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Sep 1

LinearRAG: Linear Graph Retrieval Augmented Generation on Large-scale Corpora

Retrieval-Augmented Generation (RAG) is widely used to mitigate hallucinations of Large Language Models (LLMs) by leveraging external knowledge. While effective for simple queries, traditional RAG systems struggle with large-scale, unstructured corpora where information is fragmented. Recent advances incorporate knowledge graphs to capture relational structures, enabling more comprehensive retrieval for complex, multi-hop reasoning tasks. However, existing graph-based RAG (GraphRAG) methods rely on unstable and costly relation extraction for graph construction, often producing noisy graphs with incorrect or inconsistent relations that degrade retrieval quality. In this paper, we revisit the pipeline of existing GraphRAG systems and propose LinearRAG (Linear Graph-based Retrieval-Augmented Generation), an efficient framework that enables reliable graph construction and precise passage retrieval. Specifically, LinearRAG constructs a relation-free hierarchical graph, termed Tri-Graph, using only lightweight entity extraction and semantic linking, avoiding unstable relation modeling. This new paradigm of graph construction scales linearly with corpus size and incurs no extra token consumption, providing an economical and reliable indexing of the original passages. For retrieval, LinearRAG adopts a two-stage strategy: (i) relevant entity activation via local semantic bridging, followed by (ii) passage retrieval through global importance aggregation. Extensive experiments on four datasets demonstrate that LinearRAG significantly outperforms baseline models.

  • 8 authors
·
Oct 11, 2025

PAGER: Bridging the Semantic-Execution Gap in Point-Precise Geometric GUI Control

Large vision-language models have significantly advanced GUI agents, enabling executable interaction across web, mobile, and desktop interfaces. Yet these gains largely rely on a forgiving region-tolerant paradigm, where many nearby pixels inside the same component remain valid. Precise geometric construction breaks this assumption: actions must land on points in continuous canvas space rather than tolerant regions. Because geometric primitives carry ontological dependencies, a local coordinate error can induce cascading topological failures that distort downstream objects and invalidate the final construction. We identify this regime as precision-sensitive GUI tasks, requiring point-level accuracy, geometry-aware verification, and robustness to dependency-driven error propagation. To benchmark it, we introduce PAGE Bench, with 4,906 problems and over 224K process-supervised, pixel-level GUI actions. We further propose PAGER, a topology-aware agent that decomposes construction into dependency-structured planning and pixel-level execution. Pixel-grounded supervised tuning establishes executable action grammar, while precision-aligned reinforcement learning mitigates rollout-induced exposure bias through state-conditioned geometric feedback. Experiments reveal a pronounced Semantic-Execution Gap: general multimodal models can exceed 88% action type accuracy yet remain below 6% task success. PAGER closes this gap, delivering 4.1x higher task success than the strongest evaluated general baseline and raising step success rate from below 9% for GUI-specialized agents to over 62%, establishing a new state of the art for point-precise GUI control.

opendatalab OpenDataLab
·
May 14 1

Grounded Forcing: Bridging Time-Independent Semantics and Proximal Dynamics in Autoregressive Video Synthesis

Autoregressive video synthesis offers a promising pathway for infinite-horizon generation but is fundamentally hindered by three intertwined challenges: semantic forgetting from context limitations, visual drift due to positional extrapolation, and controllability loss during interactive instruction switching. Current methods often tackle these issues in isolation, limiting long-term coherence. We introduce Grounded Forcing, a novel framework that bridges time-independent semantics and proximal dynamics through three interlocking mechanisms. First, to address semantic forgetting, we propose a Dual Memory KV Cache that decouples local temporal dynamics from global semantic anchors, ensuring long-term semantic coherence and identity stability. Second, to suppress visual drift, we design Dual-Reference RoPE Injection, which confines positional embeddings within the training manifold while rendering global semantics time-invariant. Third, to resolve controllability issues, we develop Asymmetric Proximity Recache, which facilitates smooth semantic inheritance during prompt transitions via proximity-weighted cache updates. These components operate synergistically to tether the generative process to stable semantic cores while accommodating flexible local dynamics. Extensive experiments demonstrate that Grounded Forcing significantly enhances long-range consistency and visual stability, establishing a robust foundation for interactive long-form video synthesis.

  • 5 authors
·
Apr 12

Beyond Cosine Similarity: Taming Semantic Drift and Antonym Intrusion in a 15-Million Node Turkish Synonym Graph

Neural embeddings have a notorious blind spot: they can't reliably tell synonyms apart from antonyms. Consequently, increasing similarity thresholds often fails to prevent opposites from being grouped together. We've built a large-scale semantic clustering system specifically designed to tackle this problem head on. Our pipeline chews through 15 million lexical items, evaluates a massive 520 million potential relationships, and ultimately generates 2.9 million high-precision semantic clusters. The system makes three primary contributions. First, we introduce a labeled dataset of 843,000 concept pairs spanning synonymy, antonymy, and co-hyponymy, constructed via Gemini 2.5-Flash LLM augmentation and verified using human-curated dictionary resources. Second, we propose a specialized three-way semantic relation discriminator that achieves 90% macro-F1, enabling robust disambiguation beyond raw embedding similarity. Third, we introduce a novel soft-to-hard clustering algorithm that mitigates semantic drift preventing erroneous transitive chains (e.g., hot -> spicy -> pain -> depression) while simultaneously resolving polysemy. Our approach employs a topology-aware two-stage expansion-pruning procedure with topological voting, ensuring that each term is assigned to exactly one semantically coherent cluster. The resulting resource enables high-precision semantic search and retrieval-augmented generation, particularly for morphologically rich and low-resource languages where existing synonym databases remain sparse.

  • 4 authors
·
Jan 19 2

RAG-Anything: All-in-One RAG Framework

Retrieval-Augmented Generation (RAG) has emerged as a fundamental paradigm for expanding Large Language Models beyond their static training limitations. However, a critical misalignment exists between current RAG capabilities and real-world information environments. Modern knowledge repositories are inherently multimodal, containing rich combinations of textual content, visual elements, structured tables, and mathematical expressions. Yet existing RAG frameworks are limited to textual content, creating fundamental gaps when processing multimodal documents. We present RAG-Anything, a unified framework that enables comprehensive knowledge retrieval across all modalities. Our approach reconceptualizes multimodal content as interconnected knowledge entities rather than isolated data types. The framework introduces dual-graph construction to capture both cross-modal relationships and textual semantics within a unified representation. We develop cross-modal hybrid retrieval that combines structural knowledge navigation with semantic matching. This enables effective reasoning over heterogeneous content where relevant evidence spans multiple modalities. RAG-Anything demonstrates superior performance on challenging multimodal benchmarks, achieving significant improvements over state-of-the-art methods. Performance gains become particularly pronounced on long documents where traditional approaches fail. Our framework establishes a new paradigm for multimodal knowledge access, eliminating the architectural fragmentation that constrains current systems. Our framework is open-sourced at: https://github.com/HKUDS/RAG-Anything.

