Constraint-Driven Small Language Models Based on Agent and OpenAlex Knowledge Graph: Mining Conceptual Pathways and Discovering Innovation Points in Academic Papers

In recent years, the rapid increase in academic publications across various fields has posed severe challenges for academic paper analysis: scientists struggle to timely and comprehensively track the latest research findings and methodologies. Key concept extraction has proven to be an effective analytical paradigm, and its automation has been achieved with the widespread application of language models in industrial and scientific domains. However, existing paper databases are mostly limited to similarity matching and basic classification of key concepts, failing to deeply explore the relational networks between concepts. This paper is based on the OpenAlex opensource knowledge graph. By analyzing nearly 8,000 open-source paper data from Novosibirsk State University, we discovered a strong correlation between the distribution patterns of paper key concept paths and both innovation points and rare paths. We propose a prompt engineering-based key concept path analysis method. This method leverages small language models to achieve precise key concept extraction and innovation point identification, and constructs an agent based on a knowledge graph constraint mechanism to enhance analysis accuracy. Through fine-tuning of the Qwen and DeepSeek models, we achieved significant improvements in accuracy, with the models publicly available on the Hugging Face platform.

Less is More: Denoising Knowledge Graphs For Retrieval Augmented Generation

Retrieval-Augmented Generation (RAG) systems enable large language models (LLMs) instant access to relevant information for the generative process, demonstrating their superior performance in addressing common LLM challenges such as hallucination, factual inaccuracy, and the knowledge cutoff. Graph-based RAG further extends this paradigm by incorporating knowledge graphs (KGs) to leverage rich, structured connections for more precise and inferential responses. A critical challenge, however, is that most Graph-based RAG systems rely on LLMs for automated KG construction, often yielding noisy KGs with redundant entities and unreliable relationships. This noise degrades retrieval and generation performance while also increasing computational cost. Crucially, current research does not comprehensively address the denoising problem for LLM-generated KGs. In this paper, we introduce DEnoised knowledge Graphs for Retrieval Augmented Generation (DEG-RAG), a framework that addresses these challenges through: (1) entity resolution, which eliminates redundant entities, and (2) triple reflection, which removes erroneous relations. Together, these techniques yield more compact, higher-quality KGs that significantly outperform their unprocessed counterparts. Beyond the methods, we conduct a systematic evaluation of entity resolution for LLM-generated KGs, examining different blocking strategies, embedding choices, similarity metrics, and entity merging techniques. To the best of our knowledge, this is the first comprehensive exploration of entity resolution in LLM-generated KGs. Our experiments demonstrate that this straightforward approach not only drastically reduces graph size but also consistently improves question answering performance across diverse popular Graph-based RAG variants.

Multitask finetuning and acceleration of chemical pretrained models for small molecule drug property prediction

Chemical pretrained models, sometimes referred to as foundation models, are receiving considerable interest for drug discovery applications. The general chemical knowledge extracted from self-supervised training has the potential to improve predictions for critical drug discovery endpoints, including on-target potency and ADMET properties. Multi-task learning has previously been successfully leveraged to improve predictive models. Here, we show that enabling multitasking in finetuning of chemical pretrained graph neural network models such as Kinetic GROVER Multi-Task (KERMT), an enhanced version of the GROVER model, and Knowledge-guided Pre-training of Graph Transformer (KGPT) significantly improves performance over non-pretrained graph neural network models. Surprisingly, we find that the performance improvement from finetuning KERMT in a multitask manner is most significant at larger data sizes. Additionally, we publish two multitask ADMET data splits to enable more accurate benchmarking of multitask deep learning methods for drug property prediction. Finally, we provide an accelerated implementation of the KERMT model on GitHub, unlocking large-scale pretraining, finetuning, and inference in industrial drug discovery workflows.

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.

