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14.11.2025: Protein Language Models, Generative Molecular Design, and Equivariant Structural Prediction
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
View all episodes
By This podcast is brought to you by the Oliver Laboratory at Vanderbilt University.
----------------------------------------
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