Explore every episode of the 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

This podcast is brought to you by the Oliver Laboratory at Vanderbilt University. ---------------------------------------- 0:00 Protein Secondary Structure Prediction Using Transformers (https://arxiv.org/pdf/2512.08613.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 Chemistry Integrated Language Model using Hierarchical Molecular Representation for Polymer Informatics (https://arxiv.org/pdf/2512.06301.pdf) 4:29 Hierarchical geometric deep learning enables scalable analysis of molecular dynamics (https://arxiv.org/pdf/2512.06520.pdf) 9:35 On fine-tuning Boltz-2 for protein-protein affinity prediction (https://arxiv.org/pdf/2512.06592.pdf) 14:33 Multi-Scale Protein Structure Modelling with Geometric Graph U-Nets (https://arxiv.org/pdf/2512.06752.pdf) 18:33 Self-Supervised Learning on Molecular Graphs: A Systematic Investigation of Masking Design (https://arxiv.org/pdf/2512.07064.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 Mitigating the Antigenic Data Bottleneck: Semi-supervised Learning with Protein Language Models for Influenza A Surveillance (https://arxiv.org/pdf/2512.05222.pdf) 4:40 STAR-GO: Improving Protein Function Prediction by Learning to Hierarchically Integrate Ontology-Informed Semantic Embeddings (https://arxiv.org/pdf/2512.05245.pdf) 9:43 DMAGT: Unveiling miRNA-Drug Associations by Integrating SMILES and RNA Sequence Structures through Graph Transformer Models (https://arxiv.org/pdf/2512.05287.pdf) 14:13 Generalization Beyond Benchmarks: Evaluating Learnable Protein-Ligand Scoring Functions on Unseen Targets (https://arxiv.org/pdf/2512.05386.pdf) 18:26 PERM EQ x GRAPH EQ: Equivariant Neural Networks for Quantum Molecular Learning (https://arxiv.org/pdf/2512.05475.pdf) 23:27 NEAT: Neighborhood-Guided, Efficient, Autoregressive Set Transformer for 3D Molecular Generation (https://arxiv.org/pdf/2512.05844.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 RGE-GCN: Recursive Gene Elimination with Graph Convolutional Networks for RNA-seq based Early Cancer Detection (https://arxiv.org/pdf/2512.04333.pdf) 4:27 BioMedGPT-Mol: Multi-task Learning for Molecular Understanding and Generation (https://arxiv.org/pdf/2512.04629.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 Atomic Diffusion Models for Small Molecule Structure Elucidation from NMR Spectra (https://arxiv.org/pdf/2512.03127.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 Molecular Embedding-Based Algorithm Selection in Protein-Ligand Docking (https://arxiv.org/pdf/2512.02328.pdf) 3:59 Graph VQ-Transformer (GVT): Fast and Accurate Molecular Generation via High-Fidelity Discrete Latents (https://arxiv.org/pdf/2512.02667.pdf) 8:28 Vessel Network Topology in Molecular Communication: Insights from Experiments and Theory (https://arxiv.org/pdf/2512.02811.pdf) 12:52 Modulation of DNA rheology by a transcription factor that forms aging microgels (https://arxiv.org/pdf/2512.02864.pdf) 17:42 Imperfect molecular detection renormalizes apparent kinetic rates in stochastic gene regulatory networks (https://arxiv.org/pdf/2512.02908.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 Predicting COVID-19 Prevalence Using Wastewater RNA Surveillance: A Semi-Supervised Learning Approach with Temporal Feature Trust (https://arxiv.org/pdf/2512.00100.pdf) 5:37 RadDiff: Retrieval-Augmented Denoising Diffusion for Protein Inverse Folding (https://arxiv.org/pdf/2512.00126.pdf) 10:05 Layer Probing Improves Kinase Functional Prediction with Protein Language Models (https://arxiv.org/pdf/2512.00376.pdf) 14:19 Rep3Net: An Approach Exploiting Multimodal Representation for Molecular Bioactivity