokens in Text-to-Image Models

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.

  • 5 authors
·
Apr 1, 2025

Binding Language Models in Symbolic Languages

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 .

  • 12 authors
·
Oct 6, 2022

FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction

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.

  • 4 authors
·
Jun 3, 2024

OmniBind: Large-scale Omni Multimodal Representation via Binding Spaces

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.

  • 8 authors
·
Jul 16, 2024 3

Large-Scale Multi-omic Biosequence Transformers for Modeling Peptide-Nucleotide Interactions

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.

  • 5 authors
·
Aug 28, 2024 1

FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction

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.

  • 2 authors
·
Dec 14, 2024

Token Merging for Training-Free Semantic Binding in Text-to-Image Synthesis

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.

  • 9 authors
·
Nov 11, 2024

Matching Table Metadata with Business Glossaries Using Large Language Models

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.

  • 6 authors
·
Sep 7, 2023 2

ImageBind-LLM: Multi-modality Instruction Tuning

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.

  • 17 authors
·
Sep 7, 2023 5

Joint Reasoning on Hybrid-knowledge sources for Task-Oriented Dialog

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.

  • 3 authors
·
Oct 13, 2022 2

Mixing Mechanisms: How Language Models Retrieve Bound Entities In-Context

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.

tau Tel Aviv University
·
Oct 7, 2025 2

Learning the Wrong Lessons: Syntactic-Domain Spurious Correlations in Language Models

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.

  • 5 authors
·
Sep 25, 2025

MultiBind: A Benchmark for Attribute Misbinding in Multi-Subject Generation

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.

  • 7 authors
·
Mar 23 2

A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications

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.

  • 17 authors
·
Oct 8, 2024

The Condition Number as a Scale-Invariant Proxy for Information Encoding in Neural Units

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.

  • 1 authors
·
Jun 19, 2025 1

Text-to-Image Synthesis for Any Artistic Styles: Advancements in Personalized Artistic Image Generation via Subdivision and Dual Binding

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.

  • 3 authors
·
Apr 8, 2024

A Semantic Generalization of Shannon's Information Theory and Applications

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.

  • 1 authors
·
May 6, 2025

Foundation Models for Natural Language Processing -- Pre-trained Language Models Integrating Media

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.

  • 2 authors
·
Feb 16, 2023

VSC: Visual Search Compositional Text-to-Image Diffusion Model

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.

  • 4 authors
·
May 2, 2025

Reverse Region-to-Entity Annotation for Pixel-Level Visual Entity Linking

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.

  • 9 authors
·
Dec 18, 2024

MolFM: A Multimodal Molecular Foundation Model

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.

  • 5 authors
·
Jun 6, 2023

LanguageBind: Extending Video-Language Pretraining to N-modality by Language-based Semantic Alignment

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.

  • 14 authors
·
Oct 3, 2023

On Relation-Specific Neurons in Large Language Models

In large language models (LLMs), certain neurons can store distinct pieces of knowledge learned during pretraining. While knowledge typically appears as a combination of relations and entities, it remains unclear whether some neurons focus on a relation itself -- independent of any entity. We hypothesize such neurons detect a relation in the input text and guide generation involving such a relation. To investigate this, we study the Llama-2 family on a chosen set of relations with a statistics-based method. Our experiments demonstrate the existence of relation-specific neurons. We measure the effect of selectively deactivating candidate neurons specific to relation r on the LLM's ability to handle (1) facts whose relation is r and (2) facts whose relation is a different relation r' neq r. With respect to their capacity for encoding relation information, we give evidence for the following three properties of relation-specific neurons. (i) Neuron cumulativity. The neurons for r present a cumulative effect so that deactivating a larger portion of them results in the degradation of more facts in r. (ii) Neuron versatility. Neurons can be shared across multiple closely related as well as less related relations. Some relation neurons transfer across languages. (iii) Neuron interference. Deactivating neurons specific to one relation can improve LLM generation performance for facts of other relations. We will make our code publicly available at https://github.com/cisnlp/relation-specific-neurons.

cis-lmu CIS, LMU Munich
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Feb 24, 2025 2

