Sign in

Jorge FdCD

@jorgefdcd.bsky.social
819 followers 1.5K following 44 posts

CNRS researcher working at the Institut de Physique Théorique (IPhT) in Paris-Saclay. Interested in statistical physics, machine learning, and biological data modeling. Website: sites.google.com/view/jorgefdcd

PostsRepliesMedia
Jorge FdCD @jorgefdcd.bsky.social · 01/07/2026
www.inp.cnrs.fr/en/cnrsinfo/...
inp.cnrs.fr
Different Brains share a common neural grammar
040
Jorge FdCD @jorgefdcd.bsky.social · 01/07/2026
@cnrs.fr published a popular summary of our recent work: Using recordings of whole-brain activity in zebrafish larvae, a French team has shown that it is possible to translate spontaneous neural activity between individuals without matching neurons one-to-one.
150
Jorge FdCD @jorgefdcd.bsky.social · 16/06/2026
Full preprint: arxiv.org/abs/2605.09031
arxiv.org
Spherical Boltzmann machines: a solvable theory of learning and generation in energy-based models
Energy-based models (EBMs) are flexible generative architectures inspired by statistical physics, but their learning and generative properties remain poorly understood. Here, we analyze a solvable EBM...
010
Jorge FdCD @jorgefdcd.bsky.social · 16/06/2026
... sampling temperature tuning, double descent as a function of regularization strength, tempered posterior effects, and out-of-equilibrium effects during training that induce biases in the trained model.
110
Jorge FdCD @jorgefdcd.bsky.social · 16/06/2026
We relate phase transitions that occur during training and as a function of hyper parameters, to various generative phenomena in a teacher-student scenario, including:
100
Jorge FdCD @jorgefdcd.bsky.social · 16/06/2026
Here we focus on Spherical Boltzmann machines, a solvable model allowing us to study the rich phenomenology of EBMs analytically in high-dimensions.
120
Jorge FdCD @jorgefdcd.bsky.social · 16/06/2026
Energy-based models (EBMs) are flexible generative architectures inspired by statistical physics, but their learning and generative properties remain poorly understood.
110
Jorge FdCD @jorgefdcd.bsky.social · 16/06/2026
New preprint: Spherical Boltzmann machines: a solvable theory of learning and generation in energy-based models with Thomas Tulinski, Simona Cocco, Rémi Monasson 🧵
121
Jorge FdCD @jorgefdcd.bsky.social · 16/06/2026
See the full preprint here: arxiv.org/abs/2604.17936
arxiv.org
Replica Theory of Spherical Boltzmann Machine Ensembles
Training in machine learning generally consists in finding one model, whose parameters minimize a data-dependent loss. Yet, empirical work shows that ensemble learning, an approach in which multiple m...
010
Jorge FdCD @jorgefdcd.bsky.social · 16/06/2026
We build an analytical framework to study ensembles of Boltzmann machines, exploiting a duality between ensemble learning and large deviations of the free energy in spin-glass models.
110
Jorge FdCD @jorgefdcd.bsky.social · 16/06/2026
New preprint: Replica Theory of Spherical Boltzmann Machine Ensembles, with Thomas Tulinski, Simona Cocco, and Rémi Monasson Training usually means finding one model whose parameters minimize a loss. But sampling multiple models — ensemble learning — can sometimes do better.
130
Jorge FdCD @jorgefdcd.bsky.social · 30/05/2026
icml.cc/virtual/2026...
icml.cc
ICML Steering Sequence Generation in Protein Language Models through Iterative Lookback Monte Carlo SamplingICML 2026
010
Jorge FdCD @jorgefdcd.bsky.social · 26/05/2026
Our work has been selected as a Spotlight Talk in the GenBio Workshop at ICML @icmlconf.bsky.social
130
Jorge FdCD @jorgefdcd.bsky.social · 23/05/2026
It delivers highly diverse protein designs, including variants with up to a 12°C increase in predicted melting temperature. Full paper here: www.biorxiv.org/content/10.6...
biorxiv.org
010
Jorge FdCD @jorgefdcd.bsky.social · 23/05/2026
How can we steer protein language models toward specific traits, without losing sequence diversity? In our new preprint, we introduce Iterative Lookback Monte Carlo (ILMC)—a training-free sampling strategy that balances generation quality, steering constraints, and diversity.