VCU-Bridge: Hierarchical Visual Connotation Understanding via Semantic Bridging

While Multimodal Large Language Models (MLLMs) excel on benchmarks, their processing paradigm differs from the human ability to integrate visual information. Unlike humans who naturally bridge details and high-level concepts, models tend to treat these elements in isolation. Prevailing evaluation protocols often decouple low-level perception from high-level reasoning, overlooking their semantic and causal dependencies, which yields non-diagnostic results and obscures performance bottlenecks. We present VCU-Bridge, a framework that operationalizes a human-like hierarchy of visual connotation understanding: multi-level reasoning that advances from foundational perception through semantic bridging to abstract connotation, with an explicit evidence-to-inference trace from concrete cues to abstract conclusions. Building on this framework, we construct HVCU-Bench, a benchmark for hierarchical visual connotation understanding with explicit, level-wise diagnostics. Comprehensive experiments demonstrate a consistent decline in performance as reasoning progresses to higher levels. We further develop a data generation pipeline for instruction tuning guided by Monte Carlo Tree Search (MCTS) and show that strengthening low-level capabilities yields measurable gains at higher levels. Interestingly, it not only improves on HVCU-Bench but also brings benefits on general benchmarks (average +2.53%), especially with substantial gains on MMStar (+7.26%), demonstrating the significance of the hierarchical thinking pattern and its effectiveness in enhancing MLLM capabilities. The project page is at https://vcu-bridge.github.io .

  • 9 authors
·
Nov 22, 2025

A Massive Scale Semantic Similarity Dataset of Historical English

A diversity of tasks use language models trained on semantic similarity data. While there are a variety of datasets that capture semantic similarity, they are either constructed from modern web data or are relatively small datasets created in the past decade by human annotators. This study utilizes a novel source, newly digitized articles from off-copyright, local U.S. newspapers, to assemble a massive-scale semantic similarity dataset spanning 70 years from 1920 to 1989 and containing nearly 400M positive semantic similarity pairs. Historically, around half of articles in U.S. local newspapers came from newswires like the Associated Press. While local papers reproduced articles from the newswire, they wrote their own headlines, which form abstractive summaries of the associated articles. We associate articles and their headlines by exploiting document layouts and language understanding. We then use deep neural methods to detect which articles are from the same underlying source, in the presence of substantial noise and abridgement. The headlines of reproduced articles form positive semantic similarity pairs. The resulting publicly available HEADLINES dataset is significantly larger than most existing semantic similarity datasets and covers a much longer span of time. It will facilitate the application of contrastively trained semantic similarity models to a variety of tasks, including the study of semantic change across space and time.

  • 2 authors
·
Jun 30, 2023

Higher-Order Knowledge Representations for Agentic Scientific Reasoning

Scientific inquiry requires systems-level reasoning that integrates heterogeneous experimental data, cross-domain knowledge, and mechanistic evidence into coherent explanations. While Large Language Models (LLMs) offer inferential capabilities, they often depend on retrieval-augmented contexts that lack structural depth. Traditional Knowledge Graphs (KGs) attempt to bridge this gap, yet their pairwise constraints fail to capture the irreducible higher-order interactions that govern emergent physical behavior. To address this, we introduce a methodology for constructing hypergraph-based knowledge representations that faithfully encode multi-entity relationships. Applied to a corpus of ~1,100 manuscripts on biocomposite scaffolds, our framework constructs a global hypergraph of 161,172 nodes and 320,201 hyperedges, revealing a scale-free topology (power law exponent ~1.23) organized around highly connected conceptual hubs. This representation prevents the combinatorial explosion typical of pairwise expansions and explicitly preserves the co-occurrence context of scientific formulations. We further demonstrate that equipping agentic systems with hypergraph traversal tools, specifically using node-intersection constraints, enables them to bridge semantically distant concepts. By exploiting these higher-order pathways, the system successfully generates grounded mechanistic hypotheses for novel composite materials, such as linking cerium oxide to PCL scaffolds via chitosan intermediates. This work establishes a "teacherless" agentic reasoning system where hypergraph topology acts as a verifiable guardrail, accelerating scientific discovery by uncovering relationships obscured by traditional graph methods.

  • 2 authors
·
Jan 8

LeanRAG: Knowledge-Graph-Based Generation with Semantic Aggregation and Hierarchical Retrieval

Retrieval-Augmented Generation (RAG) plays a crucial role in grounding Large Language Models by leveraging external knowledge, whereas the effectiveness is often compromised by the retrieval of contextually flawed or incomplete information. To address this, knowledge graph-based RAG methods have evolved towards hierarchical structures, organizing knowledge into multi-level summaries. However, these approaches still suffer from two critical, unaddressed challenges: high-level conceptual summaries exist as disconnected ``semantic islands'', lacking the explicit relations needed for cross-community reasoning; and the retrieval process itself remains structurally unaware, often degenerating into an inefficient flat search that fails to exploit the graph's rich topology. To overcome these limitations, we introduce LeanRAG, a framework that features a deeply collaborative design combining knowledge aggregation and retrieval strategies. LeanRAG first employs a novel semantic aggregation algorithm that forms entity clusters and constructs new explicit relations among aggregation-level summaries, creating a fully navigable semantic network. Then, a bottom-up, structure-guided retrieval strategy anchors queries to the most relevant fine-grained entities and then systematically traverses the graph's semantic pathways to gather concise yet contextually comprehensive evidence sets. The LeanRAG can mitigate the substantial overhead associated with path retrieval on graphs and minimizes redundant information retrieval. Extensive experiments on four challenging QA benchmarks with different domains demonstrate that LeanRAG significantly outperforming existing methods in response quality while reducing 46\% retrieval redundancy. Code is available at: https://github.com/RaZzzyz/LeanRAG

  • 8 authors
·
Aug 14, 2025 1

Exploring Non-Verbal Predicates in Semantic Role Labeling: Challenges and Opportunities

Although we have witnessed impressive progress in Semantic Role Labeling (SRL), most of the research in the area is carried out assuming that the majority of predicates are verbs. Conversely, predicates can also be expressed using other parts of speech, e.g., nouns and adjectives. However, non-verbal predicates appear in the benchmarks we commonly use to measure progress in SRL less frequently than in some real-world settings -- newspaper headlines, dialogues, and tweets, among others. In this paper, we put forward a new PropBank dataset which boasts wide coverage of multiple predicate types. Thanks to it, we demonstrate empirically that standard benchmarks do not provide an accurate picture of the current situation in SRL and that state-of-the-art systems are still incapable of transferring knowledge across different predicate types. Having observed these issues, we also present a novel, manually-annotated challenge set designed to give equal importance to verbal, nominal, and adjectival predicate-argument structures. We use such dataset to investigate whether we can leverage different linguistic resources to promote knowledge transfer. In conclusion, we claim that SRL is far from "solved", and its integration with other semantic tasks might enable significant improvements in the future, especially for the long tail of non-verbal predicates, thereby facilitating further research on SRL for non-verbal predicates.