Fine Tuning LLM for Enterprise: Practical Guidelines and Recommendations

There is a compelling necessity from enterprises for fine tuning LLMs (Large Language Models) o get them trained on proprietary domain knowledge. The challenge is to imbibe the LLMs with domain specific knowledge using the most optimial resource and cost and in the best possible time. Many enterprises rely on RAG (Retrieval Augmented Generation) which does not need LLMs to be ine-tuned but they are limited by the quality of vector databases and their retrieval capabilities rather than the intrinsic capabilities of the LLMs themselves. In our current work we focus on fine tuning LLaMA, an open source LLM using proprietary documents and code from an enterprise repository and use the fine tuned models to evaluate the quality of responses. As part of this work, we aim to guide beginners on how to start with fine tuning an LLM for documentation and code by making educated guesses on size of GPU required and options that are available for formatting the data. We also propose pre processing recipes for both documentation and code to prepare dataset in different formats. The proposed methods of data preparation for document datasets are forming paragraph chunks, forming question and answer pairs and forming keyword and paragraph chunk pairs. For code dataset we propose forming summary and function pairs. Further, we qualitatively evaluate the results of the models for domain specific queries. Finally, we also propose practical guidelines and recommendations for fine tuning LLMs.

  • 4 authors
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Mar 23, 2024

DOM-LM: Learning Generalizable Representations for HTML Documents

HTML documents are an important medium for disseminating information on the Web for human consumption. An HTML document presents information in multiple text formats including unstructured text, structured key-value pairs, and tables. Effective representation of these documents is essential for machine understanding to enable a wide range of applications, such as Question Answering, Web Search, and Personalization. Existing work has either represented these documents using visual features extracted by rendering them in a browser, which is typically computationally expensive, or has simply treated them as plain text documents, thereby failing to capture useful information presented in their HTML structure. We argue that the text and HTML structure together convey important semantics of the content and therefore warrant a special treatment for their representation learning. In this paper, we introduce a novel representation learning approach for web pages, dubbed DOM-LM, which addresses the limitations of existing approaches by encoding both text and DOM tree structure with a transformer-based encoder and learning generalizable representations for HTML documents via self-supervised pre-training. We evaluate DOM-LM on a variety of webpage understanding tasks, including Attribute Extraction, Open Information Extraction, and Question Answering. Our extensive experiments show that DOM-LM consistently outperforms all baselines designed for these tasks. In particular, DOM-LM demonstrates better generalization performance both in few-shot and zero-shot settings, making it attractive for making it suitable for real-world application settings with limited labeled data.

  • 5 authors
·
Jan 25, 2022

Any-to-3D Generation via Hybrid Diffusion Supervision

Recent progress in 3D object generation has been fueled by the strong priors offered by diffusion models. However, existing models are tailored to specific tasks, accommodating only one modality at a time and necessitating retraining to change modalities. Given an image-to-3D model and a text prompt, a naive approach is to convert text prompts to images and then use the image-to-3D model for generation. This approach is both time-consuming and labor-intensive, resulting in unavoidable information loss during modality conversion. To address this, we introduce XBind, a unified framework for any-to-3D generation using cross-modal pre-alignment techniques. XBind integrates an multimodal-aligned encoder with pre-trained diffusion models to generate 3D objects from any modalities, including text, images, and audio. We subsequently present a novel loss function, termed Modality Similarity (MS) Loss, which aligns the embeddings of the modality prompts and the rendered images, facilitating improved alignment of the 3D objects with multiple modalities. Additionally, Hybrid Diffusion Supervision combined with a Three-Phase Optimization process improves the quality of the generated 3D objects. Extensive experiments showcase XBind's broad generation capabilities in any-to-3D scenarios. To our knowledge, this is the first method to generate 3D objects from any modality prompts. Project page: https://zeroooooooow1440.github.io/.

  • 5 authors
·
Nov 21, 2024

MagicLens: Self-Supervised Image Retrieval with Open-Ended Instructions

Image retrieval, i.e., finding desired images given a reference image, inherently encompasses rich, multi-faceted search intents that are difficult to capture solely using image-based measures. Recent work leverages text instructions to allow users to more freely express their search intents. However, existing work primarily focuses on image pairs that are visually similar and/or can be characterized by a small set of pre-defined relations. The core thesis of this paper is that text instructions can enable retrieving images with richer relations beyond visual similarity. To show this, we introduce MagicLens, a series of self-supervised image retrieval models that support open-ended instructions. MagicLens is built on a key novel insight: image pairs that naturally occur on the same web pages contain a wide range of implicit relations (e.g., inside view of), and we can bring those implicit relations explicit by synthesizing instructions via large multimodal models (LMMs) and large language models (LLMs). Trained on 36.7M (query image, instruction, target image) triplets with rich semantic relations mined from the web, MagicLens achieves comparable or better results on eight benchmarks of various image retrieval tasks than prior state-of-the-art (SOTA) methods. Remarkably, it outperforms previous SOTA but with a 50X smaller model size on multiple benchmarks. Additional human analyses on a 1.4M-image unseen corpus further demonstrate the diversity of search intents supported by MagicLens.

