arXiv:2509.12266v3 Announce Type: replace-cross Abstract: We introduce Genome-Factory, the first integrated Python library for tuning, deploying, and interpreting genomic foundation models. Our core...
arXiv:2509.23552v2 Announce Type: replace-cross Abstract: Antimicrobial Resistance (AMR) is a rapidly escalating global health crisis. While genomic sequencing enables rapid prediction of resistance...
arXiv:2512. 17678v2 Announce Type: replace-cross Abstract: Selecting compact and informative gene subsets from single-cell transcriptomic data is essential for biomarker discovery, improving interpretability, and cost-effective profiling.
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:2607. 00931v1 Announce Type: new Abstract: Predicting cancer drug response from transcriptomic profiles is a cornerstone of precision oncology, yet the scientific value of machine learning models hinges not solely on predictive accuracy, but also on their capacity to generate reliable biological insights.
arXiv:2606. 09558v1 Announce Type: cross Abstract: Motivation: Transformer-based models are increasingly applied to large-scale single-cell transcriptomics, showing strong performance through self-supervised learning on millions of cells.
arXiv:2606. 08147v1 Announce Type: cross Abstract: DNA cis-regulatory elements (CREs) such as enhancers control gene expression levels.
arXiv:2606. 07607v1 Announce Type: new Abstract: Advances in machine learning and computational power have unlocked the predictive potential of the human genome, yet biologists now demand that these models also elucidate the underlying biological mechanisms.
CellMSA introduces a novel single‑cell representation learning framework that leverages a multiple‑sequence‑alignment‑inspired context model. For each target cell, it retrieves relevant cells across batches and related cell types, summarizing cross‑cell patterns into a context‑dependent gene‑pair representation that is fed into a pair‑aware encoder. Pretraining on a massive human single‑cell corpus (≈109 million cells) and subsequent benchmarks demonstrate consistent performance gains over existing methods.
SoftGene is a new framework that enhances gene set annotation by combining protein language model representations with a hybrid prompting scheme. It uses a hierarchical attention-based encoder built on ESM to encode gene sets from protein amino acid sequences, then merges soft prompts derived from these embeddings with hard prompts generated by a large language model. The approach is evaluated on Gene Ontology and MSigDB datasets, showing that integrating protein-sequence information with textual context improves overall annotation performance, though the benefit varies across biological domains.
arXiv:2603. 02221v2 Announce Type: replace-cross Abstract: In clinical tabular prediction, classical machine learning models with feature engineering often outperform neural methods.
arXiv:2603.02221v3 Announce Type: replace-cross Abstract: In clinical tabular prediction, classical machine learning models with feature engineering often outperform neural methods. LLMs are increasi...