iiinova — where your digital self keeps evolving

Reposted by Bence Szalai

Eric Kernfeld @ekernf01.bsky.social · 28/07/2025

In October 2024, I twote that "something is deeply wrong" with what we now call virtual cell models. A lot has happened since then. How am I updating? New blog post: ekernf01.github.io/virtual-cell...

ekernf01.github.io

A recap of virtual cell releases circa June 2025

In October 2024, I twote that “something is deeply wrong” with what we now call virtual cell models. A lot has happened since then: modelers are advancing new architectures and mining new sources of i...

1122

Reposted by Bence Szalai

Constantin Ahlmann-Eltze @const-ae.bsky.social · 04/08/2025

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉 www.nature.com/articles/s41... We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures! 🧵

Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.

Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.

212557

Bence Szalai @benceszalai.bsky.social · 15/07/2025

Our tool, RIDDEN (Receptor actIvity Data Driven inferENce) for predicting #receptor activity from #transcriptomics data is published in PLOS Computational Biology journals.plos.org/ploscompbiol... 1/n

131

Bence Szalai @benceszalai.bsky.social · 25/04/2025

Single-cell foundation models, trained on large-scale scRNA-seq datasets, are increasingly used for post-perturbation RNA-seq prediction. But how do they actually perform? Our new paper from @turbine-ai.bsky.social is now out in BMC Genomics. bmcgenomics.biomedcentral.com/articles/10.... 1/5

121

Reposted by Bence Szalai

Saez-Rodriguez Group @saezlab.bsky.social · 22/04/2025

We have an opening for a PhD/Postdoc in Spatial Omics for Cardiology in Heidelberg 🫀 #job #academicjob #phd #postdoc #cadiology 👇 jobrxiv.org/job/heidelbe...

jobrxiv.org

PhD/Postdoc in Spatial Omics for Cardiology

Post a job in 3min, or find thousands of job offers like this one at jobRxiv!

068

Reposted by Bence Szalai

Kris Szalay @kristofszalay.com · 16/04/2025

Turns out the way we usually pre-train foundational cell models adds very little information to the system - definitely not enough to make drug effect predictions work. Not what I've expected. #virtualcells #foundationalmodels #compbio blog.turbine.ai/p/pretrainin...

blog.turbine.ai

Pretraining virtual cells is useless

the way we do it now

022

Bence Szalai @benceszalai.bsky.social · 03/04/2025

easter holiday is coming: 2 revised versions submitted today

000

Reposted by Bence Szalai

Sung Kim @sungkim.bsky.social · 31/03/2025

You’ve probably heard about how AI/LLMs can solve Math Olympiad problems ( deepmind.google/discover/blo... ). So naturally, some people put it to the test — hours after the 2025 US Math Olympiad problems were released. The result: They all sucked!

917350

Reposted by Bence Szalai

Michael Hoffman @michaelhoffman.bsky.social · 30/03/2025

Does @iscb.bsky.social have a statement on this? We need to be there to support bioinformatics researchers.

0239

Bence Szalai @benceszalai.bsky.social · 30/03/2025

based on some recent papers / presentations, the hill(s) I'll die on: 1) Raw IC50 values != good metrics for comparing cancer drug sensitivity 2) Raw TPMs / counts are meaningless for comparing gene expression similarity 3) Diverging color palettes need a meaningful midpoint.

010

Reposted by Bence Szalai

Julio Saez-Rodriguez @juliosaezrod.bsky.social · 11/02/2025

Post-doc opening to join our lab @ebi.embl.org to develop&apply #bioinformatics and #machine-learning methods to study intra-/extra cellular networks to extract disease mechanisms from #single-cell and #spatial multiomic data - please share 🙏 : embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

embl.wd103.myworkdayjobs.com

Postdoctoral fellow - Saez-Rodriguez Group

Your group Saez-Rodriguez Research Group Your supervisor Julio Saez-Rodriguez Your role As a postdoctoral fellow in the Saez Rodriguez group, you will develop and apply computational methods and tools...

05846

Reposted by Bence Szalai

Colm Ryan @colmr.bsky.social · 29/01/2025

We will be hosting the International Conference on Systems Biology (ICSB) in Dublin this year – 5-9th October icsb2025.com/registration/ #ICSB2025

Flier for the ICSB2025 conference in Dublin 5-9 October 2025

0127

Reposted by Bence Szalai

Eric Wastl @was.tl · 26/12/2024

It's been over 24 hours since #AdventOfCode 2024 ended! This AoC season: - 273,313 users collected at least one star - 3,654,949 stars were collected Since 2015: - 779 users have all 500 stars - 1,077,226 users collected at least one star - 23,170,305 were collected

1727320

Bence Szalai @benceszalai.bsky.social · 10/12/2024

holiday season is coming: 2 papers submitted today

011

Bence Szalai @benceszalai.bsky.social · 09/12/2024

[first 🦋] Receptors are essential for cell-cell communication, yet most comp CCC tools focus on ligand/receptor expression, not receptor activity. To address this, we developed RIDDEN, a model that infers activity for 229 receptors from transcriptomics data. 1/n www.biorxiv.org/content/10.1...

110

Bence Szalai @benceszalai.bsky.social · 01/12/2024

I just completed "Historian Hysteria" - Day 1 - Advent of Code 2024 #AdventOfCode adventofcode.com/2024/day/1

030

Reposted by Bence Szalai

Saez-Rodriguez Group @saezlab.bsky.social · 20/11/2024

We have created a starterpack to make it easier to follow current members and alumni from our lab, check it out 👇 (DM us if we forgot about you) Also juliosaezrod.bsky.social has recently joined Bluesky go.bsky.app/5ZtPHPz

13012

Reposted by Bence Szalai

Saez-Rodriguez Group @saezlab.bsky.social · 11/11/2024

Hi 🦋 This is the saezlab (saezlab.org) bluesky account. We integrate #omics data with mechanistic molecular knowledge into statistical and machine learning #ML methods, and we share our tools as free #opensource packages (github.com/saezlab/) #systemsbiology #biology #compbio

saezlab.org

Saez-Rodriguez GroupSaez-Rodriguez Group – Systems Biomedicine

05518