Prediction (https://arxiv.org/pdf/2512.00521.pdf) 18:29 DeepFRI Demystified: Interpretability vs. Accuracy in AI Protein Function Prediction (https://arxiv.org/pdf/2512.00642.pdf) 22:33 Hierarchical Molecular Language Models (HMLMs) (https://arxiv.org/pdf/2512.00696.pdf) 28:14 Towards Precision Protein-Ligand Affinity Prediction Benchmark: A Complete and Modification-Aware DAVIS Dataset (https://arxiv.org/pdf/2512.00708.pdf) 33:20 From Atomic to Composite: Reinforcement Learning Enables Generalization in Complementary Reasoning (https://arxiv.org/pdf/2512.01970.pdf) 37:44 Consistent Synthetic Sequences Unlock Structural Diversity in Fully Atomistic De Novo Protein Design (https://arxiv.org/pdf/2512.01976.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 QuantumChem-200K: A Large-Scale Open Organic Molecular Dataset for Quantum-Chemistry Property Screening and Language Model Benchmarking (https://arxiv.org/pdf/2511.21747.pdf) 4:41 BeeRNA: tertiary structure-based RNA inverse folding using Artificial Bee Colony (https://arxiv.org/pdf/2511.21781.pdf) 9:48 Beyond Atoms: Evaluating Electron Density Representation for 3D Molecular Learning (https://arxiv.org/pdf/2511.21900.pdf) 14:45 DeepPNI: Language- and graph-based model for mutation-driven protein-nucleic acid energetics (https://arxiv.org/pdf/2511.22239.pdf) 19:49 Swarms of Large Language Model Agents for Protein Sequence Design with Experimental Validation (https://arxiv.org/pdf/2511.22311.pdf) 25:02 FoldSAE: Learning to Steer Protein Folding Through Sparse Representations (https://arxiv.org/pdf/2511.22519.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 Learning Cell-Aware Hierarchical Multi-Modal Representations for Robust Molecular Modeling (https://arxiv.org/pdf/2511.21120.pdf) 4:40 Guiding Generative Models for Protein Design: Prompting, Steering and Aligning (https://arxiv.org/pdf/2511.21476.pdf) 9:20 Automated Protein Motif Localization using Concept Activation Vectors in Protein Language Model Embedding Space (https://arxiv.org/pdf/2511.21614.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 MXtalTools: A Toolkit for Machine Learning on Molecular Crystals (https://arxiv.org/pdf/2511.20327.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 RTMol: Rethinking Molecule-text Alignment in a Round-trip View (https://arxiv.org/pdf/2511.12135.pdf) 4:26 Diffusion Models are Molecular Dynamics Simulators (https://arxiv.org/pdf/2511.17741.pdf) 8:42 TRIDENT: A Trimodal Cascade Generative Framework for Drug and RNA-Conditioned Cellular Morphology Synthesis (https://arxiv.org/pdf/2511.18287.pdf) 13:49 Pre-training Graph Neural Networks on 2D and 3D Molecular Structures by using Multi-View Conditional Information Bottleneck (https://arxiv.org/pdf/2511.18404.pdf) 18:46 A universal phase-plane model for in vivo protein aggregation (https://arxiv.org/pdf/2511.18893.pdf) 23:46 Torsion-Space Diffusion for Protein Backbone Generation with Geometric Refinement (https://arxiv.org/pdf/2511.19184.pdf) 27:38 Beyond Protein Language Models: An Agentic LLM Framework for Mechanistic Enzyme Design (https://arxiv.org/pdf/2511.19423.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 Joint Design of Protein Surface and Structure Using a Diffusion Bridge Model (https://arxiv.org/pdf/2511.16675.pdf) 4:24 Hash Collisions in Molecular Fingerprints: Effects on Property Prediction and Bayesian Optimization (https://arxiv.org/pdf/2511.17078.pdf) 8:33 FlexiFlow: decomposable flow matching for generation of flexible molecular ensemble (https://arxiv.org/pdf/2511.17249.