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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

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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

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

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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)

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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 MOSAIC: Codon Harmonization of Monte Carlo-Based Simulated Annealing for Linked Codons in Heterologous Protein Expression (https://arxiv.org/pdf/2511.10708.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 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)

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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 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)

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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 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)

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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 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)

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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 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)

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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 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)

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

Contact: oliverlaboratory.com

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