Enhanced Pre-training of Graph Neural Networks for Million-Scale Heterogeneous Graphs

In recent years, graph neural networks (GNNs) have facilitated the development of graph data mining. However, training GNNs requires sufficient labeled task-specific data, which is expensive and sometimes unavailable. To be less dependent on labeled data, recent studies propose to pre-train GNNs in a self-supervised manner and then apply the pre-trained GNNs to downstream tasks with limited labeled data. However, most existing methods are designed solely for homogeneous graphs (real-world graphs are mostly heterogeneous) and do not consider semantic mismatch (the semantic difference between the original data and the ideal data containing more transferable semantic information). In this paper, we propose an effective framework to pre-train GNNs on the large-scale heterogeneous graph. We first design a structure-aware pre-training task, which aims to capture structural properties in heterogeneous graphs. Then, we design a semantic-aware pre-training task to tackle the mismatch. Specifically, we construct a perturbation subspace composed of semantic neighbors to help deal with the semantic mismatch. Semantic neighbors make the model focus more on the general knowledge in the semantic space, which in turn assists the model in learning knowledge with better transferability. Finally, extensive experiments are conducted on real-world large-scale heterogeneous graphs to demonstrate the superiority of the proposed method over state-of-the-art baselines. Code available at https://github.com/sunshy-1/PHE.

PRoH: Dynamic Planning and Reasoning over Knowledge Hypergraphs for Retrieval-Augmented Generation

Knowledge Hypergraphs (KHs) have recently emerged as a knowledge representation for retrieval-augmented generation (RAG), offering a paradigm to model multi-entity relations into a structured form. However, existing KH-based RAG methods suffer from three major limitations: static retrieval planning, non-adaptive retrieval execution, and superficial use of KH structure and semantics, which constrain their ability to perform effective multi-hop question answering. To overcome these limitations, we propose PRoH, a dynamic Planning and Reasoning over Knowledge Hypergraphs framework. PRoH incorporates three core innovations: (i) a context-aware planning module that sketches the local KH neighborhood to guide structurally grounded reasoning plan generation; (ii) a structured question decomposition process that organizes subquestions as a dynamically evolving Directed Acyclic Graph (DAG) to enable adaptive, multi-trajectory exploration; and (iii) an Entity-Weighted Overlap (EWO)-guided reasoning path retrieval algorithm that prioritizes semantically coherent hyperedge traversals. Experiments across multiple domains demonstrate that PRoH achieves state-of-the-art performance, surpassing the prior SOTA model HyperGraphRAG by an average of 19.73% in F1 and 8.41% in Generation Evaluation (G-E) score, while maintaining strong robustness in long-range multi-hop reasoning tasks.

GraphMERT: Efficient and Scalable Distillation of Reliable Knowledge Graphs from Unstructured Data

Researchers have pursued neurosymbolic artificial intelligence (AI) applications for nearly three decades because symbolic components provide abstraction while neural components provide generalization. Thus, a marriage of the two components can lead to rapid advancements in AI. Yet, the field has not realized this promise since most neurosymbolic AI frameworks fail to scale. In addition, the implicit representations and approximate reasoning of neural approaches limit interpretability and trust. Knowledge graphs (KGs), a gold-standard representation of explicit semantic knowledge, can address the symbolic side. However, automatically deriving reliable KGs from text corpora has remained an open problem. We address these challenges by introducing GraphMERT, a tiny graphical encoder-only model that distills high-quality KGs from unstructured text corpora and its own internal representations. GraphMERT and its equivalent KG form a modular neurosymbolic stack: neural learning of abstractions; symbolic KGs for verifiable reasoning. GraphMERT + KG is the first efficient and scalable neurosymbolic model to achieve state-of-the-art benchmark accuracy along with superior symbolic representations relative to baselines. Concretely, we target reliable domain-specific KGs that are both (1) factual (with provenance) and (2) valid (ontology-consistent relations with domain-appropriate semantics). When a large language model (LLM), e.g., Qwen3-32B, generates domain-specific KGs, it falls short on reliability due to prompt sensitivity, shallow domain expertise, and hallucinated relations. On text obtained from PubMed papers on diabetes, our 80M-parameter GraphMERT yields a KG with a 69.8% FActScore; a 32B-parameter baseline LLM yields a KG that achieves only 40.2% FActScore. The GraphMERT KG also attains a higher ValidityScore of 68.8%, versus 43.0% for the LLM baseline.