  • 8 authors
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Mar 28, 2024 4

ActionBert: Leveraging User Actions for Semantic Understanding of User Interfaces

As mobile devices are becoming ubiquitous, regularly interacting with a variety of user interfaces (UIs) is a common aspect of daily life for many people. To improve the accessibility of these devices and to enable their usage in a variety of settings, building models that can assist users and accomplish tasks through the UI is vitally important. However, there are several challenges to achieve this. First, UI components of similar appearance can have different functionalities, making understanding their function more important than just analyzing their appearance. Second, domain-specific features like Document Object Model (DOM) in web pages and View Hierarchy (VH) in mobile applications provide important signals about the semantics of UI elements, but these features are not in a natural language format. Third, owing to a large diversity in UIs and absence of standard DOM or VH representations, building a UI understanding model with high coverage requires large amounts of training data. Inspired by the success of pre-training based approaches in NLP for tackling a variety of problems in a data-efficient way, we introduce a new pre-trained UI representation model called ActionBert. Our methodology is designed to leverage visual, linguistic and domain-specific features in user interaction traces to pre-train generic feature representations of UIs and their components. Our key intuition is that user actions, e.g., a sequence of clicks on different UI components, reveals important information about their functionality. We evaluate the proposed model on a wide variety of downstream tasks, ranging from icon classification to UI component retrieval based on its natural language description. Experiments show that the proposed ActionBert model outperforms multi-modal baselines across all downstream tasks by up to 15.5%.

  • 10 authors
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Dec 22, 2020

The Impact of Element Ordering on LM Agent Performance

There has been a surge of interest in language model agents that can navigate virtual environments such as the web or desktop. To navigate such environments, agents benefit from information on the various elements (e.g., buttons, text, or images) present. It remains unclear which element attributes have the greatest impact on agent performance, especially in environments that only provide a graphical representation (i.e., pixels). Here we find that the ordering in which elements are presented to the language model is surprisingly impactful--randomizing element ordering in a webpage degrades agent performance comparably to removing all visible text from an agent's state representation. While a webpage provides a hierarchical ordering of elements, there is no such ordering when parsing elements directly from pixels. Moreover, as tasks become more challenging and models more sophisticated, our experiments suggest that the impact of ordering increases. Finding an effective ordering is non-trivial. We investigate the impact of various element ordering methods in web and desktop environments. We find that dimensionality reduction provides a viable ordering for pixel-only environments. We train a UI element detection model to derive elements from pixels and apply our findings to an agent benchmark--OmniACT--where we only have access to pixels. Our method completes more than two times as many tasks on average relative to the previous state-of-the-art.

  • 3 authors
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Sep 18, 2024

A Parse-Then-Place Approach for Generating Graphic Layouts from Textual Descriptions

Creating layouts is a fundamental step in graphic design. In this work, we propose to use text as the guidance to create graphic layouts, i.e., Text-to-Layout, aiming to lower the design barriers. Text-to-Layout is a challenging task, because it needs to consider the implicit, combined, and incomplete layout constraints from text, each of which has not been studied in previous work. To address this, we present a two-stage approach, named parse-then-place. The approach introduces an intermediate representation (IR) between text and layout to represent diverse layout constraints. With IR, Text-to-Layout is decomposed into a parse stage and a place stage. The parse stage takes a textual description as input and generates an IR, in which the implicit constraints from the text are transformed into explicit ones. The place stage generates layouts based on the IR. To model combined and incomplete constraints, we use a Transformer-based layout generation model and carefully design a way to represent constraints and layouts as sequences. Besides, we adopt the pretrain-then-finetune strategy to boost the performance of the layout generation model with large-scale unlabeled layouts. To evaluate our approach, we construct two Text-to-Layout datasets and conduct experiments on them. Quantitative results, qualitative analysis, and user studies demonstrate the effectiveness of our approach.

