Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2506.03145

Entity-Augmented Neuroscience Knowledge Retrieval Using Ontology and Semantic Understanding Capability of LLM

Pralaypati Ta·Sriram Venkatesaperumal·Keerthi Ram·Mohanasankar Sivaprakasam
View original source ↗Read source document ↗Export metadata ↓

Abstract

Neuroscience research publications encompass a vast wealth of knowledge. Accurately retrieving existing information and discovering new insights from this extensive literature is essential for advancing the field. However, when knowledge is dispersed across multiple sources, current state-of-the-art retrieval methods often struggle to extract the necessary information. A knowledge graph (KG) can integrate and link knowledge from multiple sources. However, existing methods for constructing KGs in neuroscience often rely on labeled data and require domain expertise. Acquiring large-scale, labeled data for a specialized area like neuroscience presents significant challenges. This work proposes novel methods for constructing KG from unlabeled large-scale neuroscience research corpus utilizing large language models (LLM), neuroscience ontology, and text embeddings. We analyze the semantic relevance of neuroscience text segments identified by LLM for building the knowledge graph. We also introduce an entity-augmented information retrieval algorithm to extract knowledge from the KG. Several experiments were conducted to evaluate the proposed approaches. The results demonstrate that our methods significantly enhance knowledge discovery from the unlabeled neuroscience research corpus. The performance of the proposed entity and relation extraction method is comparable to the existing supervised method. It achieves an F1 score of 0.84 for entity extraction from the unlabeled data. The knowledge obtained from the KG improves answers to over 52% of neuroscience questions from the PubMedQA dataset and questions generated using selected neuroscience entities.

Explore related subjects

cs.CLcs.AI

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Pralaypati Ta, Sriram Venkatesaperumal, Keerthi Ram, Mohanasankar Sivaprakasam. 2025-10-26. Entity-Augmented Neuroscience Knowledge Retrieval Using Ontology and Semantic Understanding Capability of LLM. https://arxiv.org/abs/2506.03145

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

DA-Cramming: Enhancing Cost-Effective Language Model Pretraining with Dependency Agreement Integration

Pretraining language models is still a challenge for many researchers due to its substantial computational costs. As such, there is growing interest in developing more affordable pretraining methods. One notable advancement in this area is the Cramming technique (Geiping and Goldstein, 2022), which enables the pretraining of BERT-style language models using just one GPU in a single day. Building on this innovative approach, we introduce the Dependency Agreement Cramming (DA-Cramming), an efficient framework that integrates information about dependency agreements into the pretraining process. Unlike existing methods that leverage similar semantic information during finetuning, our approach represents a pioneering effort focusing on enhancing the foundational language understanding with semantic information during pretraining. We meticulously design a dual-stage pretraining work flow with four dedicated submodels to capture representative dependency agreements at the chunk level, effectively transforming these agreements into embeddings to benefit the pretraining. Extensive empirical results demonstrate that our method significantly outperforms previous methods across various tasks.

cs.CL↗
arXiv2026

BigO(Bench): Can LLMs Generate Code with Controlled Time and Space Complexity?

We introduce BigO(Bench), a novel coding benchmark designed to evaluate the capabilities of generative language models in understanding and generating code with specified time and space complexities. This benchmark addresses the gap in current evaluations that often overlook the ability of models to comprehend and produce code constrained by computational complexity. BigO(Bench) includes tooling to infer the algorithmic complexity of any Python function from profiling measurements, including human- or LLM-generated solutions. BigO(Bench) also includes of set of 3,105 coding problems and 1,190,250 solutions from Code Contests annotated with inferred (synthetic) time and space complexity labels from the complexity framework, as well as corresponding runtime and memory footprint values for a large set of input sizes. We present results from evaluating multiple state-of-the-art language models on this benchmark, highlighting their strengths and weaknesses in handling complexity requirements. In particular, token-space reasoning models are unrivaled in code generation but not in complexity understanding, hinting that they may not generalize well to tasks for which no reward was given at training time.

cs.CL↗
arXiv2026

UR$^2$: Unify RAG and Reasoning through Reinforcement Learning

Large Language Models (LLMs) have shown strong capabilities through two complementary paradigms: Retrieval-Augmented Generation (RAG) for knowledge grounding and Reinforcement Learning from Verifiable Rewards (RLVR) for complex reasoning. However, existing attempts to unify these paradigms remain narrow in scope, typically limited to open-domain QA with fixed retrieval settings, which constrains generalization to broader domains. To address this limitation, we propose UR$^2$ (Unified RAG and Reasoning)), a general reinforcement learning framework that dynamically coordinates retrieval and reasoning. UR$^2$ introduces two key designs: a difficulty-aware curriculum that selectively invokes retrieval only for challenging instances, and a hybrid knowledge access strategy that combines domain-specific offline corpora with on-the-fly LLM-generated summaries. Together, these components mitigate the imbalance between retrieval and reasoning and improve robustness to noisy information. Experiments on open-domain QA, MMLU-Pro, medical, and mathematical reasoning tasks show that UR$^2$, built on Qwen-2.5-3/7B and LLaMA-3.1-8B, consistently outperforms existing RAG and RL baselines, and achieves performance comparable to GPT-4o-mini and GPT-4.1-mini on several benchmarks. Code, models, and data are available at https://github.com/Tsinghua-dhy/UR2.

cs.CL↗