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 Unified all-atom molecule generation with neural fields (https://arxiv.org/pdf/2511.15906.pdf) 5:00 AssayMatch: Learning to Select Data for Molecular Activity Models (https://arxiv.org/pdf/2511.16087.pdf) 9:58 ProtT-Affinity: Sequence-Based Protein-Protein Binding Affinity Prediction Using ProtT5 Embeddings (https://arxiv.org/pdf/2511.16113.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 Quantifying the Role of OpenFold Components in Protein Structure Prediction (https://arxiv.org/pdf/2511.14781.pdf) 4:09 Deep Pathomic Learning Defines Prognostic Subtypes and Molecular Drivers in Colorectal Cancer (https://arxiv.org/pdf/2511.15067.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 XAI-Driven Deep Learning for Protein Sequence Functional Group Classification (https://arxiv.org/pdf/2511.13791.pdf) 4:42 Structural Flexibility of the TCF7L2-DNA Complex with the Type 2 Diabetes SNP rs7903146 (https://arxiv.org/pdf/2511.13916.pdf) 9:01 MiAD: Mirage Atom Diffusion for De Novo Crystal Generation (https://arxiv.org/pdf/2511.14426.pdf) 13:34 Full Atom Peptide Design via Riemannian Euclidean Bayesian Flow Networks (https://arxiv.org/pdf/2511.14516.pdf) 18:36 Apo2Mol: 3D Molecule Generation via Dynamic Pocket-Aware Diffusion Models (https://arxiv.org/pdf/2511.14559.pdf) 23:44 Near-Lossless Model Compression Enables Longer Context Inference in DNA Large Language Models (https://arxiv.org/pdf/2511.14694.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 Protein Structure Tokenization via Geometric Byte Pair Encoding (https://arxiv.org/pdf/2511.11758.pdf) 4:44 Understanding Molecular Basis of PTPN11-Related Diseases (https://arxiv.org/pdf/2511.11860.pdf) 9:02 Chain-of-Generation: Progressive Latent Diffusion for Text-Guided Molecular Design (https://arxiv.org/pdf/2511.11894.pdf) 13:17 RTMol: Rethinking Molecule-text Alignment in a Round-trip View (https://arxiv.org/pdf/2511.12135.pdf) 17:41 Chemistry-Enhanced Diffusion-Based Framework for Small-to-Large Molecular Conformation Generation (https://arxiv.org/pdf/2511.12182.pdf) 22:48 MolEdit: Knowledge Editing for Multimodal Molecule Language Models (https://arxiv.org/pdf/2511.12770.pdf) 27:08 cryoSENSE: Compressive Sensing Enables High-throughput Microscopy with Sparse and Generative Priors on the Protein Cryo-EM Image Manifold (https://arxiv.org/pdf/2511.12931.pdf) 31:07 MDIntrinsicDimension: Dimensionality-Based Analysis of Collective Motions in Macromolecules from Molecular Dynamics Trajectories (https://arxiv.org/pdf/2511.13550.pdf) 35:37 Evaluating and Scoring Ebolavirus Protein-protein Docking Models Using PIsToN (https://arxiv.org/pdf/2511.13583.pdf) 39:33 Protein Secondary Structure Prediction Using 3D Graphs and Relation-Aware Message Passing Transformers (https://arxiv.org/pdf/2511.13685.pdf) 44:19 Rare Genomic Subtype Discovery from RNA-seq via Autoencoder Embeddings and Stability-Aware Clustering (https://arxiv.org/pdf/2511.13705.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 MOSAIC: Codon Harmonization of Monte Carlo-Based Simulated Annealing for Linked Codons in Heterologous Protein Expression (https://arxiv.org/pdf/2511.10708.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 Mamba-driven multi-perspective structural understanding for molecular ground-state conformation prediction (https://arxiv.org/pdf/2511.09564.pdf) 4:51 VEDA: 3D Molecular Generation via Variance-Exploding Diffusion with Annealing (https://arxiv.org/pdf/2511.09568.pdf) 9:22 HAMscope: a snapshot Hyperspectral Autofluorescence Miniscope for real-time molecular imaging (https://arxiv.org/pdf/2511.09574.pdf) 14:19 Solvaformer: an SE(3)-equivariant graph transformer for small molecule solubility prediction (https://arxiv.org/pdf/2511.09774.pdf) 18:53 Boosting In-Silicon Directed Evolution with Fine-Tuned Protein