Has detailed setup for ELBO
https://arxiv.org/abs/1906.02691
Kingma, D. P., & Welling, M. (2019). An introduction to variational autoencoders. Foundations and Trends® in Machine Learning, 12(4), 307–392. https://doi.org/10.1561/2200000056
Archive for the 'SciLit' Category
1906.02691 An Introduction to Variational Autoencoders
March 2, 2025Investigating spatial dynamics in spatial omics data with StarTrail | bioRxiv
March 2, 2025https://www.biorxiv.org/content/10.1101/2024.05.08.593025v1
Chen, J., Xiong, C., Sun, Q., Wang, G. W., Gupta, G. P., Halder, A., Li, Y., & Li, D. (2024). Investigating spatial dynamics in spatial omics data with StarTrail. bioRxiv (Cold Spring Harbor Laboratory). https://doi.org/10.1101/2024.05.08.593025
1803.00567 Computational Optimal Transport
March 1, 2025https://arxiv.org/abs/1803.00567
explains the dual problem well
Peyré, G., & Cuturi, M. (2018, March 1). Computational Optimal transport. arXiv.org. https://arxiv.org/abs/1803.00567
tutorial_on_optimal_transport.pdf
2312.07511 A Hitchhiker’s Guide to Geometric GNNs for 3D Atomic Systems
March 1, 2025https://arxiv.org/abs/2312.07511
Duval, A., Mathis, S., V., Joshi, C. K., Schmidt, V., Miret, S., Malliaros, F. D., Cohen, T., Liò, P., Bengio, Y., & Bronstein, M. (2023, December 12). A Hitchhiker’s guide to Geometric GNNs for 3D atomic Systems. arXiv.org. https://arxiv.org/abs/2312.07511
Good intuition on spherical harmonics
1906.02691 An Introduction to Variational Autoencoders
February 18, 2025https://arxiv.org/abs/1906.02691
Kingma, D. P., & Welling, M. (2019). An introduction to variational autoencoders. Foundations and Trends® in Machine Learning, 12(4), 307–392. https://doi.org/10.1561/2200000056
Conformational sampling and interpolation using language-based protein folding neural networks
February 7, 2025Principal component analysis | Nature Reviews Methods Primers
February 4, 2025https://www.nature.com/articles/s43586-022-00184-w
Greenacre, M., Groenen, P. J. F., Hastie, T., D’Enza, A. I., Markos, A., & Tuzhilina, E. (2022). Principal component analysis. Nature Reviews Methods Primers, 2(1).
https://doi.org/10.1038/s43586-022-00184-w
Network Analysis as a Grand Unifier in Biomedical Data Science | Annual Reviews
February 4, 2025https://www.annualreviews.org/content/journals/10.1146/annurev-biodatasci-080917-013444
McGillivray, P., Clarke, D., Meyerson, W., Zhang, J., Lee, D., Gu, M., Kumar, S., Zhou, H., & Gerstein, M. (2018). Network analysis as a grand unifier in biomedical data science. Annual Review of Biomedical Data Science, 1(1), 153–180.
https://doi.org/10.1146/annurev-biodatasci-080917-013444
Hazard Ratio in Clinical Trials – PMC
January 26, 2025https://pmc.ncbi.nlm.nih.gov/articles/PMC478551/
Spruance, S. L., Reid, J. E., Grace, M., & Samore, M. (2004). Hazard ratio in clinical trials. Antimicrobial Agents and Chemotherapy, 48(8), 2787–2792. https://doi.org/10.1128/aac.48.8.2787-2792.2004
Paper on human reads in microbiome data
January 25, 2025Interesting paper on how the incomplete human genome can cause privacy issues in analyzing metagenomic data.
https://www.nature.com/articles/s41467-025-56077-5
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