Advertise on podcast: Machine Learning in Computational Biology: Daily Digest

This podcast is brought to you by the Oliver Laboratory at Vanderbilt University. ---------------------------------------- 0:00 Surface-based Molecular Design with Multi-modal Flow Matching (https://arxiv.org/pdf/2601.04506.pdf) 4:42 A Semi-supervised Molecular Learning Framework for Activity Cliff Estimation (https://arxiv.org/pdf/2601.04507.pdf) ---------------------------------------- Source code: https://github.com/OliverLaboratory/arxivreader Contact: oliverlaboratory.com Source code: https://github.com/OliverLaboratory/arxivreader

This podcast is brought to you by the Oliver Laboratory at Vanderbilt University. ---------------------------------------- 0:00 Inferring Clinically Relevant Molecular Subtypes of Pancreatic Cancer from Routine Histopathology Using Deep Learning (https://arxiv.org/pdf/2601.03410.pdf) 4:21 Interleaved Tool-Call Reasoning for Protein Function Understanding (https://arxiv.org/pdf/2601.03604.pdf) 8:50 Investigating Knowledge Distillation Through Neural Networks for Protein Binding Affinity Prediction (https://arxiv.org/pdf/2601.03704.pdf) ---------------------------------------- Source code: https://github.com/OliverLaboratory/arxivreader Contact: oliverlaboratory.com Source code: https://github.com/OliverLaboratory/arxivreader

This podcast is brought to you by the Oliver Laboratory at Vanderbilt University. ---------------------------------------- 0:00 Multi-scale Graph Autoregressive Modeling: Molecular Property Prediction via Next Token Prediction (https://arxiv.org/pdf/2601.02530.pdf) 4:35 DNACHUNKER: Learnable Tokenization for DNA Language Models (https://arxiv.org/pdf/2601.03019.pdf) ---------------------------------------- Source code: https://github.com/OliverLaboratory/arxivreader Contact: oliverlaboratory.com Source code: https://github.com/OliverLaboratory/arxivreader

This podcast is brought to you by the Oliver Laboratory at Vanderbilt University. ---------------------------------------- 0:00 Deep Learning Framework for RNA Inverse Folding with Geometric Structure Potentials (https://arxiv.org/pdf/2601.00895.pdf) 4:56 MDAgent2: Large Language Model for Code Generation and Knowledge Q&A in Molecular Dynamics (https://arxiv.org/pdf/2601.02075.pdf) 10:05 Edge-aware GAT-based protein binding site prediction (https://arxiv.org/pdf/2601.02138.pdf) 14:23 Quantized SO(3)-Equivariant Graph Neural Networks for Efficient Molecular Property Prediction (https://arxiv.org/pdf/2601.02213.pdf) ---------------------------------------- Source code: https://github.com/OliverLaboratory/arxivreader Contact: oliverlaboratory.com Source code: https://github.com/OliverLaboratory/arxivreader

This podcast is brought to you by the Oliver Laboratory at Vanderbilt University. ---------------------------------------- 0:00 Rule-Based Approaches to Atomic Sentence Extraction (https://arxiv.org/pdf/2601.00506.pdf) 3:44 Quantifying the uncertainty of molecular dynamics simulations : Good-Turing statistics revisited (https://arxiv.org/pdf/2601.00618.pdf) 8:23 Physio-DPO: Aligning Large Language Models with the Protein Energy Landscape to Eliminate Structural Hallucinations (https://arxiv.org/pdf/2601.00647.pdf) 13:03 Quantum Simulation of Protein Fragment Electronic Structure Using Moment-based Adaptive Variational Quantum Algorithms (https://arxiv.org/pdf/2601.00656.pdf) ---------------------------------------- Source code: https://github.com/OliverLaboratory/arxivreader Contact: oliverlaboratory.com Source code: https://github.com/OliverLaboratory/arxivreader

