arXiv:2607. 19376v1 Announce Type: cross Abstract: Machine learning models trained on biochemical data are routinely evaluated using splits that fail to account for relational structure, causing information leakage and over-optimistic performance estimates.
arXiv:2608. 06713v1 Announce Type: new Abstract: Biomedical knowledge graphs (KGs) accelerate drug discovery, but standard pipelines assume query molecules already exist as graph entities, leaving unregistered molecules disconnected.
arXiv:2509. 00123v2 Announce Type: replace-cross Abstract: A fundamental challenge in microbial ecology is determining whether bacteria compete or cooperate in different environmental conditions.
arXiv:2607. 20539v1 Announce Type: cross Abstract: While deep learning has accelerated drug discovery, its impact on biomanufacturing has been considerably more limited.
arXiv:2602. 02320v4 Announce Type: replace-cross Abstract: Molecular function is largely determined by structure.
arXiv:2608. 02027v1 Announce Type: new Abstract: We present scikit-fingerprints, a comprehensive, fully scikit-learn compatible library for molecular machine learning in Python, based on RDKit.
arXiv:2607. 01627v1 Announce Type: cross Abstract: Accurate protein-protein interaction (PPI) prediction is central to functional genomics, disease mechanism discovery, and drug development.
arXiv:2607. 06224v1 Announce Type: new Abstract: Designing microbial strains that produce high-value chemicals at commercially viable titers remains a central challenge in metabolic engineering.
arXiv:2604. 16648v2 Announce Type: replace Abstract: Tandem mass spectrometry is prominent in scientific discovery workflows for identifying unknown small molecules, yet high-throughput structural elucidation remains challenging.
arXiv:2607. 02212v1 Announce Type: cross Abstract: Aqueous solubility is a key property in early-stage drug discovery, but most predictive models merge physicochemical descriptors and molecular graph information into a single representation, obscuring whether a prediction is driven by global chemistry, molecular structure, or both.
arXiv:2608. 08182v1 Announce Type: cross Abstract: Machine learning models for MALDI-TOF mass spectrometry have shown considerable promise for clinical microbiology tasks such as microbial identification and antimicrobial resistance prediction.
arXiv:2509. 26405v2 Announce Type: replace Abstract: We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules.
arXiv:2606. 04287v1 Announce Type: cross Abstract: Generating realistic and diverse graphs is a key problem in machine learning, with applications in molecular discovery, circuit design, cybersecurity, and beyond.