Pablo Rodriguez-Mier
pablormier.bsky.social
Pablo Rodriguez-Mier
@pablormier.bsky.social
Scientist at @saezlab.bsky.social, Heidelberg University. EMBL-EBI Visitor. Mathematical modeling / ML & AI for biological systems
https://pablormier.github.io/
Reposted by Pablo Rodriguez-Mier
🚨 New preprint

We present an extended version of ScAPE, the method that won one of the prizes 🏆 in the @neuripsconf.bsky.social 2023 Single-Cell Perturbation Prediction challenge.

📄 preprint: doi.org/10.1101/2025...
🧬 code: github.com/scapeML/scape
September 19, 2025 at 7:45 AM
Reposted by Pablo Rodriguez-Mier
ScAPE: A lightweight multitask learning baseline method to predict transcriptomic responses to perturbations https://www.biorxiv.org/content/10.1101/2025.09.08.674873v1
September 9, 2025 at 7:47 PM
Reposted by Pablo Rodriguez-Mier
We present our MetaProViz #Rpackage for #metabolomics analysis & prior knowledge integration to generate mechanistic hypotheses on how metabolic changes affect metabolite classes, pathways & environment interaction

🔗
www.biorxiv.org/content/10.1...

📦
saezlab.github.io/MetaProViz/

🧵 Thread ⬇️
August 25, 2025 at 7:07 AM
Reposted by Pablo Rodriguez-Mier
New course announced!

We're thrilled to be hosting the @embo.org Practical Course 'Causality in biomedicine: going beyond associations' from 4 – 9 October 2026.

Register your interest and be the first to hear when the course opens for applications: www.ebi.ac.uk/training/eve...
August 12, 2025 at 11:50 AM
Reposted by Pablo Rodriguez-Mier
New course “EMBO Causality in Biomedicine”: We have organised the first EMBO course in *causal* stats/ML methods for quantitative biomedicine. @sjoerdvbeentjes.bsky.social @nimahejazi.org @pablormier.bsky.social @DariaSokolova @CarolineUhler

Very much looking forward to teaching and discussing!
New course announced!

We're thrilled to be hosting the @embo.org Practical Course 'Causality in biomedicine: going beyond associations' from 4 – 9 October 2026.

Register your interest and be the first to hear when the course opens for applications: www.ebi.ac.uk/training/eve...
August 12, 2025 at 2:03 PM
Reposted by Pablo Rodriguez-Mier
This project has been in the making for quite some time. CORNETO not only integrates key concepts and methodologies in biological network inference, but also introduces a novel framework for multi-condition analysis. Congrats to the team, and especially to @pablormier.bsky.social for leading this.
🎉 The revised version of CORNETO, our unified Python framework for knowledge-driven network inference from omics data, is published in peer reviewed form
🔗 Paper: www.nature.com/articles/s42...
📖 News & Views: www.nature.com/articles/s42...
💻 Code: corneto.org
🧵 Thread 👇
July 24, 2025 at 7:51 AM
Reposted by Pablo Rodriguez-Mier
🎉 The revised version of CORNETO, our unified Python framework for knowledge-driven network inference from omics data, is published in peer reviewed form
🔗 Paper: www.nature.com/articles/s42...
📖 News & Views: www.nature.com/articles/s42...
💻 Code: corneto.org
🧵 Thread 👇
July 22, 2025 at 3:23 PM
Reposted by Pablo Rodriguez-Mier
How can we find out what’s really going on inside cells when we’re generating so much complex data?

CORNETO is an open-source tool that uses machine learning to turn tangled omics datasets into clear maps of how genes, proteins, and signalling pathways interact.

www.ebi.ac.uk/about/news/r... 🧪
CORNETO: machine learning to decode complex omics data
New tool combines biological knowledge with machine learning to help researchers extract meaningful insights from complex omics data.
www.ebi.ac.uk
July 22, 2025 at 9:20 AM
Reposted by Pablo Rodriguez-Mier
The latest version of the Kasumi manuscript is now published in Nature Comms www.nature.com/articles/s41... Kasumi identifies patterns in tissue patches, enabling analysis of disease progression and treatment response while providing insights into spatial coordination at cell-type or marker level
Learning tissue representation by identification of persistent local patterns in spatial omics data - Nature Communications
Spatial omics reveal tissue structures and can aid patient stratification. The authors present a method to identify patterns in tissue patches, enabling analysis of disease progression and treatment r...
www.nature.com
May 7, 2025 at 1:11 PM
Reposted by Pablo Rodriguez-Mier
🚨 New preprint: Topography Aware Optimal Transport for Alignment of Spatial Omics Data

