Giovanni Palla

work with @jmtomczak.bsky.social sudarshan babu Payam Dibaeinia Donghui Li, PhD Aly A. Khan @tkaraletsos.bsky.social

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.

Virtual Cell Perturbation Metrics Reloaded Thoughts on metrics for perturbation prediction models

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...

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...

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

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...

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.

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.

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.

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

Fantastic lineup of panelists to discuss everything agentic coding in bioinformatics, still time to register here:
www.eventbrite.com/e/scverse-co...

Been hearing this often lately: 'Did you see Valentine’s blogging again?' 🎉

GitHub - quadbio/cell-annotator: Automatically annotate cell types, consistently across samples. Automatically annotate cell types, consistently across samples. - quadbio/cell-annotator

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.

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 🧵 👇

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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)

🚨 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...

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! 📝

hi @davidsebfischer.bsky.social could I be added? thanks!

📢 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 🙌