Hierarchical Indexing with Knowledge Enrichment for Multilingual Video Corpus Retrieval

Retrieving relevant instructional videos from multilingual medical archives is crucial for answering complex, multi-hop questions across language boundaries. However, existing systems either compress hour-long videos into coarse embeddings or incur prohibitive costs for fine-grained matching. We tackle the Multilingual Video Corpus Retrieval (mVCR) task in the NLPCC-2025 M4IVQA challenge with a multi-stage framework that integrates multilingual semantics, domain terminology, and efficient long-form processing. Video subtitles are divided into semantically coherent chunks, enriched with concise knowledge-graph (KG) facts, and organized into a hierarchical tree whose node embeddings are generated by a language-agnostic multilingual encoder. At query time, the same encoder embeds the input question; a coarse-to-fine tree search prunes irrelevant branches, and only the top-ranked chunks are re-scored by a lightweight large language model (LLM). This design avoids exhaustive cross-encoder scoring while preserving chunk-level precision. Experiments on the mVCR test set demonstrate state-of-the-art performance, and ablation studies confirm the complementary contributions of KG enrichment, hierarchical indexing, and targeted LLM re-ranking. The proposed method offers an accurate and scalable solution for multilingual retrieval in specialized medical video collections.

SUBQRAG: sub-question driven dynamic graph rag

Graph Retrieval-Augmented Generation (Graph RAG) effectively builds a knowledge graph (KG) to connect disparate facts across a large document corpus. However, this broad-view approach often lacks the deep structured reasoning needed for complex multi-hop question answering (QA), leading to incomplete evidence and error accumulation. To address these limitations, we propose SubQRAG, a sub-question-driven framework that enhances reasoning depth. SubQRAG decomposes a complex question into an ordered chain of verifiable sub-questions. For each sub-question, it retrieves relevant triples from the graph. When the existing graph is insufficient, the system dynamically expands it by extracting new triples from source documents in real time. All triples used in the reasoning process are aggregated into a "graph memory," forming a structured and traceable evidence path for final answer generation. Experiments on three multi-hop QA benchmarks demonstrate that SubQRAG achieves consistent and significant improvements, especially in Exact Match scores.

FedBook: A Unified Federated Graph Foundation Codebook with Intra-domain and Inter-domain Knowledge Modeling

Foundation models have shown remarkable cross-domain generalization in language and vision, inspiring the development of graph foundation models (GFMs). However, existing GFMs typically assume centralized access to multi-domain graphs, which is often infeasible due to privacy and institutional constraints. Federated Graph Foundation Models (FedGFMs) address this limitation, but their effectiveness fundamentally hinges on constructing a robust global codebook that achieves intra-domain coherence by consolidating mutually reinforcing semantics within each domain, while also maintaining inter-domain diversity by retaining heterogeneous knowledge across domains. To this end, we propose FedBook, a unified federated graph foundation codebook that systematically aggregates clients' local codebooks during server-side federated pre-training. FedBook follows a two-phase process: (1) Intra-domain Collaboration, where low-frequency tokens are refined by referencing more semantically reliable high-frequency tokens across clients to enhance domain-specific coherence; and (2) Inter-domain Integration, where client contributions are weighted by the semantic distinctiveness of their codebooks during the aggregation of the global GFM, thereby preserving cross-domain diversity. Extensive experiments on 8 benchmarks across multiple domains and tasks demonstrate that FedBook consistently outperforms 21 baselines, including isolated supervised learning, FL/FGL, federated adaptations of centralized GFMs, and FedGFM techniques.