Language Model and Tree Search (https://arxiv.org/pdf/2511.09900.pdf) 23:40 From Static Structures to Ensembles: Studying and Harnessing Protein Structure Tokenization (https://arxiv.org/pdf/2511.10056.pdf) 27:35 EPO: Diverse and Realistic Protein Ensemble Generation via Energy Preference Optimization (https://arxiv.org/pdf/2511.10165.pdf) 32:00 PepTriX: A Framework for Explainable Peptide Analysis through Protein Language Models (https://arxiv.org/pdf/2511.10244.pdf) 36:40 Pretrained Joint Predictions for Scalable Batch Bayesian Optimization of Molecular Designs (https://arxiv.org/pdf/2511.10590.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 Compact Artificial Neural Network Models for Predicting Protein Residue - RNA Base Binding (https://arxiv.org/pdf/2511.08648.pdf) 4:16 Bio AI Agent: A Multi-Agent Artificial Intelligence System for Autonomous CAR-T Cell Therapy Development with Integrated Target Discovery, Toxicity Prediction, and Rational Molecular Design (https://arxiv.org/pdf/2511.08649.pdf) 9:27 Measuring irreversibility in stochastic systems by categorizing single-molecule displacements (https://arxiv.org/pdf/2511.09183.pdf) 14:16 Controllable protein design through Feynman-Kac steering (https://arxiv.org/pdf/2511.09216.pdf) 18:16 Taming Object Hallucinations with Verified Atomic Confidence Estimation (https://arxiv.org/pdf/2511.09228.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 Hierarchical Structure-Property Alignment for Data-Efficient Molecular Generation and Editing (https://arxiv.org/pdf/2511.08080.pdf) 4:32 Hierarchical Direction Perception via Atomic Dot-Product Operators for Rotation-Invariant Point Clouds Learning (https://arxiv.org/pdf/2511.08240.pdf) 9:27 Improving the accuracy and generalizability of molecular property regression models with a substructure-substitution-rule-informed framework (https://arxiv.org/pdf/2511.08314.pdf) 13:53 Clustering Guided Residual Neural Networks for Multi-Tx Localization in Molecular Communications (https://arxiv.org/pdf/2511.08513.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 TEMPO: Temporal Multi-scale Autoregressive Generation of Protein Conformational Ensembles (https://arxiv.org/pdf/2511.05510.pdf) 4:48 Molecular Dynamics Simulations of Membrane Selectivity of Star Peptides Across Different Bacterial and Mammalian Bilipids (https://arxiv.org/pdf/2511.05513.pdf) 8:55 GastroDL-Fusion: A Dual-Modal Deep Learning Framework Integrating Protein-Ligand Complexes and Gene Sequences for Gastrointestinal Disease Drug Discovery (https://arxiv.org/pdf/2511.05726.pdf) 13:00 Breaking the Modality Barrier: Generative Modeling for Accurate Molecule Retrieval from Mass Spectra (https://arxiv.org/pdf/2511.06259.pdf) 17:04 Peeling Context from Cause for Multimodal Molecular Property Prediction (https://arxiv.org/pdf/2511.06692.pdf) 22:12 Theory of Semi-discontinuous DNA Replication (https://arxiv.org/pdf/2511.06904.pdf) 26:36 S$^2$Drug: Bridging Protein Sequence and 3D Structure in Contrastive Representation Learning for Virtual Screening (https://arxiv.org/pdf/2511.07006.pdf) 30:52 A critical assessment of the role of topology on protein thermal stability (https://arxiv.org/pdf/2511.07024.pdf) 35:12 Direct Molecular Polarizability Prediction with SO(3) Equivariant Local Frame GNNs (https://arxiv.org/pdf/2511.07087.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 SPECTRA: Spectral Target-Aware Graph Augmentation for Imbalanced Molecular Property Regression (https://arxiv.org/pdf/2511.04838.pdf) 3:49 SigmaDock: Untwisting Molecular Docking With Fragment-Based SE(3) Diffusion (https://arxiv.org/pdf/2511.04854.pdf) 9:03 Peptide2Mol: A Diffusion Model for Generating Small Molecules as Peptide Mimics for Targeted Protein Binding (https://arxiv.org/pdf/2511.04984.