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Krishnaswamylab.org

@krishnaswamylab.bsky.social
2K followers 161 following 55 posts

We develop AI methods for science, particularly deep learning methods based on data geometry, topology and dynamics systems.

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Reposted by Krishnaswamylab.org
Yale Cancer Center @yalecancer.bsky.social · 27/02/2026
Led by @virusesimmunity.bsky.social and @krishnaswamylab.bsky.social, a team of Yale researchers developed a new tool #Immunostruct that combines multiple types of data to better support the development of personalized vaccines, including vaccines for #cancer. medicine.yale.edu/news-article...
medicine.yale.edu
Using Machine Learning to Develop Personalized Vaccines for Cancer
A new tool combines multiple types of data to better support the development of vaccines that target patient-specific pathology.
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 30/11/2025
We're @neuripsconf.bsky.social HiPoNet: neurips.cc/virtual/2025... HELM: Hyperbolic LLM openreview.net/forum?id=Rnb... Talk: hyperboliclearning.github.io/events/neuri... (Unireps/Neureps) Measure Before You Look openreview.net/forum?id=5Yn... (FM4LS) CellSpliceNet: openreview.net/forum?id=gVA...
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 30/11/2025
We have 3 papers at TAG-DS @NeurIPSConf! DYMAG: Message Passing Using Dynamical-systems-based Waveforms (Oral) openreview.net/forum?id=WYi... A Graph Laplacian Eigenvector Pretraining Method for GNNs (Spotlight) openreview.net/forum?id=r5c... Reeb Graphs and Towers openreview.net/forum?id=U8I...
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 07/11/2025
(10/N) If you are interested check out our preprint and code! Thanks for reading! Arxiv: arxiv.org/abs/2502.07746 Code: github.com/Krishnaswamy...
arxiv.org
HiPoNet: A Multi-View Simplicial Complex Network for High Dimensional Point-Cloud and Single-Cell Data
In this paper, we propose HiPoNet, an end-to-end differentiable neural network for regression, classification, and representation learning on high-dimensional point clouds. Our work is motivated by si...
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 07/11/2025
(9/N) Grateful to lead authors Siddharth Viswanath and Hiren Madhu, and coauthors Dhananjay Bhaskar, Jake Kovalic, Dave Johnson, Chris Tape, Ian Adelstein, Rex Ying and Michael Perlmutter!
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 07/11/2025
(8/N) ✨ In short, HiPoNet is a neural network that takes in a whole point cloud, and utilizes methods from geometry and topology to derive features of the point cloud. → Multiple learned views → Simplicial wavelets to extract multi-scale structure
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 07/11/2025
(7/N) What’s more, HiPoNet’s learned feature weights are interpretable. For example, immune-related markers like CD11b, CD118, and FOXP3 consistently emerge as important across views, aligning with known tumor-immune biology.
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 07/11/2025
(6/N) We find that HiPONet consistently outperforms other methods on these datasets.
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 07/11/2025
(5/N) We then evaluate HiPOnet on patient level classification tasks using single cell and spatial proteomics data:
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 07/11/2025
(4/N) We first check that HiPoNet preserves topological features of datasets by predicting persistence from the datasets:
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 07/11/2025
(3/N) HiPoNet models each cloud as a simplicial complex, and uses simplicial wavelet transforms to capture point-cloud level embeddings. Not only that---it uses multiview learning, i.e. different projections of the features to capture different underlying factors in the data.
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 07/11/2025
(2/N) Modern technologies such as mass cytometry or scRNA-seq now allow large cohorts of patients to be measured. Each patient is actually a large single cell dataset creating a high-dimensional point cloud. But these point clouds are far more complex than 3D shapes that ML methods have handled..
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 07/11/2025
(1/N) Thrilled to share that our paper HiPoNet (High dimensional Point cloud Network) to be presented at NeurIPS 2025! HiPoNet treats an entire high-dimensional point cloud as a datapoint! It captures multi-scale geometry and topology of the cloud perform classification and regression tasks.
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 17/07/2025
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 · 01/07/2025
Defining and benchmarking open problems in single-cell analysis - @krishnaswamylab.bsky.social @fabiantheis.bsky.social bit.ly/4l8dsiF
bit.ly
Defining and benchmarking open problems in single-cell analysis - Nature Biotechnology
Nature Biotechnology - Defining and benchmarking open problems in single-cell analysis
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Reposted by Krishnaswamylab.org
Yale Kavli Institute for Neuroscience @kavliatyale.bsky.social · 27/05/2025
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.
Flyer for the Kavli Awards Research in Progress of June 23 showing pictures of the speakers in the Kavli logo, with a schedule:

12:00 pm Dhananjay Bhaskar, PhD
2024 Kavli Postdoctoral Fellowship
Krishnaswamy & Colón-Ramos labs

12:20 pm LaShae Nicholson, PhD
2022 Kavli Award for Academic Diversity
Strittmatter lab

12:40 pm José Jaime Martínez-Magaña, PhD
2023 Kavli Award for Academic Diversity
Montalvo-Ortiz lab