  • 3 authors
·
Jul 4, 2023

Localist LLMs with Recruitment Learning

We present a novel framework for training large language models with continuously adjustable internal representations that span the full spectrum from localist (interpretable, rule-based) to distributed (generalizable, efficient) encodings. The key innovations are (1) a locality dial, a tunable parameter that dynamically controls the degree of localization during both training and inference without requiring model retraining, (2) an information-theoretic recruitment mechanism that adaptively allocates semantic blocks as needed, eliminating the requirement for complete domain knowledge at initialization, and (3) a hierarchical recruitment framework that extends capacity allocation to entire specialized LLMs, enabling multi-granularity architectural adaptation. This is achieved through group sparsity penalties on attention mechanisms, information-theoretic anchor design, dynamic rule injection, and principled recruitment criteria based on penalized likelihood with explicit units. We provide rigorous mathematical results establishing explicit threshold conditions under which attention provably concentrates on semantically relevant blocks at stationary points, with exact bounds on attention entropy and pointer fidelity. The hierarchical recruitment mechanism provides convergence guarantees at both the block level (fine-grained, within-LLM) and the LLM level (coarse-grained, cross-domain), ensuring the system discovers semantic partitions that balance model complexity against data encoding efficiency. This framework enables practitioners to continuously interpolate between interpretable and high-performance modes while adapting architectural capacity at multiple granularities, supporting applications in regulated domains requiring both transparency and capability.

  • 1 authors
·
Oct 20, 2025

Text-Video Retrieval with Global-Local Semantic Consistent Learning

Adapting large-scale image-text pre-training models, e.g., CLIP, to the video domain represents the current state-of-the-art for text-video retrieval. The primary approaches involve transferring text-video pairs to a common embedding space and leveraging cross-modal interactions on specific entities for semantic alignment. Though effective, these paradigms entail prohibitive computational costs, leading to inefficient retrieval. To address this, we propose a simple yet effective method, Global-Local Semantic Consistent Learning (GLSCL), which capitalizes on latent shared semantics across modalities for text-video retrieval. Specifically, we introduce a parameter-free global interaction module to explore coarse-grained alignment. Then, we devise a shared local interaction module that employs several learnable queries to capture latent semantic concepts for learning fine-grained alignment. Furthermore, an Inter-Consistency Loss (ICL) is devised to accomplish the concept alignment between the visual query and corresponding textual query, and an Intra-Diversity Loss (IDL) is developed to repulse the distribution within visual (textual) queries to generate more discriminative concepts. Extensive experiments on five widely used benchmarks (i.e., MSR-VTT, MSVD, DiDeMo, LSMDC, and ActivityNet) substantiate the superior effectiveness and efficiency of the proposed method. Remarkably, our method achieves comparable performance with SOTA as well as being nearly 220 times faster in terms of computational cost. Code is available at: https://github.com/zchoi/GLSCL.

  • 7 authors
·
May 21, 2024

OpenGloss: A Synthetic Encyclopedic Dictionary and Semantic Knowledge Graph

We present OpenGloss, a synthetic encyclopedic dictionary and semantic knowledge graph for English that integrates lexicographic definitions, encyclopedic context, etymological histories, and semantic relationships in a unified resource. OpenGloss contains 537K senses across 150K lexemes, on par with WordNet 3.1 and Open English WordNet, while providing more than four times as many sense definitions. These lexemes include 9.1M semantic edges, 1M usage examples, 3M collocations, and 60M words of encyclopedic content. Generated through a multi-agent procedural generation pipeline with schema-validated LLM outputs and automated quality assurance, the entire resource was produced in under one week for under $1,000. This demonstrates that structured generation can create comprehensive lexical resources at cost and time scales impractical for manual curation, enabling rapid iteration as foundation models improve. The resource addresses gaps in pedagogical applications by providing integrated content -- definitions, examples, collocations, encyclopedias, etymology -- that supports both vocabulary learning and natural language processing tasks. As a synthetically generated resource, OpenGloss reflects both the capabilities and limitations of current foundation models. The dataset is publicly available on Hugging Face under CC-BY 4.0, enabling researchers and educators to build upon and adapt this resource.

  • 1 authors
·
Nov 23, 2025

A Joint Model for Definition Extraction with Syntactic Connection and Semantic Consistency

Definition Extraction (DE) is one of the well-known topics in Information Extraction that aims to identify terms and their corresponding definitions in unstructured texts. This task can be formalized either as a sentence classification task (i.e., containing term-definition pairs or not) or a sequential labeling task (i.e., identifying the boundaries of the terms and definitions). The previous works for DE have only focused on one of the two approaches, failing to model the inter-dependencies between the two tasks. In this work, we propose a novel model for DE that simultaneously performs the two tasks in a single framework to benefit from their inter-dependencies. Our model features deep learning architectures to exploit the global structures of the input sentences as well as the semantic consistencies between the terms and the definitions, thereby improving the quality of the representation vectors for DE. Besides the joint inference between sentence classification and sequential labeling, the proposed model is fundamentally different from the prior work for DE in that the prior work has only employed the local structures of the input sentences (i.e., word-to-word relations), and not yet considered the semantic consistencies between terms and definitions. In order to implement these novel ideas, our model presents a multi-task learning framework that employs graph convolutional neural networks and predicts the dependency paths between the terms and the definitions. We also seek to enforce the consistency between the representations of the terms and definitions both globally (i.e., increasing semantic consistency between the representations of the entire sentences and the terms/definitions) and locally (i.e., promoting the similarity between the representations of the terms and the definitions).

  • 4 authors
·
Nov 5, 2019

HELP: HyperNode Expansion and Logical Path-Guided Evidence Localization for Accurate and Efficient GraphRAG

Large Language Models (LLMs) often struggle with inherent knowledge boundaries and hallucinations, limiting their reliability in knowledge-intensive tasks. While Retrieval-Augmented Generation (RAG) mitigates these issues, it frequently overlooks structural interdependencies essential for multi-hop reasoning. Graph-based RAG approaches attempt to bridge this gap, yet they typically face trade-offs between accuracy and efficiency due to challenges such as costly graph traversals and semantic noise in LLM-generated summaries. In this paper, we propose HyperNode Expansion and Logical Path-Guided Evidence Localization strategies for GraphRAG (HELP), a novel framework designed to balance accuracy with practical efficiency through two core strategies: 1) HyperNode Expansion, which iteratively chains knowledge triplets into coherent reasoning paths abstracted as HyperNodes to capture complex structural dependencies and ensure retrieval accuracy; and 2) Logical Path-Guided Evidence Localization, which leverages precomputed graph-text correlations to map these paths directly to the corpus for superior efficiency. HELP avoids expensive random walks and semantic distortion, preserving knowledge integrity while drastically reducing retrieval latency. Extensive experiments demonstrate that HELP achieves competitive performance across multiple simple and multi-hop QA benchmarks and up to a 28.8times speedup over leading Graph-based RAG baselines.

  • 7 authors
·
Feb 24

Augmenting Textual Generation via Topology Aware Retrieval

Despite the impressive advancements of Large Language Models (LLMs) in generating text, they are often limited by the knowledge contained in the input and prone to producing inaccurate or hallucinated content. To tackle these issues, Retrieval-augmented Generation (RAG) is employed as an effective strategy to enhance the available knowledge base and anchor the responses in reality by pulling additional texts from external databases. In real-world applications, texts are often linked through entities within a graph, such as citations in academic papers or comments in social networks. This paper exploits these topological relationships to guide the retrieval process in RAG. Specifically, we explore two kinds of topological connections: proximity-based, focusing on closely connected nodes, and role-based, which looks at nodes sharing similar subgraph structures. Our empirical research confirms their relevance to text relationships, leading us to develop a Topology-aware Retrieval-augmented Generation framework. This framework includes a retrieval module that selects texts based on their topological relationships and an aggregation module that integrates these texts into prompts to stimulate LLMs for text generation. We have curated established text-attributed networks and conducted comprehensive experiments to validate the effectiveness of this framework, demonstrating its potential to enhance RAG with topological awareness.