  • 7 authors
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Aug 24, 2023

When Can Models Learn From Explanations? A Formal Framework for Understanding the Roles of Explanation Data

Many methods now exist for conditioning model outputs on task instructions, retrieved documents, and user-provided explanations and feedback. Rather than relying solely on examples of task inputs and outputs, these approaches use valuable additional data for improving model correctness and aligning learned models with human priors. Meanwhile, a growing body of evidence suggests that some language models can (1) store a large amount of knowledge in their parameters, and (2) perform inference over tasks in textual inputs at test time. These results raise the possibility that, for some tasks, humans cannot explain to a model any more about the task than it already knows or could infer on its own. In this paper, we study the circumstances under which explanations of individual data points can (or cannot) improve modeling performance. In order to carefully control important properties of the data and explanations, we introduce a synthetic dataset for experiments, and we also make use of three existing datasets with explanations: e-SNLI, TACRED, and SemEval. We first give a formal framework for the available modeling approaches, in which explanation data can be used as model inputs, as targets, or as a prior. After arguing that the most promising role for explanation data is as model inputs, we propose to use a retrieval-based method and show that it solves our synthetic task with accuracies upwards of 95%, while baselines without explanation data achieve below 65% accuracy. We then identify properties of datasets for which retrieval-based modeling fails. With the three existing datasets, we find no improvements from explanation retrieval. Drawing on findings from our synthetic task, we suggest that at least one of six preconditions for successful modeling fails to hold with these datasets. Our code is publicly available at https://github.com/peterbhase/ExplanationRoles

  • 2 authors
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Feb 3, 2021

Controllable Context Sensitivity and the Knob Behind It

When making predictions, a language model must trade off how much it relies on its context vs. its prior knowledge. Choosing how sensitive the model is to its context is a fundamental functionality, as it enables the model to excel at tasks like retrieval-augmented generation and question-answering. In this paper, we search for a knob which controls this sensitivity, determining whether language models answer from the context or their prior knowledge. To guide this search, we design a task for controllable context sensitivity. In this task, we first feed the model a context (Paris is in England) and a question (Where is Paris?); we then instruct the model to either use its prior or contextual knowledge and evaluate whether it generates the correct answer for both intents (either France or England). When fine-tuned on this task, instruction-tuned versions of Llama-3.1, Mistral-v0.3, and Gemma-2 can solve it with high accuracy (85-95%). Analyzing these high-performing models, we narrow down which layers may be important to context sensitivity using a novel linear time algorithm. Then, in each model, we identify a 1-D subspace in a single layer that encodes whether the model follows context or prior knowledge. Interestingly, while we identify this subspace in a fine-tuned model, we find that the exact same subspace serves as an effective knob in not only that model but also non-fine-tuned instruct and base models of that model family. Finally, we show a strong correlation between a model's performance and how distinctly it separates context-agreeing from context-ignoring answers in this subspace. These results suggest a single subspace facilitates how the model chooses between context and prior knowledge, hinting at a simple fundamental mechanism that controls this behavior.

  • 7 authors
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Nov 11, 2024

ICLR: In-Context Learning of Representations

Recent work has demonstrated that semantics specified by pretraining data influence how representations of different concepts are organized in a large language model (LLM). However, given the open-ended nature of LLMs, e.g., their ability to in-context learn, we can ask whether models alter these pretraining semantics to adopt alternative, context-specified ones. Specifically, if we provide in-context exemplars wherein a concept plays a different role than what the pretraining data suggests, do models reorganize their representations in accordance with these novel semantics? To answer this question, we take inspiration from the theory of conceptual role semantics and define a toy "graph tracing" task wherein the nodes of the graph are referenced via concepts seen during training (e.g., apple, bird, etc.) and the connectivity of the graph is defined via some predefined structure (e.g., a square grid). Given exemplars that indicate traces of random walks on the graph, we analyze intermediate representations of the model and find that as the amount of context is scaled, there is a sudden re-organization from pretrained semantic representations to in-context representations aligned with the graph structure. Further, we find that when reference concepts have correlations in their semantics (e.g., Monday, Tuesday, etc.), the context-specified graph structure is still present in the representations, but is unable to dominate the pretrained structure. To explain these results, we analogize our task to energy minimization for a predefined graph topology, providing evidence towards an implicit optimization process to infer context-specified semantics. Overall, our findings indicate scaling context-size can flexibly re-organize model representations, possibly unlocking novel capabilities.