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 Enhancing Multimodal Protein Function Prediction Through Dual-Branch Dynamic Selection with Reconstructive Pre-Training (https://arxiv.org/pdf/2511.04040.pdf) 4:16 Protein aggregation in Huntington's disease (https://arxiv.org/pdf/2511.04174.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 Machine Learning for RNA Secondary Structure Prediction: a review of current methods and challenges (https://arxiv.org/pdf/2511.02622.pdf) 5:32 STAR-VAE: Latent Variable Transformers for Scalable and Controllable Molecular Generation (https://arxiv.org/pdf/2511.02769.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 Generative Modeling Enables Molecular Structure Retrieval from Coulomb Explosion Imaging (https://arxiv.org/pdf/2511.00179.pdf) 4:57 Transfer learning discovery of molecular modulators for perovskite solar cells (https://arxiv.org/pdf/2511.00204.pdf) 9:23 STELLAR-koff: A Transfer Learning Model for Protein-Ligand Dissociation Rate Constant Prediction Based on Interaction Landscape (https://arxiv.org/pdf/2511.01171.pdf) 13:58 Identification of Capture Phases in Nanopore Protein Sequencing Data Using a Deep Learning Model (https://arxiv.org/pdf/2511.01277.pdf) 18:22 Split-Flows: Measure Transport and Information Loss Across Molecular Resolutions (https://arxiv.org/pdf/2511.01464.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 Molecular glues stabilize water-mediated hydrogen bonds in ternary complexes (https://arxiv.org/pdf/2510.26806.pdf) 4:34 GeoPep: A geometry-aware masked language model for protein-peptide binding site prediction (https://arxiv.org/pdf/2510.27040.pdf) 8:57 The Demon Hidden Behind Life's Ultra-Energy-Efficient Information Processing -- Demonstrated by Biological Molecular Motors (https://arxiv.org/pdf/2510.27212.pdf) 12:50 InertialAR: Autoregressive 3D Molecule Generation with Inertial Frames (https://arxiv.org/pdf/2510.27497.pdf) 17:17 MolChord: Structure-Sequence Alignment for Protein-Guided Drug Design (https://arxiv.org/pdf/2510.27671.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 Discovering Interpretable Biological Concepts in Single-cell RNA-seq Foundation Models (https://arxiv.org/pdf/2510.25807.pdf) 4:13 Enabling Fast and Accurate Neutral Atom Readout through Image Denoising (https://arxiv.org/pdf/2510.25982.pdf) 9:05 Bridging the Gap Between Molecule and Textual Descriptions via Substructure-aware Alignment (https://arxiv.org/pdf/2510.26157.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 Re-evaluating sample efficiency in de novo molecule generation (https://arxiv.org/pdf/2212.01385.pdf) 4:41 Flows, straight but not so fast: Exploring the design space of Rectified Flows in Protein Design (https://arxiv.org/pdf/2510.24732.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 Structure-Aware Fusion with Progressive Injection for Multimodal Molecular Representation Learning (https://arxiv.org/pdf/2510.23640.pdf) 4:28 Test-Time Tuned Language Models Enable End-to-end De Novo Molecular Structure Generation from MS/MS Spectra (https://arxiv.org/pdf/2510.23746.pdf) 8:26 Relaxed Sequence Sampling for Diverse Protein Design (https://arxiv.org/pdf/2510.23786.pdf) 13:05 Low-N Protein Activity Optimization with FolDE (https://arxiv.org/pdf/2510.24053.pdf) 17:40 Pearl: A Foundation Model for Placing Every Atom in the Right Location (https://arxiv.org/pdf/2510.24670.