Machine Learning in Computational Biology: Daily Digest

Carlos Oliver
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Daily summaries of preprints in machine learning and computational biology. Source code: https://github.com/OliverLaboratory/arxivreader

  1. JAN 9

    09.01.2026: Multi-Modal Molecular Design, Semi-Supervised Learning, and Activity Cliff Estimation

    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

    9 min

  2. JAN 8

    08.01.2026: Knowledge Distillation, Deep Learning for Cancer Subtyping, and Protein Function Reasoning

    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

    13 min

  3. JAN 7

    07.01.2026: Molecular Property Prediction, Learnable DNA Tokenization, and Multi-Scale Graph Autoregressive Modeling

    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

    9 min

  4. JAN 6

    06.01.2026: Equivariant Models, Protein and RNA Structure Prediction, and Large Language Models for Molecular Applications

    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

    19 min

  5. JAN 5

    05.01.2026: Uncertainty Quantification, Protein Energy Alignment, and Quantum Simulation in Molecular Modeling

    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

    18 min

  6. 12/30/2025

    30.12.2025: Design Archetypes, Interpretable Machine Learning, and Benchmarking in Molecular and Protein Science

    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

    20 min

  7. 12/29/2025

    29.12.2025: Molecule Generative Models, In Vitro Evaluation, and Hit Generation

    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

    5 min

  8. 12/24/2025

    24.12.2025: Multi-Modal Molecular Elucidation, Agentic Optimization, and Advanced RNA Structure Analysis

    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

    25 min
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Daily summaries of preprints in machine learning and computational biology. Source code: https://github.com/OliverLaboratory/arxivreader

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