  • 8 authors
·
Dec 29, 2024

From Entropy to Epiplexity: Rethinking Information for Computationally Bounded Intelligence

Can we learn more from data than existed in the generating process itself? Can new and useful information be constructed from merely applying deterministic transformations to existing data? Can the learnable content in data be evaluated without considering a downstream task? On these questions, Shannon information and Kolmogorov complexity come up nearly empty-handed, in part because they assume observers with unlimited computational capacity and fail to target the useful information content. In this work, we identify and exemplify three seeming paradoxes in information theory: (1) information cannot be increased by deterministic transformations; (2) information is independent of the order of data; (3) likelihood modeling is merely distribution matching. To shed light on the tension between these results and modern practice, and to quantify the value of data, we introduce epiplexity, a formalization of information capturing what computationally bounded observers can learn from data. Epiplexity captures the structural content in data while excluding time-bounded entropy, the random unpredictable content exemplified by pseudorandom number generators and chaotic dynamical systems. With these concepts, we demonstrate how information can be created with computation, how it depends on the ordering of the data, and how likelihood modeling can produce more complex programs than present in the data generating process itself. We also present practical procedures to estimate epiplexity which we show capture differences across data sources, track with downstream performance, and highlight dataset interventions that improve out-of-distribution generalization. In contrast to principles of model selection, epiplexity provides a theoretical foundation for data selection, guiding how to select, generate, or transform data for learning systems.

  • 6 authors
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Jan 6

DreamRenderer: Taming Multi-Instance Attribute Control in Large-Scale Text-to-Image Models

Image-conditioned generation methods, such as depth- and canny-conditioned approaches, have demonstrated remarkable abilities for precise image synthesis. However, existing models still struggle to accurately control the content of multiple instances (or regions). Even state-of-the-art models like FLUX and 3DIS face challenges, such as attribute leakage between instances, which limits user control. To address these issues, we introduce DreamRenderer, a training-free approach built upon the FLUX model. DreamRenderer enables users to control the content of each instance via bounding boxes or masks, while ensuring overall visual harmony. We propose two key innovations: 1) Bridge Image Tokens for Hard Text Attribute Binding, which uses replicated image tokens as bridge tokens to ensure that T5 text embeddings, pre-trained solely on text data, bind the correct visual attributes for each instance during Joint Attention; 2) Hard Image Attribute Binding applied only to vital layers. Through our analysis of FLUX, we identify the critical layers responsible for instance attribute rendering and apply Hard Image Attribute Binding only in these layers, using soft binding in the others. This approach ensures precise control while preserving image quality. Evaluations on the COCO-POS and COCO-MIG benchmarks demonstrate that DreamRenderer improves the Image Success Ratio by 17.7% over FLUX and enhances the performance of layout-to-image models like GLIGEN and 3DIS by up to 26.8%. Project Page: https://limuloo.github.io/DreamRenderer/.

  • 4 authors
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Mar 17, 2025 3

AMELI: Enhancing Multimodal Entity Linking with Fine-Grained Attributes

We propose attribute-aware multimodal entity linking, where the input consists of a mention described with a text paragraph and images, and the goal is to predict the corresponding target entity from a multimodal knowledge base (KB) where each entity is also accompanied by a text description, visual images, and a collection of attributes that present the meta-information of the entity in a structured format. To facilitate this research endeavor, we construct AMELI, encompassing a new multimodal entity linking benchmark dataset that contains 16,735 mentions described in text and associated with 30,472 images, and a multimodal knowledge base that covers 34,690 entities along with 177,873 entity images and 798,216 attributes. To establish baseline performance on AMELI, we experiment with several state-of-the-art architectures for multimodal entity linking and further propose a new approach that incorporates attributes of entities into disambiguation. Experimental results and extensive qualitative analysis demonstrate that extracting and understanding the attributes of mentions from their text descriptions and visual images play a vital role in multimodal entity linking. To the best of our knowledge, we are the first to integrate attributes in the multimodal entity linking task. The programs, model checkpoints, and the dataset are publicly available at https://github.com/VT-NLP/Ameli.