  • 9 authors
·
May 27, 2024

LocalSearchBench: Benchmarking Agentic Search in Real-World Local Life Services

Recent advances in large reasoning models (LRMs) have enabled agentic search systems to perform complex multi-step reasoning across multiple sources. However, most studies focus on general information retrieval and rarely explores vertical domains with unique challenges. In this work, we focus on local life services and introduce LocalSearchBench, which encompass diverse and complex business scenarios. Real-world queries in this domain are often ambiguous and require multi-hop reasoning across merchants and products, remaining challenging and not fully addressed. As the first comprehensive benchmark for agentic search in local life services, LocalSearchBench includes over 150,000 high-quality entries from various cities and business types. We construct 300 multi-hop QA tasks based on real user queries, challenging agents to understand questions and retrieve information in multiple steps. We also developed LocalPlayground, a unified environment integrating multiple tools for agent interaction. Experiments show that even state-of-the-art LRMs struggle on LocalSearchBench: the best model (DeepSeek-V3.1) achieves only 34.34% correctness, and most models have issues with completeness (average 77.33%) and faithfulness (average 61.99%). This highlights the need for specialized benchmarks and domain-specific agent training in local life services. Code, Benchmark, and Leaderboard are available at localsearchbench.github.io.

  • 14 authors
·
Dec 8, 2025

Distributional semantic modeling: a revised technique to train term/word vector space models applying the ontology-related approach

We design a new technique for the distributional semantic modeling with a neural network-based approach to learn distributed term representations (or term embeddings) - term vector space models as a result, inspired by the recent ontology-related approach (using different types of contextual knowledge such as syntactic knowledge, terminological knowledge, semantic knowledge, etc.) to the identification of terms (term extraction) and relations between them (relation extraction) called semantic pre-processing technology - SPT. Our method relies on automatic term extraction from the natural language texts and subsequent formation of the problem-oriented or application-oriented (also deeply annotated) text corpora where the fundamental entity is the term (includes non-compositional and compositional terms). This gives us an opportunity to changeover from distributed word representations (or word embeddings) to distributed term representations (or term embeddings). This transition will allow to generate more accurate semantic maps of different subject domains (also, of relations between input terms - it is useful to explore clusters and oppositions, or to test your hypotheses about them). The semantic map can be represented as a graph using Vec2graph - a Python library for visualizing word embeddings (term embeddings in our case) as dynamic and interactive graphs. The Vec2graph library coupled with term embeddings will not only improve accuracy in solving standard NLP tasks, but also update the conventional concept of automated ontology development. The main practical result of our work is the development kit (set of toolkits represented as web service APIs and web application), which provides all necessary routines for the basic linguistic pre-processing and the semantic pre-processing of the natural language texts in Ukrainian for future training of term vector space models.

  • 4 authors
·
Mar 6, 2020

Probing Natural Language Inference Models through Semantic Fragments

Do state-of-the-art models for language understanding already have, or can they easily learn, abilities such as boolean coordination, quantification, conditionals, comparatives, and monotonicity reasoning (i.e., reasoning about word substitutions in sentential contexts)? While such phenomena are involved in natural language inference (NLI) and go beyond basic linguistic understanding, it is unclear the extent to which they are captured in existing NLI benchmarks and effectively learned by models. To investigate this, we propose the use of semantic fragments---systematically generated datasets that each target a different semantic phenomenon---for probing, and efficiently improving, such capabilities of linguistic models. This approach to creating challenge datasets allows direct control over the semantic diversity and complexity of the targeted linguistic phenomena, and results in a more precise characterization of a model's linguistic behavior. Our experiments, using a library of 8 such semantic fragments, reveal two remarkable findings: (a) State-of-the-art models, including BERT, that are pre-trained on existing NLI benchmark datasets perform poorly on these new fragments, even though the phenomena probed here are central to the NLI task. (b) On the other hand, with only a few minutes of additional fine-tuning---with a carefully selected learning rate and a novel variation of "inoculation"---a BERT-based model can master all of these logic and monotonicity fragments while retaining its performance on established NLI benchmarks.

  • 4 authors
·
Sep 16, 2019

DeepGen 1.0: A Lightweight Unified Multimodal Model for Advancing Image Generation and Editing

Current unified multimodal models for image generation and editing typically rely on massive parameter scales (e.g., >10B), entailing prohibitive training costs and deployment footprints. In this work, we present DeepGen 1.0, a lightweight 5B unified model that achieves comprehensive capabilities competitive with or surpassing much larger counterparts. To overcome the limitations of compact models in semantic understanding and fine-grained control, we introduce Stacked Channel Bridging (SCB), a deep alignment framework that extracts hierarchical features from multiple VLM layers and fuses them with learnable 'think tokens' to provide the generative backbone with structured, reasoning-rich guidance. We further design a data-centric training strategy spanning three progressive stages: (1) Alignment Pre-training on large-scale image-text pairs and editing triplets to synchronize VLM and DiT representations, (2) Joint Supervised Fine-tuning on a high-quality mixture of generation, editing, and reasoning tasks to foster omni-capabilities, and (3) Reinforcement Learning with MR-GRPO, which leverages a mixture of reward functions and supervision signals, resulting in substantial gains in generation quality and alignment with human preferences, while maintaining stable training progress and avoiding visual artifacts. Despite being trained on only ~50M samples, DeepGen 1.0 achieves leading performance across diverse benchmarks, surpassing the 80B HunyuanImage by 28% on WISE and the 27B Qwen-Image-Edit by 37% on UniREditBench. By open-sourcing our training code, weights, and datasets, we provide an efficient, high-performance alternative to democratize unified multimodal research.

Beyond Nearest Neighbors: Semantic Compression and Graph-Augmented Retrieval for Enhanced Vector Search

Vector databases typically rely on approximate nearest neighbor (ANN) search to retrieve the top-k closest vectors to a query in embedding space. While effective, this approach often yields semantically redundant results, missing the diversity and contextual richness required by applications such as retrieval-augmented generation (RAG), multi-hop QA, and memory-augmented agents. We introduce a new retrieval paradigm: semantic compression, which aims to select a compact, representative set of vectors that captures the broader semantic structure around a query. We formalize this objective using principles from submodular optimization and information geometry, and show that it generalizes traditional top-k retrieval by prioritizing coverage and diversity. To operationalize this idea, we propose graph-augmented vector retrieval, which overlays semantic graphs (e.g., kNN or knowledge-based links) atop vector spaces to enable multi-hop, context-aware search. We theoretically analyze the limitations of proximity-based retrieval under high-dimensional concentration and highlight how graph structures can improve semantic coverage. Our work outlines a foundation for meaning-centric vector search systems, emphasizing hybrid indexing, diversity-aware querying, and structured semantic retrieval. We make our implementation publicly available to foster future research in this area.

