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

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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)

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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 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)

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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 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)

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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 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)

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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 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)

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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 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)

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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 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)

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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 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)

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

Contact: oliverlaboratory.com

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