arXiv:2606. 04525v1 Announce Type: cross Abstract: Progress in genomic foundation models is difficult to assess due to fragmented benchmarks, incompatible evaluation protocols, and task-specific reporting.
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".
The paper introduces Balance of Benchmarks (BoB), a framework that improves task-conditioned model comparison by weighting benchmark evidence based on semantic density, equating scores across varying difficulty levels, and pooling task-relevant residuals. BoB retains all eligible benchmark data while adjusting its influence, outperforming uniform averaging on the WildScores dataset with higher Spearman correlation, lower MAE, and better shortlist hit rates. The method also reduces ranking instability when benchmarks are repeated or paraphrased, and lowers retrospective regret in model selection.
arXiv:2602. 12147v4 Announce Type: replace Abstract: Time series foundation models (TSFMs) are revolutionizing the forecasting landscape from specific dataset modeling to generalizable task evaluation.
arXiv:2606. 30410v1 Announce Type: cross Abstract: Foundation models for predictive machine learning on tabular data have recently gained significant traction in academia and industry.
arXiv:2609.05818v1 Announce Type: new Abstract: We introduce ABLE, a benchmark for evaluating LLM agents' ability to use biological AI models (BAIMs), such as ProteinMPNN and AlphaFold3, in dual-use...
The paper investigates how synthetic pretraining priors used in tabular foundation models (TFMs) influence downstream performance. By reconstructing the synthetic data generators of four TFMs and comparing their generated tasks to two popular tabular benchmarks using structural descriptors, the authors measure structural coverage and normalized density. They find that some generators provide broader and denser support for benchmark tasks, and that stronger synthetic-to-benchmark support generally correlates with better model performance.
arXiv:2606. 27997v1 Announce Type: new Abstract: Benchmarks of machine learning models often include many datasets, making evaluation expensive.
arXiv:2606. 08679v1 Announce Type: cross Abstract: Pretrained models are often evaluated on multi-task leaderboards to measure their applicability in diverse contexts.
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.
arXiv:2606. 11459v1 Announce Type: cross Abstract: Large Language Models are highly sensitive to prompt formulation, necessitating automatic prompt optimization to unlock their full potential.
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:2512. 22240v5 Announce Type: replace-cross Abstract: Machine learning models are primarily judged by predictive performance, especially in applied genomics, where explanations are read as biological findings.