This podcast is brought to you by the Oliver Laboratory at Vanderbilt University. ---------------------------------------- 0:00 On the comparison of models and experiments in the study of DNA open states: the problem of degrees of freedom (https://arxiv.org/pdf/2512.22160.pdf) 4:32 LiveProteinBench: A Contamination-Free Benchmark for Assessing Models' Specialized Capabilities in Protein Science (https://arxiv.org/pdf/2512.22257.pdf) 9:51 INSIGHT: Spatially resolved survival modelling from routine histology crosslinked with molecular profiling reveals prognostic epithelial-immune axes in stage II/III colorectal cancer (https://arxiv.org/pdf/2512.22262.pdf) 14:43 Revealing design archetypes and flexibility in e-molecule import pathways using Modeling to Generate Alternatives and interpretable machine learning (https://arxiv.org/pdf/2512.23284.pdf) ---------------------------------------- Source code: https://github.com/OliverLaboratory/arxivreader Contact: oliverlaboratory.com Source code: https://github.com/OliverLaboratory/arxivreader

This podcast is brought to you by the Oliver Laboratory at Vanderbilt University. ---------------------------------------- 0:00 From In Silico to In Vitro: Evaluating Molecule Generative Models for Hit Generation (https://arxiv.org/pdf/2512.22031.pdf) ---------------------------------------- Source code: https://github.com/OliverLaboratory/arxivreader Contact: oliverlaboratory.com Source code: https://github.com/OliverLaboratory/arxivreader

This podcast is brought to you by the Oliver Laboratory at Vanderbilt University. ---------------------------------------- 0:00 NMIRacle: Multi-modal Generative Molecular Elucidation from IR and NMR Spectra (https://arxiv.org/pdf/2512.19733.pdf) 4:51 Methods for Analyzing RNA Pseudoknots via Chord Diagrams and Intersection Graphs (https://arxiv.org/pdf/2512.19939.pdf) 9:14 MolAct: An Agentic RL Framework for Molecular Editing and Property Optimization (https://arxiv.org/pdf/2512.20135.pdf) 14:26 SynCraft: Guiding Large Language Models to Predict Edit Sequences for Molecular Synthesizability Optimization (https://arxiv.org/pdf/2512.20333.pdf) 19:44 MERGE-RNA: a physics-based model to predict RNA secondary structure ensembles with chemical probing (https://arxiv.org/pdf/2512.20581.pdf) ---------------------------------------- Source code: https://github.com/OliverLaboratory/arxivreader Contact: oliverlaboratory.com Source code: https://github.com/OliverLaboratory/arxivreader

This podcast is brought to you by the Oliver Laboratory at Vanderbilt University. ---------------------------------------- 0:00 Greater than the Sum of Its Parts: Building Substructure into Protein Encoding Models (https://arxiv.org/pdf/2512.18114.pdf) ---------------------------------------- Source code: https://github.com/OliverLaboratory/arxivreader Contact: oliverlaboratory.com Source code: https://github.com/OliverLaboratory/arxivreader

This podcast is brought to you by the Oliver Laboratory at Vanderbilt University. ---------------------------------------- 0:00 Atom: Efficient On-Device Video-Language Pipelines Through Modular Reuse (https://arxiv.org/pdf/2512.17108.pdf) 5:34 SafeBench-Seq: A Homology-Clustered, CPU-Only Baseline for Protein Hazard Screening with Physicochemical/Composition Features and Cluster-Aware Confidence Intervals (https://arxiv.org/pdf/2512.17527.pdf) 10:07 Generative Multi-Objective Bayesian Optimization with Scalable Batch Evaluations for Sample-Efficient De Novo Molecular Design (https://arxiv.org/pdf/2512.17659.pdf) ---------------------------------------- Source code: https://github.com/OliverLaboratory/arxivreader Contact: oliverlaboratory.com Source code: https://github.com/OliverLaboratory/arxivreader