  • 2 authors
·
Jul 25, 2025

AILA--First Experiments with Localist Language Models

This paper presents the first empirical demonstration of controllable locality in transformer language models, a novel architectural framework that enables continuous control over the degree of representation localization through a tunable locality dial parameter. Unlike traditional language models that rely exclusively on distributed representations, our approach allows dynamic interpolation between highly interpretable localist encodings and efficient distributed representations without requiring model retraining. We conducted experiments on the WikiText corpus using a two-layer transformer architecture, systematically varying the locality parameter λ across the full spectrum from 1.0 (fully localist) to 0.0 (fully distributed). Our results demonstrate that localist configurations achieve dramatically lower attention entropy, with λ = 1.0 yielding 5.36 bits compared to 7.18 bits at λ = 0.0, while maintaining substantially higher pointer fidelity scores reflecting stronger alignment with rule-specified targets. Prediction experiments reveal that intermediate locality values optimize the tradeoff between interpretability and performance, with λ = 0.6 achieving test perplexity of 4.65 and accuracy of 84.7%. These findings establish that localist language models provide a practical framework for applications in regulated domains requiring both transparency and capability, offering precise mathematical control over the interpretability-performance spectrum through explicit penalty thresholds and information-theoretic design principles.

  • 1 authors
·
Nov 5, 2025

GraspLLM: Towards Zero-Shot Generalization on Text-Attributed Graphs with LLMs

Research on Text-Attributed Graphs (TAGs) has gained significant attention recently due to its broad applications across various real-world data scenarios, such as citation networks, e-commerce platforms, social media, and web pages. Inspired by the remarkable semantic understanding ability of Large Language Models (LLMs), there have been numerous attempts to integrate LLMs into TAGs. However, existing methods still struggle to generalize across diverse graphs and tasks, and their ability to capture transferable graph structural patterns remains limited. To address this, we introduce the GraspLLM, a framework that combines Graph structural comprehension with semantic understanding prowess of LLMs to enhance the cross-dataset and cross-task generalizability. Specifically, we represent node texts from different graphs in a unified semantic space with a frozen general embedding model, on top of which we perform motif-aware contrastive learning across multiple motif-induced adjacency matrices to extract dataset-agnostic structural information. Then, with our proposed optimal contextual subgraph, we extract the most contextually relevant subgraph for each target node and align these subgraphs to the token space of LLM via an alignment projector. Extensive experiments on TAG benchmark datasets spanning diverse domains reveal that GraspLLM consistently outperforms previous LLM-based methods for TAGs, especially in zero-shot scenarios, highlighting its strong generalizability across different datasets and tasks. Our code is available at https://github.com/Heinz217/GraspLLM.

  • 5 authors
·
Jun 10

Large Language Models Meet Text-Attributed Graphs: A Survey of Integration Frameworks and Applications

Large Language Models (LLMs) have achieved remarkable success in natural language processing through strong semantic understanding and generation. However, their black-box nature limits structured and multi-hop reasoning. In contrast, Text-Attributed Graphs (TAGs) provide explicit relational structures enriched with textual context, yet often lack semantic depth. Recent research shows that combining LLMs and TAGs yields complementary benefits: enhancing TAG representation learning and improving the reasoning and interpretability of LLMs. This survey provides the first systematic review of LLM--TAG integration from an orchestration perspective. We introduce a novel taxonomy covering two fundamental directions: LLM for TAG, where LLMs enrich graph-based tasks, and TAG for LLM, where structured graphs improve LLM reasoning. We categorize orchestration strategies into sequential, parallel, and multi-module frameworks, and discuss advances in TAG-specific pretraining, prompting, and parameter-efficient fine-tuning. Beyond methodology, we summarize empirical insights, curate available datasets, and highlight diverse applications across recommendation systems, biomedical analysis, and knowledge-intensive question answering. Finally, we outline open challenges and promising research directions, aiming to guide future work at the intersection of language and graph learning.

  • 6 authors
·
Oct 23, 2025

Do LLMs Really Adapt to Domains? An Ontology Learning Perspective

Large Language Models (LLMs) have demonstrated unprecedented prowess across various natural language processing tasks in various application domains. Recent studies show that LLMs can be leveraged to perform lexical semantic tasks, such as Knowledge Base Completion (KBC) or Ontology Learning (OL). However, it has not effectively been verified whether their success is due to their ability to reason over unstructured or semi-structured data, or their effective learning of linguistic patterns and senses alone. This unresolved question is particularly crucial when dealing with domain-specific data, where the lexical senses and their meaning can completely differ from what a LLM has learned during its training stage. This paper investigates the following question: Do LLMs really adapt to domains and remain consistent in the extraction of structured knowledge, or do they only learn lexical senses instead of reasoning? To answer this question and, we devise a controlled experiment setup that uses WordNet to synthesize parallel corpora, with English and gibberish terms. We examine the differences in the outputs of LLMs for each corpus in two OL tasks: relation extraction and taxonomy discovery. Empirical results show that, while adapting to the gibberish corpora, off-the-shelf LLMs do not consistently reason over semantic relationships between concepts, and instead leverage senses and their frame. However, fine-tuning improves the performance of LLMs on lexical semantic tasks even when the domain-specific terms are arbitrary and unseen during pre-training, hinting at the applicability of pre-trained LLMs for OL.

  • 3 authors
·
Jul 29, 2024

Agentic Deep Graph Reasoning Yields Self-Organizing Knowledge Networks

We present an agentic, autonomous graph expansion framework that iteratively structures and refines knowledge in situ. Unlike conventional knowledge graph construction methods relying on static extraction or single-pass learning, our approach couples a reasoning-native large language model with a continually updated graph representation. At each step, the system actively generates new concepts and relationships, merges them into a global graph, and formulates subsequent prompts based on its evolving structure. Through this feedback-driven loop, the model organizes information into a scale-free network characterized by hub formation, stable modularity, and bridging nodes that link disparate knowledge clusters. Over hundreds of iterations, new nodes and edges continue to appear without saturating, while centrality measures and shortest path distributions evolve to yield increasingly distributed connectivity. Our analysis reveals emergent patterns, such as the rise of highly connected 'hub' concepts and the shifting influence of 'bridge' nodes, indicating that agentic, self-reinforcing graph construction can yield open-ended, coherent knowledge structures. Applied to materials design problems, we present compositional reasoning experiments by extracting node-specific and synergy-level principles to foster genuinely novel knowledge synthesis, yielding cross-domain ideas that transcend rote summarization and strengthen the framework's potential for open-ended scientific discovery. We discuss other applications in scientific discovery and outline future directions for enhancing scalability and interpretability.

