The study introduces a dual‑rule contrastive learning framework that aligns neural dynamics from mice and humans by learning representations organized by biological state rather than species. It demonstrates that this cross‑species representation can recover conserved sensory‑response structures, differentiate disease phenotypes, and track drug efficacy in epilepsy models. The framework also identifies shared disease‑associated neural dynamics between genetically distinct mouse models and human carriers of 16p11.2 copy‑number variants.
arXiv:2608. 02688v1 Announce Type: cross Abstract: Phenotypic drug discovery enables the discovery of functional relationships between molecular structures and cellular responses.
arXiv:2606. 29577v1 Announce Type: cross Abstract: Positron Emission Tomography (PET) reveals brain metabolism and is clinically central to neurodegenerative disease assessment, yet existing 3D brain foundation models treat PET as generic volumetric data, missing the structured regional metabolic information that distinguishes it from structural neuroimaging.
BrainWideBench is a benchmark that evaluates across‑animal transfer on multi‑region neural recordings from 139 mice, covering 276 brain regions. It comprises three task suites—behavior decoding, neural activity prediction, and anatomical organization recovery—to test whether learned representations support diverse downstream objectives. The benchmark shows that while pretraining improves performance over single‑session baselines, current methods vary in transfer ability and none perform uniformly well across all suites, highlighting the challenge of developing general‑purpose neural representations.
Positron Emission Tomography (PET) reveals brain metabolism and is clinically central to neurodegenerative disease assessment, yet existing 3D brain foundation models treat PET as generic volumetric data, missing the structured regional metabolic information that distinguishes it from structural neuroimaging. To address these limitations, we propose ReMAP-PET, a framework that moves beyond visual encoding by supervising a partially-tuned MedicalNet 3D ResNet-50 with brain regional standardized uptake value ratio (SUVR) profiles through joint regression and contrastive objectives, enabling the encoder to learn the metabolic semantics underlying PET modality.
arXiv:2607. 04557v1 Announce Type: cross Abstract: Accurate prediction of patient-specific therapeutic response from pre-treatment transcriptomes is hindered by the scarcity of matched clinical response labels and post-treatment molecular profiles.
Accurate prediction of patient-specific therapeutic response from pre-treatment transcriptomes is hindered by the scarcity of matched clinical response labels and post-treatment molecular profiles. Preclinical transfer-learning models can simulate drug-induced expression changes but are often hard to interpret and unstable, whereas knowledge-graph methods provide mechanistic context yet remain static and fail to capture drug-induced transcriptomic perturbation dynamics.
VINCENT is a post‑training framework that provides validated, chemically coherent explanations for drug synergy predictions by extracting atom‑pair evidence from attention and gradient signals, grouping them into motifs, and refining these motifs through repeated local perturbations. On a literature‑annotated subset of 25 drug pairs, VINCENT achieves a mean motif recall of 0.826, outperforming baselines (0.49–0.66). Across 71 test pairs, its validated interaction scores yield a TP/TN separation of 3.36, indicating more accurate recovery of literature‑supported molecular regions and better alignment with predictor behavior.
arXiv:2609.37024v1 Announce Type: new Abstract: Integrating transcriptomic and electrophysiological data is essential for building multimodal foundation models for neuroscience. Patch-seq provides pa...
arXiv:2607. 25322v1 Announce Type: new Abstract: Multimodal drug discovery enables drug representation learning beyond chemical structure by incorporating cellular responses such as gene expression and cell morphology.
Drug synergy prediction estimates whether two drugs produce a stronger joint effect than expected from their individual activities. For drug combination discovery, a single synergy score is often not...
arXiv:2608. 14293v1 Announce Type: cross Abstract: High-content microscopy enables systematic profiling of cellular responses to chemical perturbations, but the scale of the chemical space makes exhaustive phenotypic characterization experimentally infeasible.
arXiv:2606. 06094v1 Announce Type: cross Abstract: Advances in computational modeling, neuroimaging, and artificial intelligence are revolutionizing the modeling of neurological disorders for improved diagnostics, prognosis, and treatment planning.