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Krishnaswamylab.org @krishnaswamylab.bsky.social · Jul 17

Good morning from Vancouver! 🌞⛰️ We’re at #ICML2025 presenting at GenBio + MAS. Come chat with us about machine learning in biology!

With @RobertXiangruTang, @ChenLiu, @DanqiLiao. Views like this make the science even sweeter.🧬🧠

#ML #ComputationalBiology #ICML #Vancouver

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Reposted by Krishnaswamylab.org

Nature Biotechnology @natbiotech.nature.com · Jul 1

Defining and benchmarking open problems in single-cell analysis - @krishnaswamylab.bsky.social @fabiantheis.bsky.social bit.ly/4l8dsiF

Defining and benchmarking open problems in single-cell analysis - Nature Biotechnology

Nature Biotechnology - Defining and benchmarking open problems in single-cell analysis

bit.ly

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Reposted by Krishnaswamylab.org

Yale Kavli Institute for Neuroscience @kavliatyale.bsky.social · May 27

Mark your calendars 🗓️ for June 23 for a Kavli Awards Research in Progress!🧠

Hear from Drs. Bhaskar (@krishnaswamylab.bsky.social‬), @lashaeneuroxp.bsky.social‬, Chen (@emonetlab.bsky.social)‬, Martinez-Magaña (@janitzamontalvo.bsky.social), @kuanawanda.bsky.social‬, Teefe, & ‪‪@haohy.bsky.social‬.

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Reposted by Krishnaswamylab.org

Erica Busch @elbusch.bsky.social · Apr 3

New preprint! Excited to share our latest work “Accelerated learning of a noninvasive human brain-computer interface via manifold geometry” ft. outstanding former undergraduate Chandra Fincke, @glajoie.bsky.social, @krishnaswamylab.bsky.social, and @wutsaiyale.bsky.social's Nick Turk-Browne 1/8

Accelerated learning of a noninvasive human brain-computer interface via manifold geometry

Brain-computer interfaces (BCIs) promise to restore and enhance a wide range of human capabilities. However, a barrier to the adoption of BCIs is how long it can take users to learn to control them. W...

doi.org

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Jan 26

Excited to organize this! Should be an exciting event!!

Graph Signal Processing Workshop 2025 @gsp-workshop.bsky.social · Jan 26

The 8th annual Graph Signal Processing Workshop is back this May 14-16! Held in Montreal, CA, at MILA! GSP covers all things graphs, signals, learning, & applications!

🔗: gspworkshop.org

👉🏻Abstract submission opens Feb 1

👉🏻 Registration opens Mar 20

Graph Signal Processing Workshop

GSP Workshop 2025.

gspworkshop.org

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Jan 25

Great ideas to introduce to the community!! Enjoyed the talk!

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Jan 10

Join us for an exciting session in @jointmath.bsky.social tomorrow! Here is our revised schedule!

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Jan 8

We are at @jointmath.bsky.social Jan 8-11!
1/8: My talk at Topological Machine Learning I
1/8: Dhananjay Bhaskar at Contributed Paper session on Topology
1/11 join our special session on Mathematical and Computational Oncology
Also check out @pseudomanifold.topology.rocks on 1/9!!

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Dec 25

Merry Xmas!

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Dec 24

Looking for talented postdocs in deep learning for neuroscience and neuromodulation with the Murat Gunel lab in neurosurgery (medicine.yale.edu/lab/gunel/)! Projects include brain signal decoding, dynamics modeling for neuromodulation ASD and other conditions. See: krishnaswamylab.org/join

Join the Krishnaswamy Lab

We work on developing foundational mathematical <span class=

krishnaswamylab.org

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Dec 24

Frohe Weinachten!

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Dec 21

(10/n) For code see github.com/Krishnaswamy.... Thanks for reading!

GitHub - KrishnaswamyLab/GSPA-manuscript-analyses: Learning meaningful representations of genes

Learning meaningful representations of genes. Contribute to KrishnaswamyLab/GSPA-manuscript-analyses development by creating an account on GitHub.

github.com

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Dec 21

(9/n) GSPA-Pt can be used to map patient sample manifolds. We mapped 48 melanoma patient scRNA-seq samples and classified response from the patient embedding using logistic regression. The GSPA-Pt gene embeddings achieved the highest classification performance.

