Decoding Biomolecular Languages

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

  1. 6 de jul.

    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 de jun.

    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 de jun.

    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 de jun.

    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 de jun.

    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 de jun.

    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 de mai.

    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 de mai.

    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

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

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