This podcast is brought to you by the Oliver Laboratory at Vanderbilt University. ---------------------------------------- 0:00 Multiscale Cross-Modal Mapping of Molecular, Pathologic, and Radiologic Phenotypes in Lipid-Deficient Clear Cell Renal CellCarcinoma (https://arxiv.org/pdf/2512.14750.pdf) 5:00 HD-Prot: A Protein Language Model for Joint Sequence-Structure Modeling with Continuous Structure Tokens (https://arxiv.org/pdf/2512.15133.pdf) ---------------------------------------- Source code: https://github.com/OliverLaboratory/arxivreader Contact: oliverlaboratory.com Source code: https://github.com/OliverLaboratory/arxivreader

This podcast is brought to you by the Oliver Laboratory at Vanderbilt University. ---------------------------------------- 0:00 Modeling Dabrafenib Response Using Multi-Omics Modality Fusion and Protein Network Embeddings Based on Graph Convolutional Networks (https://arxiv.org/pdf/2512.12134.pdf) 5:01 MolGuidance: Advanced Guidance Strategies for Conditional Molecular Generation with Flow Matching (https://arxiv.org/pdf/2512.12198.pdf) 9:20 GoMS: Graph of Molecule Substructure Network for Molecule Property Prediction (https://arxiv.org/pdf/2512.12489.pdf) ---------------------------------------- Source code: https://github.com/OliverLaboratory/arxivreader Contact: oliverlaboratory.com Source code: https://github.com/OliverLaboratory/arxivreader

This podcast is brought to you by the Oliver Laboratory at Vanderbilt University. ---------------------------------------- 0:00 MolSculpt: Sculpting 3D Molecular Geometries from Chemical Syntax (https://arxiv.org/pdf/2512.10991.pdf) 4:09 Task-Specific Sparse Feature Masks for Molecular Toxicity Prediction with Chemical Language Models (https://arxiv.org/pdf/2512.11412.pdf) 8:02 Atomic Action Slicing: Planner-Aligned Options for Generalist VLA Agents (https://arxiv.org/pdf/2512.11584.pdf) ---------------------------------------- Source code: https://github.com/OliverLaboratory/arxivreader Contact: oliverlaboratory.com Source code: https://github.com/OliverLaboratory/arxivreader

This podcast is brought to you by the Oliver Laboratory at Vanderbilt University. ---------------------------------------- 0:00 DynaMate: An Autonomous Agent for Protein-Ligand Molecular Dynamics Simulations (https://arxiv.org/pdf/2512.10034.pdf) 4:54 UNAAGI: Atom-Level Diffusion for Generating Non-Canonical Amino Acid Substitutions (https://arxiv.org/pdf/2512.10515.pdf) 9:37 Optimal transport unlocks end-to-end learning for single-molecule localization (https://arxiv.org/pdf/2512.10683.pdf) ---------------------------------------- Source code: https://github.com/OliverLaboratory/arxivreader Contact: oliverlaboratory.com Source code: https://github.com/OliverLaboratory/arxivreader

This podcast is brought to you by the Oliver Laboratory at Vanderbilt University. ---------------------------------------- 0:00 Self Distillation Fine-Tuning of Protein Language Models Improves Versatility in Protein Design (https://arxiv.org/pdf/2512.09329.pdf) 3:55 KGOT: Unified Knowledge Graph and Optimal Transport Pseudo-Labeling for Molecule-Protein Interaction Prediction (https://arxiv.org/pdf/2512.09365.pdf) 8:46 Toward Closed-loop Molecular Discovery via Language Model, Property Alignment and Strategic Search (https://arxiv.org/pdf/2512.09566.pdf) 13:31 Circuits, Features, and Heuristics in Molecular Transformers (https://arxiv.org/pdf/2512.09757.pdf) 18:07 Exploring Protein Language Model Architecture-Induced Biases for Antibody Comprehension (https://arxiv.org/pdf/2512.09894.pdf) ---------------------------------------- Source code: https://github.com/OliverLaboratory/arxivreader Contact: oliverlaboratory.com Source code: https://github.com/OliverLaboratory/arxivreader