Iterative Lookback Monte Carlo (ILMC)
131
Jorge FdCD @jorgefdcd.bsky.social · 14/05/2026
Just published in PNAS: www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
021
Jorge FdCD @jorgefdcd.bsky.social · 12/01/2026
Link: www.biorxiv.org/content/10.6...
biorxiv.org
Design and experimental characterization of specificity-switching mutational paths of WW domains
Specific interactions between proteins and other biomolecules are ubiquitous in cellular processes. How specificity is encoded in the protein sequence and can be modified through a minimal set of conc...
031
Jorge FdCD @jorgefdcd.bsky.social · 12/01/2026
We use energy-based generative models (RBM) to design full mutational paths connecting two natural proteins of different binding specificities, and verify experimentally that intermediate sequences stay functional.
110
Jorge FdCD @jorgefdcd.bsky.social · 12/01/2026
New preprint: Design and experimental characterization of specificity-switching mutational paths of WW domains.
120
Jorge FdCD @jorgefdcd.bsky.social · 12/01/2026
Link: www.biorxiv.org/content/10.6...
biorxiv.org
Cross-individual translation of spontaneous zebrafish brain activity through a shared latent representation
Spontaneous activity is a hallmark of brain function, reflecting the underlying circuit organization. Identifying conserved structure across individuals in this self-sustained activity has remained a ...
010
Jorge FdCD @jorgefdcd.bsky.social · 12/01/2026
We develop latent-aligned RBMs, to uncover a common representational space from cell-resolved whole-brain recordings spanning several distinct larval zebrafish individuals.
110
Jorge FdCD @jorgefdcd.bsky.social · 12/01/2026
New preprint: Cross-individual translation of spontaneous zebrafish brain activity through a shared latent representation
110
Jorge FdCD @jorgefdcd.bsky.social · 21/12/2025
Just published in @natcomms.nature.com : Designing molecular RNA switches with Restricted Boltzmann machines. Full paper: www.nature.com/articles/s41...
nature.com
Designing molecular RNA switches with Restricted Boltzmann machines - Nature Communications
Riboswitches are allosteric RNA molecules that change conformation upon ligand binding to regulate downstream genes. Here, the authors use Restricted Boltzmann machines trained on natural sequences to...
021
Jorge FdCD @jorgefdcd.bsky.social · 02/11/2025
Master internship position available, with possibility of PhD after. More details here: sites.google.com/view/jorgefd...
021
Jorge FdCD @jorgefdcd.bsky.social · 30/06/2025
See www.cofund-physics.universite-paris-saclay.fr for more information. Deadline to apply is July 31 2025.
cofund-physics.universite-paris-saclay.fr
UPSaclay STAR φ – Become a STAR φ Fellow!
010
Jorge FdCD @jorgefdcd.bsky.social · 30/06/2025
We invite early-career researchers to apply for the STARφ programme of Université Paris-Saclay, funded by the European Union under the Marie Skłodowska-Curie COFUND action. Our team at the IPhT at CEA-Saclay is among the participating laboratories.
110
Jorge FdCD @jorgefdcd.bsky.social · 23/06/2025
The candidate is expected to have a strong background in machine learning, computational biology and statistical physics. For more details and to apply contact me (DM or email).
010
Jorge FdCD @jorgefdcd.bsky.social · 23/06/2025
The work will be carried out in close collaboration with the experimental team of Frédéric Ducongé, at MIRCen, Institut de Biologie François Jacob of CEA.
110
Jorge FdCD @jorgefdcd.bsky.social · 23/06/2025
The goal of the project is to develop machine learning approaches to infer fitness landscapes from large sequencing datasets obtained in such experiments.
110
Jorge FdCD @jorgefdcd.bsky.social · 23/06/2025
Aptamers are often obtained through rounds of in vitro competitive selection (SELEX), starting from random artificial libraries of ~10^15 distinct distinct sequences. However, engineered libraries cannot fully explore sequence space diversity.
