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:2608. 19201v1 Announce Type: cross Abstract: Bioinformatics software and databases are essential components of modern life science research, yet their mentions in the scientific literature are often inconsistent and difficult to systematically identify at scale.
The paper introduces pre‑trained models for extracting variant‑phenotype relations from biomedical text, focusing on the SNPPhenA corpus. Fine‑tuning small BERT‑based models, especially DeBERTa, achieves performance close to the current state‑of‑the‑art. Moreover, careful fine‑tuning of Google’s Gemini Pro 1.0 surpasses existing benchmarks on both sentence‑level and abstract‑level relation extraction tasks.
arXiv:2609.37675v1 Announce Type: new Abstract: Protein Language Models (PLMs) have made remarkable progress following scaling laws established in natural language processing across sequence- and str...
arXiv:2607. 08803v1 Announce Type: cross Abstract: The push toward large language models for biology (BioLM) has created a need for training corpora that can endow models with a genuine understanding of biology.
arXiv:2608.25466v2 Announce Type: replace-cross Abstract: The functional annotation of genes in non-model organisms remains a significant challenge in computational biology, with 20-70% of sequenced...
EvoLen is a tokenization method for DNA language models that incorporates evolutionary information to prioritize functional sequence patterns such as regulatory motifs. It groups DNA sequences by cross-species evolutionary signals, trains separate BPE tokenizers for each group, merges vocabularies with a rule that favors preserved patterns, and uses length-aware decoding with dynamic programming. Experiments show EvoLen better preserves functional motifs, differentiates genomic contexts, and aligns with evolutionary constraints while matching or surpassing standard BPE on various DNALM benchmarks.
The paper introduces MiNER, a fine‑tuned biomedical NLP system that uses BioBERT to extract malaria‑related named entities from scientific literature. It builds a large, annotated corpus of malaria articles, preprocesses the text, and applies supervised learning to improve extraction performance. Experiments show that MiNER outperforms other encoding and machine‑learning methods in precision, recall, and accuracy, and the authors release the human‑labeled dataset for further research.
arXiv:2602. 02320v4 Announce Type: replace-cross Abstract: Molecular function is largely determined by structure.
arXiv:2402. 18121v2 Announce Type: replace-cross Abstract: This study assesses four cutting-edge language models in the underexplored Aminoacian language.
arXiv:2602. 17162v3 Announce Type: replace Abstract: Genomic Foundation Models (GFMs) typically rely on Masked Language Modeling (MLM) or Next-Token Prediction (NTP) to learn the "Laws of Nature".
arXiv:2604. 04287v2 Announce Type: replace Abstract: Foundation models in genomics have shown mixed success compared to their counterparts in natural language processing.
arXiv:2601. 12805v4 Announce Type: replace-cross Abstract: Large language models (LLMs) have shown growing promise in biomedical research, particularly for knowledge-driven interpretation tasks.