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

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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)

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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 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)

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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 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)

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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 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)

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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 MXtalTools: A Toolkit for Machine Learning on Molecular Crystals (https://arxiv.org/pdf/2511.20327.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 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)

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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 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)

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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 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)

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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 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)

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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 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)

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

Contact: oliverlaboratory.com

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