  • 8 authors
·
May 24, 2023

When Does Metadata Conditioning (NOT) Work for Language Model Pre-Training? A Study with Context-Free Grammars

The ability to acquire latent semantics is one of the key properties that determines the performance of language models. One convenient approach to invoke this ability is to prepend metadata (e.g. URLs, domains, and styles) at the beginning of texts in the pre-training data, making it easier for the model to access latent semantics before observing the entire text. Previous studies have reported that this technique actually improves the performance of trained models in downstream tasks; however, this improvement has been observed only in specific downstream tasks, without consistent enhancement in average next-token prediction loss. To understand this phenomenon, we closely investigate how prepending metadata during pre-training affects model performance by examining its behavior using artificial data. Interestingly, we found that this approach produces both positive and negative effects on the downstream tasks. We demonstrate that the effectiveness of the approach depends on whether latent semantics can be inferred from the downstream task's prompt. Specifically, through investigations using data generated by probabilistic context-free grammars, we show that training with metadata helps improve model's performance when the given context is long enough to infer the latent semantics. In contrast, the technique negatively impacts performance when the context lacks the necessary information to make an accurate posterior inference.

  • 10 authors
·
Apr 24, 2025

3D-MolT5: Towards Unified 3D Molecule-Text Modeling with 3D Molecular Tokenization

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

  • 5 authors
·
Jun 9, 2024

Evaluating Relational Reasoning in LLMs with REL

Relational reasoning is the ability to infer relations that jointly bind multiple entities, attributes, or variables. This ability is central to scientific reasoning, but existing evaluations of relational reasoning in large language models often focus on structured inputs such as tables, graphs, or synthetic tasks, and do not isolate the difficulty introduced by higher-arity relational binding. We study this problem through the lens of Relational Complexity (RC), which we define as the minimum number of independent entities or operands that must be simultaneously bound to apply a relation. RC provides a principled way to vary reasoning difficulty while controlling for confounders such as input size, vocabulary, and representational choices. Building on RC, we introduce REL, a generative benchmark framework spanning algebra, chemistry, and biology that varies RC within each domain. Across frontier LLMs, performance degrades consistently and monotonically as RC increases, even when the total number of entities is held fixed. This failure mode persists with increased test-time compute and in-context learning, suggesting a limitation tied to the arity of the required relational binding rather than to insufficient inference steps or lack of exposure to examples. Our results identify a regime of higher-arity reasoning in which current models struggle, and motivate re-examining benchmarks through the lens of relational complexity.

  • 5 authors
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Apr 13

Knowledge-Augmented Large Language Models for Personalized Contextual Query Suggestion

Large Language Models (LLMs) excel at tackling various natural language tasks. However, due to the significant costs involved in re-training or fine-tuning them, they remain largely static and difficult to personalize. Nevertheless, a variety of applications could benefit from generations that are tailored to users' preferences, goals, and knowledge. Among them is web search, where knowing what a user is trying to accomplish, what they care about, and what they know can lead to improved search experiences. In this work, we propose a novel and general approach that augments an LLM with relevant context from users' interaction histories with a search engine in order to personalize its outputs. Specifically, we construct an entity-centric knowledge store for each user based on their search and browsing activities on the web, which is then leveraged to provide contextually relevant LLM prompt augmentations. This knowledge store is light-weight, since it only produces user-specific aggregate projections of interests and knowledge onto public knowledge graphs, and leverages existing search log infrastructure, thereby mitigating the privacy, compliance, and scalability concerns associated with building deep user profiles for personalization. We then validate our approach on the task of contextual query suggestion, which requires understanding not only the user's current search context but also what they historically know and care about. Through a number of experiments based on human evaluation, we show that our approach is significantly better than several other LLM-powered baselines, generating query suggestions that are contextually more relevant, personalized, and useful.

  • 5 authors
·
Nov 9, 2023

Multi-level Matching Network for Multimodal Entity Linking

Multimodal entity linking (MEL) aims to link ambiguous mentions within multimodal contexts to corresponding entities in a multimodal knowledge base. Most existing approaches to MEL are based on representation learning or vision-and-language pre-training mechanisms for exploring the complementary effect among multiple modalities. However, these methods suffer from two limitations. On the one hand, they overlook the possibility of considering negative samples from the same modality. On the other hand, they lack mechanisms to capture bidirectional cross-modal interaction. To address these issues, we propose a Multi-level Matching network for Multimodal Entity Linking (M3EL). Specifically, M3EL is composed of three different modules: (i) a Multimodal Feature Extraction module, which extracts modality-specific representations with a multimodal encoder and introduces an intra-modal contrastive learning sub-module to obtain better discriminative embeddings based on uni-modal differences; (ii) an Intra-modal Matching Network module, which contains two levels of matching granularity: Coarse-grained Global-to-Global and Fine-grained Global-to-Local, to achieve local and global level intra-modal interaction; (iii) a Cross-modal Matching Network module, which applies bidirectional strategies, Textual-to-Visual and Visual-to-Textual matching, to implement bidirectional cross-modal interaction. Extensive experiments conducted on WikiMEL, RichpediaMEL, and WikiDiverse datasets demonstrate the outstanding performance of M3EL when compared to the state-of-the-art baselines.