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 A Multimodal Human Protein Embeddings Database: DeepDrug Protein Embeddings Bank (DPEB) (https://arxiv.org/pdf/2510.22008.pdf) 4:47 Learning 3D Anisotropic Noise Distributions Improves Molecular Force Field Modeling (https://arxiv.org/pdf/2510.22123.pdf) 9:44 CAP: Commutative Algebra Prediction of Protein-Nucleic Acid Binding Affinities (https://arxiv.org/pdf/2510.22130.pdf) 14:20 ATOM: AdapTive and OptiMized dynamic temporal knowledge graph construction using LLMs (https://arxiv.org/pdf/2510.22590.pdf) 19:21 A Novel Framework for Multi-Modal Protein Representation Learning (https://arxiv.org/pdf/2510.23273.pdf) 23:42 Improving Predictions of Molecular Properties with Graph Featurisation and Heterogeneous Ensemble Models (https://arxiv.org/pdf/2510.23428.pdf) 28:14 Quantum Phase Classification of Rydberg Atom Systems Using Resource-Efficient Variational Quantum Circuits and Classical Shadows (https://arxiv.org/pdf/2510.23489.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 Meta-Learning for Cross-Task Generalization in Protein Mutation Property Prediction (https://arxiv.org/pdf/2510.20943.pdf) 4:55 M-GLC: Motif-Driven Global-Local Context Graphs for Few-shot Molecular Property Prediction (https://arxiv.org/pdf/2510.21088.pdf) 8:39 Uncertainty-Aware Multi-Objective Reinforcement Learning-Guided Diffusion Models for 3D De Novo Molecular Design (https://arxiv.org/pdf/2510.21153.pdf) 13:37 RiboPO: Preference Optimization for Structure- and Stability-Aware RNA Design (https://arxiv.org/pdf/2510.21161.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 Speak to a Protein: An Interactive Multimodal Co-Scientist for Protein Analysis (https://arxiv.org/pdf/2510.17826.pdf) 5:17 Atomic Literary Styling: Mechanistic Manipulation of Prose Generation in Neural Language Models (https://arxiv.org/pdf/2510.17909.pdf) 9:50 HyperDiffusionFields (HyDiF): Diffusion-Guided Hypernetworks for Learning Implicit Molecular Neural Fields (https://arxiv.org/pdf/2510.18122.pdf) 14:20 Protein generation with embedding learning for motif diversification (https://arxiv.org/pdf/2510.18790.pdf) 19:06 SO(3)-invariant PCA with application to molecular data (https://arxiv.org/pdf/2510.18827.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 Interpretable RNA-Seq Clustering with an LLM-Based Agentic Evidence-Grounded Framework (https://arxiv.org/pdf/2510.16082.pdf) 5:02 AtomBench: A Benchmark for Generative Atomic Structure Models using GPT, Diffusion, and Flow Architectures (https://arxiv.org/pdf/2510.16165.pdf) 9:17 Protein Folding with Neural Ordinary Differential Equations (https://arxiv.org/pdf/2510.16253.pdf) 14:03 Parameter Identifiability of RNA Dynamics in PDE Transport Models of Fluorescence Recovery After Photobleaching (https://arxiv.org/pdf/2510.16304.pdf) 18:10 CryoDyna: Multiscale end-to-end modeling of cryo-EM macromolecule dynamics with physics-aware neural network (https://arxiv.org/pdf/2510.16510.pdf) 23:23 Atom-anchored LLMs speak Chemistry: A Retrosynthesis Demonstration (https://arxiv.org/pdf/2510.16590.pdf) 27:57 Evaluating protein binding interfaces with PUMBA (https://arxiv.org/pdf/2510.16674.pdf) 32:26 3D-GSRD: 3D Molecular Graph Auto-Encoder with Selective Re-mask Decoding (https://arxiv.org/pdf/2510.16780.pdf) 37:09 ProtoMol: Enhancing Molecular Property Prediction via Prototype-Guided Multimodal Learning (https://arxiv.org/pdf/2510.16824.pdf) 41:22 DeepChem Equivariant: SE(3)-Equivariant Support in an Open-Source Molecular Machine Learning Library (https://arxiv.org/pdf/2510.16897.pdf) 45:24 The Atomic Instruction Gap: Instruction-Tuned LLMs Struggle with Simple, Self-Contained Directives (https://arxiv.org/pdf/2510.17388.pdf) ---------------------------------------- Source code: https://github.com/OliverLaboratory/arxivreader Contact: oliverlaboratory.com Source code: https://github.com/OliverLaboratory/arxivreader