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Dec 21

(8/n) GSPA-LR concatenates ligand (L) and receptor (R) for a pair representation. LR pair modules captures a diverse range of LR profiles, finer the cluster-level analysis. For example, in skin cells, Module 5 includes Ccl5–Ccr5 link present in AG and AG CPI, epithelial, myeloid and T cells.

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Dec 21

(7/n) With the Nik Joshi Lab at Yale we presented a new dataset of 39K CD8+ cells from LCMV infections. Interestingly only GSPA-based gene localization finds genes associated with type 1 interferon signaling. DE requires clustering, but DE genes in clusters do not reveal this signature!

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Dec 21

(6/n) GSPA facilitates a measure called gene localization, via comparison to a uniform distribution. For PBMCs, cell embeddings using all genes versus only top localized genes showed similar structure, suggesting that localized genes capture cell-type variation and geometry.

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Dec 21

(5/n) We show that for (PBMCs), GSPA with compressed wavelets grouped cell-type specific genes from PanglaoDB. In embryoid-body lineages early trajectory genes linked to embryonic stem cells (NANOG, POU5F1) and late trajectory genes linked to hemangioblast-specific signatures (CD34, PECAM1, TAL1).

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Dec 21

(4/n) Rather than transposing the cellxgene matrix for gene embeddings, we frame genes as signals on a cell–cell graph, decomposed using graph-based diffusion wavelets. Diffusion wavelets use differences of powers of P. Then we then reduce dimensionality with an autoencoder.

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Dec 21

(3/n) Low dimensional embeddings like UMAP, PHATE, tSNE have been vital in understanding geometry and subpopulations from single cell data. Gene expression is also highly organized (pathways etc). But due to noise, directly apply these embeddings to genes has not worked.

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Dec 21

(2/n)This work is lead by Aarthi Venkat, Sam Leone. We couldn't have done it without our collaborators Scott Youlton, Eric Fagerberg, John Attanasio from Nik Joshi Lab at Yale and Michael Perlmutter from Boise State University!

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Reposted by Krishnaswamylab.org

Nature Computational Science @natcomputsci.nature.com · Dec 20

📢Out now! @krishnaswamylab.bsky.social presents a graph signal processing method that learns gene representations from single-cell data. www.nature.com/articles/s43...

🔓https://rdcu.be/d4kPz

Mapping the gene space at single-cell resolution with gene signal pattern analysis - Nature Computational Science

This work presents a graph signal processing method, gene signal pattern analysis, to embed gene signals from single-cell sequencing data. In diverse experimental set-ups and case studies, GSPA establ...

www.nature.com

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Dec 20

(1/n) Excited to share our work on gene signal pattern analysis (GSPA)---our new method for analyzing gene expression over cellular manifolds! www.nature.com/articles/s43...

Mapping the gene space at single-cell resolution with gene signal pattern analysis - Nature Computational Science

This work presents a graph signal processing method, gene signal pattern analysis, to embed gene signals from single-cell sequencing data. In diverse experimental set-ups and case studies, GSPA establ...

www.nature.com

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Dec 5

us :) [See Diffusion EMD, Geodesic Sinkhorn, TrajectoryNet, PhEMD, Trellis, Mioflow]

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Krishnaswamylab.org @krishnaswamylab.bsky.social · Dec 2

Last day to apply for our @wutsaiyale.bsky.social
open rank faculty position in one of several relevant fields including computer science, data science, engineering in addition to psychology, neuroscience and cognitive science!! apply.interfolio.com/153378

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Reposted by Krishnaswamylab.org

logconference.bsky.social @logconference.bsky.social · Nov 29

🏆 Best Paper Award & Honorable Mention 🏆

Congratulations to our outstanding authors for their exceptional contributions to LoG 2024! 🎉

📜 Your work inspires the entire graph and geometric ML community!

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