This podcast is brought to you by the Oliver Laboratory at Vanderbilt University.

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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)

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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.

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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)

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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.

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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)

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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.

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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)

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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.

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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)

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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.

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0:00 Protein Secondary Structure Prediction Using Transformers (https://arxiv.org/pdf/2512.08613.pdf)

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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.

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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)

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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.

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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)

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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.

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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)

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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.

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0:00 Atomic Diffusion Models for Small Molecule Structure Elucidation from NMR Spectra (https://arxiv.org/pdf/2512.03127.pdf)

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Source code: https://github.com/OliverLaboratory/arxivreader

Contact: oliverlaboratory.com

Source code: https://github.com/OliverLaboratory/arxivreader