  • 1 authors
·
Feb 18, 2025

Heterogeneous LLM Methods for Ontology Learning (Few-Shot Prompting, Ensemble Typing, and Attention-Based Taxonomies)

We present a comprehensive system for addressing Tasks A, B, and C of the LLMs4OL 2025 challenge, which together span the full ontology construction pipeline: term extraction, typing, and taxonomy discovery. Our approach combines retrieval-augmented prompting, zero-shot classification, and attention-based graph modeling -- each tailored to the demands of the respective task. For Task A, we jointly extract domain-specific terms and their ontological types using a retrieval-augmented generation (RAG) pipeline. Training data was reformulated into a document to terms and types correspondence, while test-time inference leverages semantically similar training examples. This single-pass method requires no model finetuning and improves overall performance through lexical augmentation Task B, which involves assigning types to given terms, is handled via a dual strategy. In the few-shot setting (for domains with labeled training data), we reuse the RAG scheme with few-shot prompting. In the zero-shot setting (for previously unseen domains), we use a zero-shot classifier that combines cosine similarity scores from multiple embedding models using confidence-based weighting. In Task C, we model taxonomy discovery as graph inference. Using embeddings of type labels, we train a lightweight cross-attention layer to predict is-a relations by approximating a soft adjacency matrix. These modular, task-specific solutions enabled us to achieve top-ranking results in the official leaderboard across all three tasks. Taken together these strategies showcase the scalability, adaptability, and robustness of LLM-based architectures for ontology learning across heterogeneous domains. Code is available at: https://github.com/BelyaevaAlex/LLMs4OL-Challenge-Alexbek

  • 2 authors
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Aug 26, 2025

Relative Representations of Latent Spaces enable Efficient Semantic Channel Equalization

In multi-user semantic communication, language mismatche poses a significant challenge when independently trained agents interact. We present a novel semantic equalization algorithm that enables communication between agents with different languages without additional retraining. Our algorithm is based on relative representations, a framework that enables different agents employing different neural network models to have unified representation. It proceeds by projecting the latent vectors of different models into a common space defined relative to a set of data samples called anchors, whose number equals the dimension of the resulting space. A communication between different agents translates to a communication of semantic symbols sampled from this relative space. This approach, in addition to aligning the semantic representations of different agents, allows compressing the amount of information being exchanged, by appropriately selecting the number of anchors. Eventually, we introduce a novel anchor selection strategy, which advantageously determines prototypical anchors, capturing the most relevant information for the downstream task. Our numerical results show the effectiveness of the proposed approach allowing seamless communication between agents with radically different models, including differences in terms of neural network architecture and datasets used for initial training.

  • 5 authors
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Nov 29, 2024

Locality Alignment Improves Vision-Language Models

Vision language models (VLMs) have seen growing adoption in recent years, but many still struggle with basic spatial reasoning errors. We hypothesize that this is due to VLMs adopting pre-trained vision backbones, specifically vision transformers (ViTs) trained with image-level supervision and minimal inductive biases. Such models may fail to encode the class contents at each position in the image, and our goal is to resolve this by ensuring that the vision backbone effectively captures both local and global image semantics. Our main insight is that we do not require new supervision to learn this capability -- pre-trained models contain significant knowledge of local semantics that we can extract and use for scalable self-supervision. We propose a new efficient post-training stage for ViTs called locality alignment and a novel fine-tuning procedure called MaskEmbed that uses a masked reconstruction loss to learn semantic contributions for each image patch. We first evaluate locality alignment with a vision-only benchmark, finding that it improves a model's performance at a patch-level semantic segmentation task, especially for strong backbones trained with image-caption pairs (e.g., CLIP and SigLIP). We then train a series of VLMs with and without locality alignment, and show that locality-aligned backbones improve performance across a range of benchmarks, particularly ones that involve spatial understanding (e.g., RefCOCO, OCID-Ref, TallyQA, VSR, AI2D). Overall, we demonstrate that we can efficiently learn local semantic extraction via a locality alignment stage, and that this procedure complements existing VLM training recipes that use off-the-shelf vision backbones.

  • 4 authors
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Oct 14, 2024

TheoremGraph: Bridging Formal and Informal Mathematics

Mathematical knowledge is organized around statements and their dependencies, but this structure is exposed unevenly: informal papers cite mostly at the document level, while formal libraries record fine-grained dependencies over a much smaller body of mathematics. We introduce TheoremGraph, a unified statement-level dependency graph spanning both informal and formal mathematics. On the informal side, we parse 11.7M theorem-like environments from mathematics arXiv and recover 18.3M candidate directed dependencies, each labeled by the extractor that proposed it so downstream users can trade coverage for precision. On the formal side, we release LeanGraph, a Lean 4 elaborator-level extractor producing 388,105 declaration nodes and 11.3M typed edges across 25 Lean projects. We bridge the two graphs by embedding generated natural-language slogans into a shared semantic space, linking related statements across papers and across the informal/formal divide; an LLM judge affirms 47,952 such matches above a 0.8 cosine floor, with the judge-acceptance rate rising from 48% across the floor to 87% in the >=0.9 tier. On formal concept retrieval, our name-and-signature representation with graph expansion comes within 0.5pp of LeanSearch v2's reranked Recall@10 (0.775 vs. 0.780) without an LM reranker. We release the dataset, extractors, HTTP API, and MCP interface as infrastructure for mathematical search, attribution, and retrieval-augmented reasoning, available at theoremsearch.com and huggingface.co/datasets/uw-math-ai/theorem-matching.

Unveiling LLMs: The Evolution of Latent Representations in a Dynamic Knowledge Graph

Large Language Models (LLMs) demonstrate an impressive capacity to recall a vast range of factual knowledge. However, understanding their underlying reasoning and internal mechanisms in exploiting this knowledge remains a key research area. This work unveils the factual information an LLM represents internally for sentence-level claim verification. We propose an end-to-end framework to decode factual knowledge embedded in token representations from a vector space to a set of ground predicates, showing its layer-wise evolution using a dynamic knowledge graph. Our framework employs activation patching, a vector-level technique that alters a token representation during inference, to extract encoded knowledge. Accordingly, we neither rely on training nor external models. Using factual and common-sense claims from two claim verification datasets, we showcase interpretability analyses at local and global levels. The local analysis highlights entity centrality in LLM reasoning, from claim-related information and multi-hop reasoning to representation errors causing erroneous evaluation. On the other hand, the global reveals trends in the underlying evolution, such as word-based knowledge evolving into claim-related facts. By interpreting semantics from LLM latent representations and enabling graph-related analyses, this work enhances the understanding of the factual knowledge resolution process.

  • 5 authors
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Apr 4, 2024

Accelerating Diffusion LLM Inference via Local Determinism Propagation

Diffusion large language models (dLLMs) represent a significant advancement in text generation, offering parallel token decoding capabilities. However, existing open-source implementations suffer from quality-speed trade-offs that impede their practical deployment. Conservative sampling strategies typically decode only the most confident token per step to ensure quality (i.e., greedy decoding), at the cost of inference efficiency due to repeated redundant refinement iterations--a phenomenon we term delayed decoding. Through systematic analysis of dLLM decoding dynamics, we characterize this delayed decoding behavior and propose a training-free adaptive parallel decoding strategy, named LocalLeap, to address these inefficiencies. LocalLeap is built on two fundamental empirical principles: local determinism propagation centered on high-confidence anchors and progressive spatial consistency decay. By applying these principles, LocalLeap identifies anchors and performs localized relaxed parallel decoding within bounded neighborhoods, achieving substantial inference step reduction through early commitment of already-determined tokens without compromising output quality. Comprehensive evaluation on various benchmarks demonstrates that LocalLeap achieves 6.94times throughput improvements and reduces decoding steps to just 14.2\% of the original requirement, achieving these gains with negligible performance impact. The source codes are available at: https://github.com/friedrichor/LocalLeap.