110
Jorge FdCD @jorgefdcd.bsky.social · 23/06/2025
An 14 months months postdoctoral positions is available in my team, to work on computational models of artificial evolution for aptamer design.
110
Reposted by Jorge FdCD
Jorge FdCD @jorgefdcd.bsky.social · 23/01/2025
The summer school “Molecular Evolution and Design: from Computational Models to Biological and Medical Applications”, which we are organizing in Cargèse on Corsica island, will take place from August 19-29 2025 - the place is fantastic in summer ! 🧵
131
Jorge FdCD @jorgefdcd.bsky.social · 08/05/2025
For more details and to apply: adum.fr/as/ed/voirpr.... Deadline to apply is May 23, 2025. DM if you have questions.
adum.fr
110
Jorge FdCD @jorgefdcd.bsky.social · 08/05/2025
By addressing the inherent biases and noise structures in these datasets, we will create more accurate computational frameworks for protein fitness landscape modeling.
110
Jorge FdCD @jorgefdcd.bsky.social · 08/05/2025
This PhD project aims to develop novel machine learning approaches for robust characterization and modeling of noise in deep sequencing data from selection-amplification experiments.
110
Jorge FdCD @jorgefdcd.bsky.social · 08/05/2025
We are looking for a candidate for a PhD position shared between Gen&Chem group (BGE/IRIG) at CEA-Grenoble and IPhT at CEA-Saclay, combining expertise in statistical physics, computational biology and computer science. 🧵
120
Jorge FdCD @jorgefdcd.bsky.social · 23/01/2025
We would like to invite applications and propositions for contributed talks or posters from students, postdocs and young researchers. To register and for more details, see the website: sites.google.com/view/coevolc...
sites.google.com
2025
This summer school will cover different topics in protein and RNA design as listed below, and will focus on teaching modern modeling approaches in this domain, from statistical physics, computer scien...
020
Jorge FdCD @jorgefdcd.bsky.social · 23/01/2025
The school will cover different topics in protein and RNA design, and will focus on teaching modern modeling approaches in this domain, from statistical physics, computer science, and machine learning fields to recent experimental approaches.
120
Jorge FdCD @jorgefdcd.bsky.social · 23/01/2025
The summer school “Molecular Evolution and Design: from Computational Models to Biological and Medical Applications”, which we are organizing in Cargèse on Corsica island, will take place from August 19-29 2025 - the place is fantastic in summer ! 🧵
131
Jorge FdCD @jorgefdcd.bsky.social · 11/01/2025
See sites.google.com/view/jorgefd... for more details.
sites.google.com
Personal website - Open positions
Jorge FERNANDEZ-DE-COSSIO-DIAZ CNRS Junior Professor Institut de Physique Théorique Contact: jorge[dot]fdcd[at]icloud[dot]com
010
Jorge FdCD @jorgefdcd.bsky.social · 11/01/2025
I have an 18 months postdoc position available in Paris-Saclay, starting in March 2025, to work at the interface of machine learning, computational biology and statistical physics.
150
Reposted by Jorge FdCD
Willie Neiswanger @willieneis.bsky.social · 20/11/2024
The first list filled up, so here's a second list of AI for Science researchers on bluesky. Let me know if I missed you / if you'd like to join! bsky.app/starter-pack...
577129
Reposted by Jorge FdCD
Jacob S. Zelko @thecedarprince.bsky.social · 08/11/2024
Hey folks! I got a bit swamped with all the new #julialang BlueSky people and made my own mega Julia #programmer starter pack! go.bsky.app/Hv4RKzM What other starter packs would you want to see? I'm in health research, mathematics, and open source/science. 🧪🛟🩺 📊
83513
Jorge FdCD @jorgefdcd.bsky.social · 25/11/2024
Thanks please add me
000
Jorge FdCD @jorgefdcd.bsky.social · 24/11/2024
Hello, I'd love to join
110
Jorge FdCD @jorgefdcd.bsky.social · 24/11/2024
Thanks ! Please add me :)
000
Jorge FdCD @jorgefdcd.bsky.social · 24/11/2024
Thanks ! Please add me :)
010