We present our new alignment framework TOAST www.biorxiv.org/content/10.1...
April 22, 2025 at 9:37 AM
Reposted by Pablo Rodriguez-Mier
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...
Pretraining virtual cells is useless
the way we do it now
blog.turbine.ai
April 16, 2025 at 5:03 PM
Reposted by Pablo Rodriguez-Mier
📄 Update on our preprint about Gene Regulatory Net (GRN) benchmarking 📄
We have included the original and decoupled version of SCENIC+, added a new metric and two more databases. Dictys and SCENIC+ outperformed others, but still performed poorly in causal mechanistic tasks.
doi.org/10.1101/2024... 👇
March 14, 2025 at 10:34 AM
Haha, Peyman Milanfar blocked me within milliseconds after I liked a reply of somebody else defending @hardmaru.bsky.social and Sakana AI against his attacks.

Fastest block ever!
March 16, 2025 at 10:55 PM
Stephen Boyd's reaction when a student says they're using Genetic Algorithms for optimization is priceless 😂
youtu.be/kV1ru-Inzl4?...
Stanford EE364A Convex Optimization I Stephen Boyd I 2023 I Lecture 1
YouTube video by Stanford Online
youtu.be
March 16, 2025 at 5:15 PM
Reposted by Pablo Rodriguez-Mier
In many countries we're seeing voters that have never known anything other than stability and a certain level of competence voting for anti- system candidates because they have convinced themselves of two things: things right now are awful; change will only be for the better.
February 3, 2025 at 8:27 AM
Reposted by Pablo Rodriguez-Mier
This is also why vaccine-denial is so prevalent. People don’t have a memory of what mass death from smallpox looked like, or post-poli disability.
February 24, 2025 at 10:50 AM
No AGI until LLMs can reliably produce useful LaTeX. Haven’t seen one that truly delivers.

We need a LLM LaTeX benchmark!
February 20, 2025 at 6:34 PM
Reposted by Pablo Rodriguez-Mier
"LLaDA: Large Language Diffusion Models" Nie et al.

Just read this fascinating paper.

Scaled up Masked Diffusion Language Models to 8B params, and show that it can match #LLMs (including Llama 3) while solving some key limitations!

Let's dive in... 🧵

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#genai
February 18, 2025 at 3:05 PM
Reposted by Pablo Rodriguez-Mier
We are delighted to announce The Health Privacy Challenge, an interactive opportunity for advancement at the intersection of computational biology and privacy research, brought to you as a part of CAMDA Conference at #ISMB/ECCB2025 🫐🍅
Register to participate: benchmarks.elsa-ai.eu?ch=4
Overview - Health - ELSA Benchmarks Platform
benchmarks.elsa-ai.eu
January 15, 2025 at 9:27 AM
Reposted by Pablo Rodriguez-Mier
We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
December 23, 2024 at 8:43 AM
Reposted by Pablo Rodriguez-Mier
The final chapter of my PhD thesis is now out! 🎉 We compared the latest gene regulatory network (#GRN) inference methods for #single-cell multimodal datasets and evaluated their performance across various tasks. Hard to believe this journey started in March 2021 and has finally reached this point 😅🥳
We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
December 23, 2024 at 8:49 AM
Reposted by Pablo Rodriguez-Mier
We present NetworkCommons, a unified platform 🪐 for network biology, providing access to omics data, knowledge, and contextualization methods, all with a consistent API 👇🧵
Paper: doi.org/10.1101/2024...
Docs: networkcommons.readthedocs.io
November 26, 2024 at 9:44 AM
Reposted by Pablo Rodriguez-Mier
Very cool to see our model scAPE perform so well in this benchmark @pablormier.bsky.social !
openreview.net/forum?id=WTI...
Thanks to the organizers for this amazing competition.
A benchmark for prediction of transcriptomic responses to chemical...
Single-cell transcriptomics has revolutionized our understanding of cellular heterogeneity and drug perturbation effects. However, its high cost and the vast chemical space of potential drugs...
openreview.net
November 25, 2024 at 4:04 PM