  • 7 authors
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Oct 8, 2025

ToolTok: Tool Tokenization for Efficient and Generalizable GUI Agents

Existing GUI agent models relying on coordinate-based one-step visual grounding struggle with generalizing to varying input resolutions and aspect ratios. Alternatives introduce coordinate-free strategies yet suffer from learning under severe data scarcity. To address the limitations, we propose ToolTok, a novel paradigm of multi-step pathfinding for GUI agents, where operations are modeled as a sequence of progressive tool usage. Specifically, we devise tools aligned with human interaction habits and represent each tool using learnable token embeddings. To enable efficient embedding learning under limited supervision, ToolTok introduces a semantic anchoring mechanism that grounds each tool with semantically related concepts as natural inductive bias. To further enable a pre-trained large language model to progressively acquire tool semantics, we construct an easy-to-hard curriculum consisting of three tasks: token definition question-answering, pure text-guided tool selection, and simplified visual pathfinding. Extensive experiments on multiple benchmarks show that ToolTok achieves superior performance among models of comparable scale (4B) and remains competitive with a substantially larger model (235B). Notably, these results are obtained using less than 1% of the training data required by other post-training approaches. In addition, ToolTok demonstrates strong generalization across unseen scenarios. Our training & inference code is open-source at https://github.com/ZephinueCode/ToolTok.

  • 6 authors
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Jan 29

LEGO-GraphRAG: Modularizing Graph-based Retrieval-Augmented Generation for Design Space Exploration

GraphRAG addresses significant challenges in Retrieval-Augmented Generation (RAG) by leveraging graphs with embedded knowledge to enhance the reasoning capabilities of Large Language Models (LLMs). Despite its promising potential, the GraphRAG community currently lacks a unified framework for fine-grained decomposition of the graph-based knowledge retrieval process. Furthermore, there is no systematic categorization or evaluation of existing solutions within the retrieval process. In this paper, we present LEGO-GraphRAG, a modular framework that decomposes the retrieval process of GraphRAG into three interconnected modules: subgraph-extraction, path-filtering, and path-refinement. We systematically summarize and classify the algorithms and neural network (NN) models relevant to each module, providing a clearer understanding of the design space for GraphRAG instances. Additionally, we identify key design factors, such as Graph Coupling and Computational Cost, that influence the effectiveness of GraphRAG implementations. Through extensive empirical studies, we construct high-quality GraphRAG instances using a representative selection of solutions and analyze their impact on retrieval and reasoning performance. Our findings offer critical insights into optimizing GraphRAG instance design, ultimately contributing to the advancement of more accurate and contextually relevant LLM applications.

  • 5 authors
·
Nov 6, 2024

Unsupervised Matching of Data and Text

Entity resolution is a widely studied problem with several proposals to match records across relations. Matching textual content is a widespread task in many applications, such as question answering and search. While recent methods achieve promising results for these two tasks, there is no clear solution for the more general problem of matching textual content and structured data. We introduce a framework that supports this new task in an unsupervised setting for any pair of corpora, being relational tables or text documents. Our method builds a fine-grained graph over the content of the corpora and derives word embeddings to represent the objects to match in a low dimensional space. The learned representation enables effective and efficient matching at different granularity, from relational tuples to text sentences and paragraphs. Our flexible framework can exploit pre-trained resources, but it does not depends on their existence and achieves better quality performance in matching content when the vocabulary is domain specific. We also introduce optimizations in the graph creation process with an "expand and compress" approach that first identifies new valid relationships across elements, to improve matching, and then prunes nodes and edges, to reduce the graph size. Experiments on real use cases and public datasets show that our framework produces embeddings that outperform word embeddings and fine-tuned language models both in results' quality and in execution times.

  • 3 authors
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Dec 16, 2021

Large Language Models for History, Philosophy, and Sociology of Science: Interpretive Uses, Methodological Challenges, and Critical Perspectives

This paper explores the use of large language models (LLMs) as research tools in the history, philosophy, and sociology of science (HPSS). LLMs are remarkably effective at processing unstructured text and inferring meaning from context, offering new affordances that challenge long-standing divides between computational and interpretive methods. This raises both opportunities and challenges for HPSS, which emphasizes interpretive methodologies and understands meaning as context-dependent, ambiguous, and historically situated. We argue that HPSS is uniquely positioned not only to benefit from LLMs' capabilities but also to interrogate their epistemic assumptions and infrastructural implications. To this end, we first offer a concise primer on LLM architectures and training paradigms tailored to non-technical readers. We frame LLMs not as neutral tools but as epistemic infrastructures that encode assumptions about meaning, context, and similarity, conditioned by their training data, architecture, and patterns of use. We then examine how computational techniques enhanced by LLMs, such as structuring data, detecting patterns, and modeling dynamic processes, can be applied to support interpretive research in HPSS. Our analysis compares full-context and generative models, outlines strategies for domain and task adaptation (e.g., continued pretraining, fine-tuning, and retrieval-augmented generation), and evaluates their respective strengths and limitations for interpretive inquiry in HPSS. We conclude with four lessons for integrating LLMs into HPSS: (1) model selection involves interpretive trade-offs; (2) LLM literacy is foundational; (3) HPSS must define its own benchmarks and corpora; and (4) LLMs should enhance, not replace, interpretive methods.

  • 3 authors
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Jun 13, 2025

G-reasoner: Foundation Models for Unified Reasoning over Graph-structured Knowledge

Large language models (LLMs) excel at complex reasoning but remain limited by static and incomplete parametric knowledge. Retrieval-augmented generation (RAG) mitigates this by incorporating external knowledge, yet existing RAGs struggle with knowledge-intensive tasks due to fragmented information and weak modeling of knowledge structure. Graphs offer a natural way to model relationships within knowledge, but LLMs are inherently unstructured and cannot effectively reason over graph-structured data. Recent graph-enhanced RAG (GraphRAG) attempts to bridge this gap by constructing tailored graphs and enabling LLMs to reason on them. However, these methods often depend on ad-hoc graph designs, heuristic search, or costly agent pipelines, which hinder scalability and generalization. To address these challenges, we present G-reasoner, a unified framework that integrates graph and language foundation models for scalable reasoning over diverse graph-structured knowledge. Central to our approach is QuadGraph, a standardized four-layer abstraction that unifies heterogeneous knowledge sources into a common graph representation. Building on this, we introduce a 34M-parameter graph foundation model (GFM) that jointly captures graph topology and textual semantics, and is integrated with LLMs to enhance reasoning in downstream applications. To ensure scalability and efficiency, mixed-precision training and distributed message-passing are implemented to scale GFM with more GPUs. Extensive experiments on six benchmarks show that G-reasoner consistently outperforms state-of-the-art baselines, significantly enhances LLM reasoning, and achieves strong efficiency and cross-graph generalization.

  • 12 authors
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Feb 28

BioGraphFusion: Graph Knowledge Embedding for Biological Completion and Reasoning

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.

