Decoding Biomolecular Languages

About Decoding Biomolecular Languages

Daily summaries of preprints from arXiv and bioRxiv. Generated for Decoding Biomolecular Languages.

Language

en

Explicit

No

First episode

6 Apr 2026

Latest episode

6 Jul 2026

Latest episodes

14 episodes in the feed.

1. 

   6 Jul 2026

   06.07.2026: Fusion of GNNs and LLMs, Safety Evaluation of AI Agents, and Scientific Collaboration at Web Scale

   This podcast is brought to you by Scholar FM. ---------------------------------------- Papers included in this episode: 0:09 - Measuring Graph-to-Graph Semantic Similarity in Knowledge Graphs: An Empirical Evaluation of Knowledge Graph Embeddings https://export.arxiv.org/pdf/2606.29180.pdf 1:22 - Clarus: Coordinating Autonomous Research Agents toward Web-Scale Scientific Collaboration https://export.arxiv.org/pdf/2606.30246.pdf 2:18 - Inoculation Adapters: Improved Selective Generalization of Capabilities with Fewer Surprising Backdoors https://export.arxiv.org/pdf/2606.30252.pdf 3:24 - EMPATH: A Multilingual Auditor-Judge Benchmark for Safety Evaluation of Emotional-Support Chatbots https://export.arxiv.org/pdf/2606.30256.pdf 4:21 - PromptGNN-sim: Deep Fusion and Alignment of GNN and LLMs for Text-Attributed Graph Learning https://export.arxiv.org/pdf/2606.30291.pdf ---------------------------------------- scholarfm.com

2. 

   29 Jun 2026

   29.06.2026: Unified Multimodal Models, Structure Prediction, and Biomolecular Design

   This podcast is brought to you by Scholar FM. ---------------------------------------- Papers included in this episode: 0:09 - Molexar: A Unified Multimodal Molecular Foundation Model for Drug Design https://export.arxiv.org/pdf/2606.25865.pdf ---------------------------------------- scholarfm.com

3. 

   22 Jun 2026

   22.06.2026: Integrated Protein Dynamics, Proximity-Inducing Drug Discovery, and Equivariant Deep Learning Models

   This podcast is brought to you by Scholar FM. ---------------------------------------- Papers included in this episode: 0:09 - Predicting protein-protein interaction sites based on dynamic perception mechanism within a hierarchical E(n)-equivariant graph. https://doi.org/10.1093/bib/bbag304 1:04 - Proteomics-Driven Strategies for Proximity-Inducing Drug Discovery. https://doi.org/10.1002/anie.3307512 1:55 - DrugDL: Dual-modal deep learning framework for multi-property drug prediction and targeted therapy discovery. https://doi.org/10.1093/bioinformatics/btag392 2:49 - AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling. https://doi.org/10.1002/advs.76023 3:37 - AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling. https://doi.org/10.1002/advs.76023 ---------------------------------------- scholarfm.com

4. 

   15 Jun 2026

   15.06.2026: Salt Bridge Conservation, Diffusion Model Uncertainty, and Graph Contrastive Learning in Structural Biology

   This podcast is brought to you by Scholar FM. ---------------------------------------- Papers included in this episode: 0:09 - Evaluating the Representation Space of Diffusion Models via Self-Supervised Principles https://export.arxiv.org/pdf/2606.09718.pdf 1:10 - Uncertainty Estimation for Molecular Diffusion Models https://export.arxiv.org/pdf/2606.13451.pdf ---------------------------------------- scholarfm.com

5. 