  • 4 authors
·
Dec 11, 2024

Learning to Detect Relevant Contexts and Knowledge for Response Selection in Retrieval-based Dialogue Systems

Recently, knowledge-grounded conversations in the open domain gain great attention from researchers. Existing works on retrieval-based dialogue systems have paid tremendous efforts to utilize neural networks to build a matching model, where all of the context and knowledge contents are used to match the response candidate with various representation methods. Actually, different parts of the context and knowledge are differentially important for recognizing the proper response candidate, as many utterances are useless due to the topic shift. Those excessive useless information in the context and knowledge can influence the matching process and leads to inferior performance. To address this problem, we propose a multi-turn Response Selection Model that can Detect the relevant parts of the Context and Knowledge collection (RSM-DCK). Our model first uses the recent context as a query to pre-select relevant parts of the context and knowledge collection at the word-level and utterance-level semantics. Further, the response candidate interacts with the selected context and knowledge collection respectively. In the end, The fused representation of the context and response candidate is utilized to post-select the relevant parts of the knowledge collection more confidently for matching. We test our proposed model on two benchmark datasets. Evaluation results indicate that our model achieves better performance than the existing methods, and can effectively detect the relevant context and knowledge for response selection.

  • 5 authors
·
Sep 26, 2025

Dual-View Training for Instruction-Following Information Retrieval

Instruction-following information retrieval (IF-IR) studies retrieval systems that must not only find documents relevant to a query, but also obey explicit user constraints such as required attributes, exclusions, or output preferences. However, most retrievers are trained primarily for semantic relevance and often fail to distinguish documents that match the topic from those that satisfy the instruction. We propose a dual-view data synthesis strategy based on polarity reversal: given a query, a document that is relevant under the instruction, and a hard negative that matches the query but violates the instruction, we prompt an LLM to generate a complementary instruction under which the two documents swap relevance labels. By presenting the same document pair under complementary instructions that invert their relevance labels, the training signal forces the retriever to reconsider the same candidate set through the instruction, rather than relying on fixed topical cues. On a 305M-parameter encoder, our method improves performance on the FollowIR benchmark by 45%, surpassing general-purpose embedding models of comparable or larger scale. Through head-to-head comparisons at matched data budgets, we further show that data diversity and instruction supervision play complementary roles: the former preserves general retrieval quality, while the latter improves instruction sensitivity. These results highlight the value of targeted data synthesis for building retrieval systems that are both broadly capable and instruction-aware.

Snowflake Snowflake
·
Apr 19 2

Retrieval-Augmented Code Generation for Universal Information Extraction

Information Extraction (IE) aims to extract structural knowledge (e.g., entities, relations, events) from natural language texts, which brings challenges to existing methods due to task-specific schemas and complex text expressions. Code, as a typical kind of formalized language, is capable of describing structural knowledge under various schemas in a universal way. On the other hand, Large Language Models (LLMs) trained on both codes and texts have demonstrated powerful capabilities of transforming texts into codes, which provides a feasible solution to IE tasks. Therefore, in this paper, we propose a universal retrieval-augmented code generation framework based on LLMs, called Code4UIE, for IE tasks. Specifically, Code4UIE adopts Python classes to define task-specific schemas of various structural knowledge in a universal way. By so doing, extracting knowledge under these schemas can be transformed into generating codes that instantiate the predefined Python classes with the information in texts. To generate these codes more precisely, Code4UIE adopts the in-context learning mechanism to instruct LLMs with examples. In order to obtain appropriate examples for different tasks, Code4UIE explores several example retrieval strategies, which can retrieve examples semantically similar to the given texts. Extensive experiments on five representative IE tasks across nine datasets demonstrate the effectiveness of the Code4UIE framework.

  • 11 authors
·
Nov 6, 2023