  • 6 authors
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Jul 19, 2025

LoMo: Local Modality Substitution for Deeper Vision-Language Fusion

Vision-Language Models (VLMs) have achieved substantial progress across a wide range of understanding and reasoning tasks, driven by large-scale image-text training aimed at multimodal fusion. Ideally, replacing a textual question with its rendered-image counterpart should leave model performance essentially unaffected. In practice, however, such modality substitution induces dramatic performance degradation. We attribute this "carrier sensitivity" issue to an inherent bias in current training corpora. Across prevalent datasets such as image captioning, VQA, OCR, and web-sourced interleaved data, text and images are typically organized into distinct and asymmetric roles, with text serving as linguistic queries and images as visual references. Such data bias leads VLMs to exhibit distinct preferences for information acquisition across different modalities. Consequently, VLMs fail to align representations of semantically equivalent content across textual and visual carriers, making model reasoning fragile under modality substitution. To address this, we propose Local Modality Substitution (LoMo), a lightweight, architecture-agnostic data curation paradigm designed to provide supervision for cross-modal representational invariance between semantically equivalent text and image carriers. LoMo achieves this by reformulating single-modality prompts into seamlessly interleaved multimodal sequences. It dynamically selects target text spans and recasts them as rendered images, thereby preserving the same semantics across "text, visual, text" carriers. Extensive experiments across 13 diverse multimodal benchmarks demonstrate that LoMo significantly improves overall multimodal reasoning and yields deeper cross-modal fusion. Specifically, it delivers consistent gains across foundational models, improving over standard SFT by 2.67 points on LLaVA-OneVision-1.5-8B and 2.82 points on Qwen3.5-9B.

Memory-Orchestrated Semantic System (MOSS): An Auditable Agentic Memory Architecture

Long-term memory remains a structural weakness of AI agents. The dominant approach, retrieval-augmented generation (RAG), relies on embedding-based similarity search, which is opaque by construction, difficult to audit, and bounded by the theoretical limits of vector representations. We present the Memory-Orchestrated Semantic System (MOSS), an agentic memory architecture in which the agent drives retrieval over a structured relational database. MOSS is model-agnostic, storage-agnostic, and API-agnostic: it runs on any relational engine, connects to any LLM provider (or to deterministic non-LLM processes), and deploys on any infrastructure, local or cloud. Its retrieval execution is symbolic and reproducible (once a query is formulated, no LLM participates in the retrieval loop) and every step of the system, from indexing to answer formulation, is logged and inspectable, making MOSS auditable by construction. Rather than imposing an external ontology, MOSS derives its conceptual vocabulary from the corpus itself. We report on a longitudinal deployment unique in the agentic-memory literature: a year of continuous production over an individual scholar's working corpus--a conversational corpus reaching back to October 2024 (some 44 million tokens, retroactively indexed) comprising 110,183 segments, alongside 163,494 catalogued documents, 569 inductively derived concepts, 322,662 concept annotations, and eleven metadata graphs totaling approximately five million relations--across four successive infrastructure generations. While the present case is that of a single researcher, the architecture is in no way specific to one person: it serves a team, an institution, or any entity that accumulates knowledge over time. We argue that auditable, sovereign, structurally unbounded memory is a precondition for AI agents intended to accompany a person or an organization over years rather than sessions.

  • 3 authors
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Jul 4

Integrating Knowledge Graph embedding and pretrained Language Models in Hypercomplex Spaces

Knowledge Graphs, such as Wikidata, comprise structural and textual knowledge in order to represent knowledge. For each of the two modalities dedicated approaches for graph embedding and language models learn patterns that allow for predicting novel structural knowledge. Few approaches have integrated learning and inference with both modalities and these existing ones could only partially exploit the interaction of structural and textual knowledge. In our approach, we build on existing strong representations of single modalities and we use hypercomplex algebra to represent both, (i), single-modality embedding as well as, (ii), the interaction between different modalities and their complementary means of knowledge representation. More specifically, we suggest Dihedron and Quaternion representations of 4D hypercomplex numbers to integrate four modalities namely structural knowledge graph embedding, word-level representations (e.g.\ Word2vec, Fasttext), sentence-level representations (Sentence transformer), and document-level representations (sentence transformer, Doc2vec). Our unified vector representation scores the plausibility of labelled edges via Hamilton and Dihedron products, thus modeling pairwise interactions between different modalities. Extensive experimental evaluation on standard benchmark datasets shows the superiority of our two new models using abundant textual information besides sparse structural knowledge to enhance performance in link prediction tasks.

  • 7 authors
·
Aug 4, 2022

MechGPT, a language-based strategy for mechanics and materials modeling that connects knowledge across scales, disciplines and modalities

For centuries, researchers have sought out ways to connect disparate areas of knowledge. While early scholars (Galileo, da Vinci, etc.) were experts across fields, specialization has taken hold later. With the advent of Artificial Intelligence, we can now explore relationships across areas (e.g., mechanics-biology) or disparate domains (e.g., failure mechanics-art). To achieve this, we use a fine-tuned Large Language Model (LLM), here for a subset of knowledge in multiscale materials failure. The approach includes the use of a general-purpose LLM to distill question-answer pairs from raw sources followed by LLM fine-tuning. The resulting MechGPT LLM foundation model is used in a series of computational experiments to explore its capacity for knowledge retrieval, various language tasks, hypothesis generation, and connecting knowledge across disparate areas. While the model has some ability to recall knowledge from training, we find that LLMs are particularly useful to extract structural insights through Ontological Knowledge Graphs. These interpretable graph structures provide explanatory insights, frameworks for new research questions, and visual representations of knowledge that also can be used in retrieval-augmented generation. Three versions of MechGPT are discussed, featuring different sizes from 13 billion to 70 billion parameters, and reaching context lengths of more than 10,000 tokens. This provides ample capacity for sophisticated retrieval augmented strategies, as well as agent-based modeling where multiple LLMs interact collaboratively and/or adversarially, the incorporation of new data from the literature or web searches, as well as multimodality.

  • 1 authors
·
Oct 16, 2023

Beyond Similarity Search: Tenure and the Case for Structured Belief State in LLM Memory

Why do we need another AI to help the AI? We argue you don't. Stateless LLM sessions impose re-orientation costs on iterative, session-heavy workflows. Prior work addresses cross-session memory through retrieval-augmented approaches: store history, embed it, retrieve by semantic similarity. Cross-session memory is a state management problem, not a search problem. Similarity search fails for named entity resolution within bounded vocabulary contexts because beliefs about a shared technical domain are semantically proximate by construction. A single user is the simplest bounded vocabulary context; engineering teams converge on the same property through shared codebases and terminology. We present Tenure, a local-first proxy that maintains a typed belief store with epistemic status, versioned supersession, and scope isolation, injecting curated context into every LLM session through precision-first retrieval. Hard scope isolation provides a structural guarantee: the right beliefs surface, and only within the boundaries the user has authorized. Tenure's typed schema converts extracted facts into imperative instructions via a why it matters field, making injected beliefs directly actionable rather than raw material for the model to re-derive. A controlled evaluation on 72 retrieval cases demonstrates the gap. Cosine similarity over dense embeddings achieves mean precision of 0.12. Alias-weighted BM25 maintains mean precision of 1.0, passing 72/72 cases versus 8/72 for cosine similarity on the same corpus. Hybrid retrieval typically solves vocabulary mismatch between disparate authors; Tenure eliminates this structurally: query and belief authors are the same person, and an alias enrichment flywheel continuously indexes their specific vocabulary. Under multi-turn topic drift this worsens: the vector backend produces drift scores of 0.43--0.50 on noise-critical turns where BM25 maintains 0.

  • 1 authors
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May 10