   8 Jun 2026

   08.06.2026: Agentic Protein Design, Geospatial Foundation Models, and Reinforcement Learning for Intelligent Agents

   This podcast is brought to you by Scholar FM. ---------------------------------------- Papers included in this episode: 0:09 - Structure-Guided Adaptive Propagation for Protein-Protein Interaction Site Prediction https://export.arxiv.org/pdf/2606.01781.pdf 1:03 - COMAP: Co-Evolving World Models and Agent Policies for LLM Agents https://export.arxiv.org/pdf/2606.02372.pdf 1:58 - Harness-1: Reinforcement Learning for Search Agents with State-Externalizing Harnesses https://export.arxiv.org/pdf/2606.02373.pdf 2:53 - Spatial Representation Learning Beyond Pixels: Unifying Raster Data and Vector Semantics for Human-Centric Geospatial Foundation Models https://export.arxiv.org/pdf/2606.02374.pdf 3:51 - AgentPLM: Agentic Protein Language Models with Reasoning-Augmented Decoding for Protein Sequence Design https://export.arxiv.org/pdf/2606.02386.pdf ---------------------------------------- scholarfm.com

6. 

   1 Jun 2026

   01.06.2026: Protein and Antibody Engineering, Geometry-Based Molecular Generation, and Phenotype-Aware Editing

   This podcast is brought to you by Scholar FM. ---------------------------------------- Papers included in this episode: 0:09 - Geometric Flow Matching for Molecular Conformation Generation via Manifold Decomposition https://export.arxiv.org/pdf/2605.25577.pdf 1:09 - Co-folding model guided by structural proteomics https://export.arxiv.org/pdf/2605.26192.pdf 2:01 - PhAME: Phenotype-Aware Molecular Editing via Latent Diffusion https://export.arxiv.org/pdf/2605.28226.pdf ---------------------------------------- scholarfm.com

7. 

   25 May 2026

   25.05.2026: Causal Intelligence, Novel Optimization Methods, and New Benchmarks for Language and Vision Models

   This podcast is brought to you by Scholar FM. ---------------------------------------- Papers included in this episode: 0:09 - Causely: A Causal Intelligence Layer for Enterprise AI A Benchmark Study on SRE and Reliability Workflows https://export.arxiv.org/pdf/2605.18327.pdf 1:12 - QSTRBench: a New Benchmark to Evaluate the Ability of Language Models to Reason with Qualitative Spatial and Temporal Calculi https://export.arxiv.org/pdf/2605.18380.pdf 2:08 - When Fireflies Cluster; Enhancing Automatic Clustering via Centroid-Guided Firefly Optimization https://export.arxiv.org/pdf/2605.18460.pdf 2:58 - OCCAM: Open-set Causal Concept explAnation and Ontology induction for black-box vision Models https://export.arxiv.org/pdf/2605.18481.pdf 3:46 - A Practical Noise2Noise Denoising Pipeline for High-Throughput Raman Spectroscopy https://export.arxiv.org/pdf/2605.18511.pdf ---------------------------------------- scholarfm.com

8. 

   18 May 2026

   18.05.2026: LLM-Guided Knowledge Graphs, Model-Agnostic Protein Interaction Prediction, and Continual Learning Benchmarks

   This podcast is brought to you by Scholar FM. ---------------------------------------- Papers included in this episode: 0:10 - Evolving-RL: End-to-End Optimization of Experience-Driven Self-Evolving Capability within Agents https://export.arxiv.org/pdf/2605.10663.pdf ---------------------------------------- scholarfm.com

9. 

   11 May 2026

   11.05.2026: Fine-Grained Graph Generation, Semantic Consistency in GNNs, and Causality for Trustworthy AI

   This podcast is brought to you by Scholar FM. ---------------------------------------- Papers included in this episode: 0:09 - Counterfactual Reasoning in Automated Planning https://export.arxiv.org/pdf/2605.02603.pdf 0:52 - SCGNN: Semantic Consistency enhanced Graph Neural Network Guided by Granular-ball Computing https://export.arxiv.org/pdf/2605.02617.pdf 1:45 - SCGNN: Semantic Consistency enhanced Graph Neural Network Guided by Granular-ball Computing https://export.arxiv.org/pdf/2605.02617.pdf 2:39 - Trustworthy AI Suffers from Invariance Conflicts and Causality is The Solution https://export.arxiv.org/pdf/2605.02640.pdf 3:24 - Fine-Grained Graph Generation through Latent Mixture Scheduling https://export.arxiv.org/pdf/2605.02780.pdf ---------------------------------------- scholarfm.com

10. 

