arXiv Machine Learning
Jun 9
Active Flow Expansion for Out-of-Distribution Discovery: from Theory to Molecules
arXiv:2606. 08802v1 Announce Type: new Abstract: Standard flow and diffusion pre-training matches the distribution of available data (e.
Predicting Unseen Scientific Interactions: Conditional Flow Models Hallucinate Non-Additive Effects
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arXiv Machine Learning
Oct 28
MLIPDiff: Guiding Denoising Diffusion Models for Structure-Based Drug Design via Machine-Learned Interatomic Potentials
MLIPDiff is an inference‑time guidance technique that enhances pretrained denoising diffusion models for ligand generation by incorporating physics‑informed guidance from a machine‑learned interatomic potential (UMA). It combines four weighted energy terms—protein‑ligand interaction, ligand strain, steric clash, and pocket anchoring—to eliminate protein‑ligand collisions while preserving local geometry, without requiring model retraining. On the CrossDocked2020 benchmark, MLIPDiff produces clash‑free, physically plausible ligand poses and achieves superior binding‑affinity metrics compared to both the base diffusion model and NucleusDiff.
arXiv AI
2d ago
CellCanon: An Agentic Cellular World Model for Prediction, Explanation, and Observation-Driven Updating
CellCanon is an agentic cellular world model that integrates single‑cell expression prediction, evidence‑grounded explanation, and observation‑driven updating. Its predictive core reuses condition‑level biological evidence to generate gene‑specific readouts, while a shared world state links predictions, measurements, and source‑linked claims to support explanation and revision. On 339 held‑out SciPlex3 conditions across three cell lines, CellCanon outperforms baselines in differential‑expression AUPRC, Macro‑F1, and direction Macro‑F1, and its explanation module correctly answers all answerable questions with supporting proofs.
arXiv Machine Learning
Aug 20
Monroe: A Molecular Foundation Model for In-Context Probabilistic Inference
Monroe is a new molecular foundation model that improves upon existing models by pre‑training on over 81 million molecules from the PM6 quantum chemistry dataset, enhancing stereochemistry representation, and introducing novel training losses such as conformer denoising and embedding decorrelation. It also incorporates a prior‑data‑fitted model (TabPFN) for downstream in‑context prediction and demonstrates superior performance on Polaris benchmarks and activity cliff tests. Ablation studies show that the PFN‑based downstream approach can upgrade other models, producing state‑of‑the‑art variants MiniMol_PFN and CheMeleon_PFN.
arXiv Machine Learning
Jun 2
Genotype-Conditioned Molecular Generation via Evidence-Grounded Multi-Objective Latent Perturbation in Diffusion Models
arXiv:2606. 01461v1 Announce Type: new Abstract: Developing effective anticancer therapeutics remains challenging due to tumor heterogeneity and the absence of well-defined molecular targets across cancer subtypes.
arXiv AI
Aug 19
Leveraging generative hallucination and biophysics-informed modeling for unified biomolecular sequence-structure co-design
The paper introduces MCTH (Monte Carlo Tree Hallucination), an inference-only framework that performs all‑atom biomolecular sequence‑structure co‑design by treating pretrained folding and inverse‑folding models as black‑box operators. MCTH uses Monte Carlo Tree Search to allocate a fixed inference budget across competing design trajectories, incorporating model confidence, uncertainty, and cross‑expert consensus. Experiments across protein‑RNA, protein‑DNA, protein‑protein, and protein‑ligand design show that adaptive search outperforms simpler sampling strategies, and evaluations with AlphaFold3 and Chai‑1 demonstrate transferability beyond the search‑time oracle.
Hugging Face Trending Papers
Sep 29
Scalable Diffusion SBI for Compositional Inference under Simulator Misspecification
Simulation-based inference is challenging when many heterogeneous observations must be composed, hierarchical latent structure must be preserved, and the simulator is misspecified relative to observed...
arXiv AI
Jun 2
On the Collapse of Generative Paths: A Criterion and Correction for Diffusion Steering
arXiv:2512. 10339v2 Announce Type: replace Abstract: Inference-time steering adapts pretrained diffusion and flow models to new tasks without retraining, often utilizing ratio-of-densities constructions that reweight time-indexed marginals with fixed exponents.
Hugging Face Trending Papers
Aug 26
VINCENT: Validated Interaction Network for Cross-drug Explanation of Therapeutics
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 Machine Learning
Sep 30
Scalable Diffusion SBI for Compositional Inference under Simulator Misspecification
arXiv:2609.36950v1 Announce Type: new Abstract: Simulation-based inference is challenging when many heterogeneous observations must be composed, hierarchical latent structure must be preserved, and t...
arXiv Machine Learning
Aug 27
VINCENT: Validated Interaction Network for Cross-drug Explanation of Therapeutics
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 Machine Learning
Jul 28
PerturbPFN: Probing the Limits of Synthetic Priors in Drug Perturbation Modelling
arXiv:2607. 23447v1 Announce Type: new Abstract: Predicting cellular responses to unseen chemical perturbations is challenging due to unknown targets and mechanisms, high-dimensional expression responses, and limited experimental coverage of the large small-molecule design space.