arXiv:2607. 18249v1 Announce Type: cross Abstract: Constraint-based metabolic modeling is a powerful way to study the mechanistic basis of cellular states and disease, but its effective use demands substantial computational expertise and careful coordination of multi-step analyses.
arXiv:2606. 03435v1 Announce Type: new Abstract: Cell Painting combines multiplexed fluorescent staining, high-content imaging, and quantitative analysis to generate high-dimensional phenotypic readouts to support diverse downstream tasks such as mechanism-of-action (MoA) inference, toxicity prediction, and construction of drug-disease atlases.
arXiv:2606. 01042v1 Announce Type: cross Abstract: Perturbation experiments are central to understanding cellular mechanisms, but remain costly and sparse, motivating prediction of gene expression responses for unobserved conditions.
arXiv:2606. 31085v1 Announce Type: new Abstract: Drug-drug interaction (DDI) prediction is essential for medication safety, yet it requires reasoning over heterogeneous biomedical evidence whose relevance changes across interaction mechanisms.
arXiv:2602.00663v3 Announce Type: replace Abstract: Optimizing molecules to achieve desired properties is a central bottleneck across the chemical sciences, particularly in the pharmaceutical industr...
arXiv:2603. 11872v3 Announce Type: replace-cross Abstract: Translating single-cell RNA sequencing (scRNA-seq) data into mechanistic biological hypotheses remains a critical bottleneck, as agentic AI systems lack direct access to transcriptomic representations while expression foundation models remain opaque to natural language.
arXiv:2603. 01131v3 Announce Type: replace-cross Abstract: Clinical diagnosis is a gradual process of evidence integration, in which physicians move from symptoms and medical history to examinations, competing hypotheses, disease relations, and treatment decisions.
arXiv:2607. 18777v1 Announce Type: new Abstract: Evaluating machine learning in scientific domains requires separating correct predictions from correct reasons under realistic distribution shifts.
arXiv:2607. 16262v1 Announce Type: cross Abstract: The acceleration of automated scientific discovery has been fundamentally bottlenecked by the epistemic gap between the semantic reasoning of large language models (LLMs) and the deterministic physics of mammalian biology.
arXiv:2607. 11084v1 Announce Type: new Abstract: Agentic research systems are emerging as a new paradigm for coordinating scientific workflows beyond isolated model inference, code generation, or statistical analysis.
arXiv:2502. 18864v2 Announce Type: replace Abstract: Scientific discovery is driven by scientists generating novel hypotheses for complex problems that undergo rigorous experimental validation.
arXiv:2408. 13378v5 Announce Type: replace Abstract: Workflows in drug-target interaction (DTI) assessment require integrating heterogeneous data from predictive models, curated resources, and observations from experimental literature.
arXiv:2510. 17064v4 Announce Type: replace Abstract: Single-cell RNA sequencing has transformed our ability to identify diverse cell types and their transcriptomic signatures.