    4 May 2026

    04.05.2026: AI-Driven Protein Dynamics, Curvature-Aware Docking, and Multimodal Drug-Target Interaction Exploration

    This podcast is brought to you by Scholar FM. ---------------------------------------- Papers included in this episode: 0:08 - Learning Structure, Energy, and Dynamics: A Survey of Artificial Intelligence for Protein Dynamics https://export.arxiv.org/pdf/2604.25244.pdf ---------------------------------------- scholarfm.com

11. 

    27 Apr 2026

    27.04.2026: Contrastive 3D Learning, Multimodal Feature Fusion, and Automated Protein-Ligand Bioactivity Mining

    This podcast is brought to you by Scholar FM. ---------------------------------------- Papers included in this episode: 0:09 - Structure-guided molecular design with contrastive 3D protein-ligand learning https://export.arxiv.org/pdf/2604.19562.pdf 1:05 - BioMiner: A Multi-modal System for Automated Mining of Protein-Ligand Bioactivity Data from Literature https://export.arxiv.org/pdf/2604.21508.pdf ---------------------------------------- scholarfm.com

12. 

    20 Apr 2026

    20.04.2026: Thermodynamics-Driven Machine Learning, Protein-Molecule Interaction Mechanisms, and Controllable Molecular Optimization

    This podcast is brought to you by Scholar FM. ---------------------------------------- Papers included in this episode: 0:09 - TriFit: Trimodal Fusion with Protein Dynamics for Mutation Fitness Prediction https://export.arxiv.org/pdf/2604.12026.pdf 1:07 - Scaffold-Conditioned Preference Triplets for Controllable Molecular Optimization with Large Language Models https://export.arxiv.org/pdf/2604.12350.pdf 2:04 - Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot with Thermodynamics-Driven Machine Learning https://export.arxiv.org/pdf/2604.14906.pdf ---------------------------------------- scholarfm.com

13. 

    13 Apr 2026

    13.04.2026: Protein Dynamics Visualization, Controllable Design with AI, and 3D Structure-Aware Simulation

    This podcast is brought to you by Scholar FM. ---------------------------------------- Papers included in this episode: 0:10 - MAVEN: A Mesh-Aware Volumetric Encoding Network for Simulating 3D Flexible Deformation https://export.arxiv.org/pdf/2604.04474.pdf ---------------------------------------- scholarfm.com

14. 

    6 Apr 2026

    06.04.2026: Deep Learning for Protein States, Goal-Directed Molecular Generation, and Trillion-Scale Chemical Libraries

    This podcast is brought to you by Scholar FM. ---------------------------------------- Papers included in this episode: 0:08 - Estimating Protein Conformational States from High-Speed AFM Images with Molecular Dynamics and Deep Learning. https://doi.org/10.1021/acs.jcim.6c00142 1:01 - Discovery of WRN helicase inhibitors by 3D-CNN docking and ML consensus from traditional Chinese medicine monomers. https://doi.org/10.1016/j.jmgm.2026.109376 1:53 - Constructing and characterizing trillion-scale combinatorial chemical library. https://doi.org/10.1186/s13321-026-01185-7 2:44 - SiteContext: A Web Server for Protein Binding Site Comparison. https://doi.org/10.1016/j.jmb.2026.169791 3:38 - HybridMolGen: A Unified Framework for Goal-Directed Molecular Generation via Multi-Objective Reinforcement Learning. https://doi.org/10.1093/bioinformatics/btag170 ---------------------------------------- scholarfm.com

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