arXiv AI
Homo-RAG: Homology-Guided Retrieval-Augmented Generation for Cross-Species Gene Function Prediction
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arXiv Machine Learning
Sep 22
Tool-Augmented On-Policy Distillation for LLM Domain Adaptation in Sequence-Based Omics Tasks
The paper introduces OmicsBench, a new reasoning benchmark for multi‑omics sequences that includes 1,160 expert‑validated questions across DNA regulation, RNA processing, and protein function tasks, requiring traceable evidence chains. Evaluation of 17 large language models shows that scientific LLMs, while more accurate in classification, often lack valid evidence, suggesting shortcut learning. To address this, the authors propose tool‑augmented on‑policy distillation (TA‑OPD), a post‑training method that improves both evidence grounding and predictive performance across five Qwen3.5 models of varying sizes.
arXiv Computation and Language
Sep 2
Bridging Lexical Divergence: LLM-Assisted, Cost-Efficient, Zero-shot Scientific Entity Linking
arXiv:2609.00228v1 Announce Type: new Abstract: Scientific domain entity linking (EL) differs from general domain EL because mentions and entity names often lack lexical overlap. Another challenge is...
arXiv AI
Sep 3
BioELX: Context-Aware Cross-lingual Biomedical Entity Linking without Task-Specific Supervision
BioELX is a retrieve‑rerank framework for cross‑lingual biomedical entity linking that tackles two key problems: the English‑biased UMLS alias training data and the degradation caused by naïvely adding context. It fine‑tunes SapBERT_multi with Wikidata‑derived cross‑lingual alias supervision to create shared concept neighborhoods, and then reranks candidates using pretrained LLMs with mention‑anchored prompting to focus on the target mention. Experiments demonstrate state‑of‑the‑art performance on four benchmarks, improving Recall@1 by 4.8–18.2 percentage points without task‑specific annotations.
arXiv AI
Jul 7
Leveraging Natural Language Processing to Unravel the Mystery of Life: A Review of NLP Approaches in Genomics, Transcriptomics, and Proteomics
arXiv:2506. 02212v2 Announce Type: replace-cross Abstract: Natural Language Processing (NLP) has transformed various fields beyond linguistics by applying techniques originally developed for human language to the analysis of biological sequences.
arXiv AI
6d ago
FlyAOC: Evaluating Agentic Ontology Curation of Drosophila Scientific Knowledge Bases
FlyAOC is a benchmark that tests AI agents on end‑to‑end ontology curation of Drosophila scientific literature. Given a gene symbol, a brief description, a large paper corpus, and ontology resources, agents must search for evidence and produce structured annotations such as function terms, expression patterns, and historical synonyms. The benchmark contains 7,397 expert‑curated annotations across 100 genes and evaluates different agent harnesses, revealing system‑level failure modes that single‑task evaluations miss.
arXiv AI
Sep 7
A Semantic Model of Genetic Evidence: A Step Toward Bridging the Basic-Science-Clinic Gap
The article presents a new semantic model for representing scientific evidence, specifically tailored to genetics, that extends existing standards by adding fine‑grained, domain‑specific structure. It aligns with FHIR Evidence and SEPIO, incorporates a compact vocabulary validated by SHACL, and was tested in a human‑AI annotation pilot on six genetics papers, producing 28 evidence items and 95 source‑anchored assertions. The authors argue that this model advances trustworthy, AI‑ready infrastructure for variant interpretation by providing a reference data model and validation schema for genetic evidence.