1:00 pm Kevin Chen, PhD
2024 Kavli Postdoctoral Fellowship
Emonet & Clark labs

1:20 pm break

1:30 pm Aaron Kuan, PhD &
Joerg Bewersdorf, PhD
2024 Kavli Teams Award

1:50 pm Enock Teefe, MD
2023 Kavli Award for Academic Diversity
Pittenger & Fernandez labs

2:10 pm Hongyan Hao, PhD
2024 Kavli Postdoctoral Fellowship
Hammarlund & De Camilli labs
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Reposted by Krishnaswamylab.org
Erica Busch @elbusch.bsky.social · 04/04/2025
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
doi.org
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...
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 26/01/2025
Excited to organize this! Should be an exciting event!!
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 25/01/2025
Great ideas to introduce to the community!! Enjoyed the talk!
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 10/01/2025
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 · 08/01/2025
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 · 25/12/2024
Merry Xmas!
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 24/12/2024
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
krishnaswamylab.org
Join the Krishnaswamy Lab
We work on developing foundational mathematical <span class=
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 24/12/2024
Frohe Weinachten!
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 21/12/2024
(10/n) For code see github.com/Krishnaswamy.... Thanks for reading!
github.com
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.
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 21/12/2024
(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 · 21/12/2024
(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 · 21/12/2024
(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 · 21/12/2024
(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 · 21/12/2024
(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 · 21/12/2024
(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 · 21/12/2024
(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 · 21/12/2024
(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 · 20/12/2024
📢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
nature.com
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...
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 20/12/2024
(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...
nature.com
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...
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 05/12/2024
us :) [See Diffusion EMD, Geodesic Sinkhorn, TrajectoryNet, PhEMD, Trellis, Mioflow]
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 02/12/2024
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 · 29/11/2024
🏆 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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Krishnaswamylab.org @krishnaswamylab.bsky.social · 28/11/2024
Happy thanksgiving!!
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 28/11/2024
Up Mont Royal in the rain! For those of you who don’t know I’m on a one-semester sabbatical to Montreal!
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 26/11/2024
Pictures from @logconference.bsky.social meetup Montreal!
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 25/11/2024
If you're in Montreal tomorrow, catch us at the @logconference.bsky.social meetup @Mila_Quebec ! sites.google.com/view/log-202...
sites.google.com
LoG 2024 Montreal
About
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Reposted by Krishnaswamylab.org
logconference.bsky.social @logconference.bsky.social · 24/11/2024
✨EXCITING NEWS! We now have a Bluesky account!! AND registration for the 3rd Learning on Graphs conference is open 😊 It is virtual, free to attend, livestreamed, and recorded 📹 Sign up today! The conference is this coming week 😱 forms.gle/eYiDCopJGUc8...
Screen capture of LoG website. The conference is Nov 26-29, 2024. See our website for more details: https://logconference.org/.
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 23/11/2024
Siddharth from our lab explaining protscape and scattering to CT Governor Ned Lamont and others at the AI summit hosted by @boehringer.bsky.social and BioCT arxiv.org/abs/2410.20317!!
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 22/11/2024
(3/3) Finally @DanqiLiao73090 is previewing our new method of annotating dense microscopic images by killing and restoring diffeomorphisms DiffkillR arxiv.org/abs/2410.03058
arxiv.org
DiffKillR: Killing and Recreating Diffeomorphisms for Cell Annotation in Dense Microscopy Images
The proliferation of digital microscopy images, driven by advances in automated whole slide scanning, presents significant opportunities for biomedical research and clinical diagnostics. However, accu...
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 22/11/2024
(2/3) We also have a poster on CUTS for unsupervised presentation (to appear at MICCAI) arxiv.org/abs/2209.11359
arxiv.org
CUTS: A Deep Learning and Topological Framework for Multigranular Unsupervised Medical Image Segmentation
Segmenting medical images is critical to facilitating both patient diagnoses and quantitative research. A major limiting factor is the lack of labeled data, as obtaining expert annotations for each ne...
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 22/11/2024
(1/3) Our lab is at the New England Computer Vision Conference (NECV) right here in New Haven today! Chen Liu is presenting an oral on Imageflownet for longitudinal forecasting of medical images. arxiv.org/abs/2406.14794
arxiv.org
ImageFlowNet: Forecasting Multiscale Image-Level Trajectories of Disease Progression with Irregularly-Sampled Longitudinal Medical Images
Advances in medical imaging technologies have enabled the collection of longitudinal images, which involve repeated scanning of the same patients over time, to monitor disease progression. However, pr...
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 21/11/2024
(8/n) Applications to Cancer, Immunology, Molecular generation, Neuroscience, Psychology... Happy to provide links!
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 21/11/2024
(7/n) Geometric and topological characterizations of cellular and neural dynamics: GSTH (Moore et al. Journal of Cell Biology), Cubical Complex homology of fMRI (Rieck et al. NeurIPS 2020), NeuroGSTH (Bhaskar et al. GSTH)
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Krishnaswamylab.org @krishnaswamylab.bsky.social · 21/11/2024
(6/n) Domain transfer: Examples: FMGAN (Amodio et al., Pattterns), MAGAN (Amodio et al. ICML 2018), SAMBA (Afrasiyabi et al., under review)
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