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Giovanni Palla

@giopll.bsky.social
158 followers 323 following 11 posts

Research Scientist AI/ML @cziscience.bsky.social , PhD @www.helmholtz-munich.de , OSS @scverse.bsky.social giovannipalla.com

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Giovanni Palla @giopll.bsky.social · 06/12/2025
work with @jmtomczak.bsky.social sudarshan babu Payam Dibaeinia Donghui Li, PhD Aly A. Khan @tkaraletsos.bsky.social
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Giovanni Palla @giopll.bsky.social · 06/12/2025
I'll be at the AI Virtual Cells and Instruments: A New Era in Drug Discovery and Development. Stop by to chat about generative models and virtual cells! I'll be presenting our work @biohub.org on a scalable latent diffusion model for single-cell gene expression data.
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Giovanni Palla @giopll.bsky.social · 27/11/2025
As more single-cell perturbation data become available, it is crucial to establish a consensus on measures of success for perturbation prediction models. I reviewed recent literature and collected some thoughts on the current state of affairs. open.substack.com/pub/giovanni...
open.substack.com
Virtual Cell Perturbation Metrics Reloaded
Thoughts on metrics for perturbation prediction models
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Giovanni Palla @giopll.bsky.social · 07/11/2025
For further details, check out: 📜 our paper: arxiv.org/abs/2511.02986 💻 our code: github.com/czi-ai/scldm 🖥️ a blogpost: biohub.org/blog/scldm-a... 🤖 a model card: virtualcellmodels.cziscience.com/model/scldm
arxiv.org
Scalable Single-Cell Gene Expression Generation with Latent Diffusion Models
Computational modeling of single-cell gene expression is crucial for understanding cellular processes, but generating realistic expression profiles remains a major challenge. This difficulty arises fr...
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Giovanni Palla @giopll.bsky.social · 07/11/2025
Fantastic collaboration with @jmtomczak.bsky.social , the Biohub Chicago team sudarshan babu Payam Dibaeinia Aly A. Kahn and the team in the Bay Area James Douglas Pearce Donghui Li, PhD Theofanis Karaletsos.
arxiv.org
Scalable Single-Cell Gene Expression Generation with Latent Diffusion Models
Computational modeling of single-cell gene expression is crucial for understanding cellular processes, but generating realistic expression profiles remains a major challenge. This difficulty arises fr...
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Giovanni Palla @giopll.bsky.social · 07/11/2025
We are excited because it presents a novel way to learn "latent tokens" of gene expression variation, overcoming many of the limitations of order(less) tokenization and learning schemes. We show its performance in generative and representation learning tasks.
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Giovanni Palla @giopll.bsky.social · 07/11/2025
Yesterday, we released a new paper on a novel architecture for single-cell genomics. We call it scLDM to hint at the Latent Diffusion Model paradigm, a generative modeling framework that has been very successful across various domains.
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Reposted by Giovanni Palla
Lukas Heumos @lukasheumos.bsky.social · 06/11/2025
Excited to see a home for MCP servers in bioinformatics emerge! The community needs a central hub for developing MCP servers for key bioinfo tools. At @scverse.bsky.social we're contributing to this effort - can't wait to share what we're building
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Giovanni Palla @giopll.bsky.social · 03/10/2025
Fantastic lineup of panelists to discuss everything agentic coding in bioinformatics, still time to register here: www.eventbrite.com/e/scverse-co...
eventbrite.com
Scverse Conference 2025
From the foundational open-source software in the life sciences — to its large community coming together
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Giovanni Palla @giopll.bsky.social · 29/03/2025
Been hearing this often lately: 'Did you see Valentine’s blogging again?' 🎉
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Reposted by Giovanni Palla
mariuslange.bsky.social @mariuslange.bsky.social · 28/03/2025
Happy to share CellAnnotator, a lightweight Python package to query OpenAI models for initial cell type annotations: github.com/quadbio/cell... Inspired by ideas in www.nature.com/articles/s41... and github.com/VPetukhov/GP..., implemented as an scVerse ecosystem package with docs and tutorials.
github.com
GitHub - quadbio/cell-annotator: Automatically annotate cell types, consistently across samples.
Automatically annotate cell types, consistently across samples. - quadbio/cell-annotator
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Reposted by Giovanni Palla
Luke Zappia @lazappi.bsky.social · 18/03/2025
Our paper benchmarking feature selection for scRNA-seq integration and reference usage is out now www.nature.com/articles/s41...! Keep reading for more about how we did the study and what we found out 🧵 👇 1/16
nature.com
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Reposted by Giovanni Palla
Valentine Svensson @nxn.se · 06/03/2025
A pre-trained SCVI model of our Tahoe-100M cell atlas is now available as a HubModel! It can be used for gene expression visualization, differential expression, or cell clustering. Available at Hugging Face with instructions on how to load it (see thread)
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Giovanni Palla @giopll.bsky.social · 10/02/2025
🚨 Deadline Approaching! 🚨 Only 3 days left to submit your tiny or full workshop papers! 📝✨ Don’t miss out—deadline is February 12, 2025, at 11:59 PM AoE. 👉 Submit your work here: openreview.net/group?id=ICL...
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Reposted by Giovanni Palla
Kristina Ulicna @kristinaulicna.bsky.social · 06/02/2025
We have a date! 📅 #LMRL2025 is coming to 🇸🇬 on 28th April 2025 @iclr-conf.bsky.social to bring life into AI 🌱😜 Biological of biomedical, any bio domain helping to bring *meaningfulness* into the world should be represented at this workshop 🌏 It's not late until 12th Feb AoE to submit! 📝
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Giovanni Palla @giopll.bsky.social · 14/01/2025
hi @davidsebfischer.bsky.social could I be added? thanks!
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Reposted by Giovanni Palla
Kristina Ulicna @kristinaulicna.bsky.social · 06/01/2025
📢 Calling all researchers! The #LMRL workshop is now accepting paper submissions! 🧬✨ 🎯 Showcase complete works / early-stage ideas 💡 via your chance to inspire & connect with a non-traditional AIxBio #ICLR2025 audience 🌍 👉 Help us spread the word of lmrl.org 🙌
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