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SEES Lab

@seeslab.bsky.social
714 followers 252 following 36 posts

Marta Sales-Pardo & Roger Guimerà. Complex systems & networks; Statiscal learning; Comput. social science; Systems biology at @universitatURV @icreacommunity

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Reposted by SEES Lab
Serge Parel @spparel.bsky.social · 10/05/2026
102 organic chemists shown real vs AI-generated molecules. Couldn't tell them apart — 62% accuracy ≈ random. That's CoCoGraph: graph diffusion with 100% chemical validity, 534K params vs 4.6M for comparable models. Constraints in the math, not the model. www.nature.com/articles/s42...
nature.com
A collaborative constrained graph diffusion model for the generation of realistic synthetic molecules - Nature Machine Intelligence
The collaborative constrained graph diffusion model CoCoGraph generates novel molecules that are guaranteed to be valid and more realistic than state-of-the-art outputs, while achieving faster perform...
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Reposted by SEES Lab
Science X / Phys.org @sciencex.bsky.social · 05/05/2026
A new AI tool can generate millions of chemically valid molecules, offering a faster and more efficient approach to exploring potential compounds for drug development and materials science. doi.org/hb2mwd
phys.org
Chemistry-aware AI can generate millions of plausible new molecules
Finding and developing new molecules is one of the great research endeavors of modern chemistry. From the development of new drugs to the creation of more sustainable materials, everything depends on finding new combinations of atoms with useful properties.
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Reposted by SEES Lab
AI x Bio Discovery @aixbiobot.bsky.social · 04/05/2026
A collaborative constrained graph diffusion model for the generation of realistic synthetic molecules [new] ...that ensures generated novel molecules are valid and highly realistic.
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Reposted by SEES Lab
SEES Lab @seeslab.bsky.social · 04/05/2026
Can we design generative #AI models capable of creating new molecules, much in the same way that other generative models generate text or images? In a new paper in @natmachintell.nature.com, we introduce #CoCoGraph, which does just that Online: dx.doi.org/10.1038/s422... PDF: rdcu.be/fgNIA
dx.doi.org
A collaborative constrained graph diffusion model for the generation of realistic synthetic molecules - Nature Machine Intelligence
The collaborative constrained graph diffusion model CoCoGraph generates novel molecules that are guaranteed to be valid and more realistic than state-of-the-art outputs, while achieving faster performance with up to an order of magnitude fewer parameters.
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SEES Lab @seeslab.bsky.social · 04/05/2026
Great work by Manuel Ruiz-Botella. Congratulations!!
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SEES Lab @seeslab.bsky.social · 04/05/2026
To verify this, we implemented and analyzed the results of a Turing-like test, where experts were asked to distinguish between real and generated molecules
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SEES Lab @seeslab.bsky.social · 04/05/2026
Because chemical validity is satisfied by construction, #CoCoGraph needs much fewer parameters than the state of the art and it can focus on learning subtle chemical patterns, leading to generation of molecules that are more realistic than existing models
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SEES Lab @seeslab.bsky.social · 04/05/2026
#CoCoGraph is a collaborative constrained graph diffusion model for the generation of realistic synthetic molecules. Unlike previous generative models for molecules, we use ideas from graph theory to guarantee that all generated molecules are chemically valid
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SEES Lab @seeslab.bsky.social · 04/05/2026
Can we design generative #AI models capable of creating new molecules, much in the same way that other generative models generate text or images? In a new paper in @natmachintell.nature.com, we introduce #CoCoGraph, which does just that Online: dx.doi.org/10.1038/s422... PDF: rdcu.be/fgNIA
dx.doi.org
A collaborative constrained graph diffusion model for the generation of realistic synthetic molecules - Nature Machine Intelligence
The collaborative constrained graph diffusion model CoCoGraph generates novel molecules that are guaranteed to be valid and more realistic than state-of-the-art outputs, while achieving faster performance with up to an order of magnitude fewer parameters.
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Reposted by SEES Lab
Oscar Yanes @oyanes.bsky.social · 13/02/2026
ChemEmbed: a deep learning framework for metabolite identification using enhanced MS/MS data and multidimensional molecular embeddings url: academic.oup.com/bib/article/...
academic.oup.com
ChemEmbed: a deep learning framework for metabolite identification using enhanced MS/MS data and multidimensional molecular embeddings
Abstract. Machine learning offers a promising path to annotating the large number of unidentified MS/MS spectra in metabolomics, addressing the limited cov
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Reposted by SEES Lab
ICREA Community @icreacommunity.bsky.social · 01/10/2025
🚀A ICREA tornem a estar actius a les xarxes socials! Parlarem de: ✨ Nous descobriments de la #ComunitatICREA 📢 Convocatòries 🎉 Esdeveniments i congressos 🧪 I molta recerca d'excel·lència! Segueix-nos a X x.com/icreacommunity i LinkedIn www.linkedin.com/company/icrea i no et perdis cap novetat!
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Reposted by SEES Lab
Amaral Lab @amarallab.bsky.social · 04/08/2025
🧵 1/ New from @reeserichardson.bsky.social, @jabyrnesci.bsky.social, and our lab in @pnas.org : A growing body of evidence shows that "systematic" scientific fraud is an emerging threat to the integrity of science. Our latest study investigates how this fraud is organized and sustained.
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Reposted by SEES Lab
SEES Lab @seeslab.bsky.social · 14/07/2025
New paper out in Briefings in Bioinformatics 📰SingleFrag: a deep learning tool for MS/MS fragment and spectral prediction and metabolite annotation academic.oup.com/bib/article/...
academic.oup.com
SingleFrag: a deep learning tool for MS/MS fragment and spectral prediction and metabolite annotation
Abstract. Metabolite and small molecule identification via tandem mass spectrometry (MS/MS) involves matching experimental spectra with prerecorded spectra
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SEES Lab @seeslab.bsky.social · 14/07/2025
Yet another great collaboration with @oyanes.bsky.social
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SEES Lab @seeslab.bsky.social · 14/07/2025
As a proof of concept, we successfully annotate three previously unidentified compounds frequently found in human samples
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SEES Lab @seeslab.bsky.social · 14/07/2025
Our results demonstrate that SingleFrag surpasses state-of-the-art in silico fragmentation tools, providing a powerful method for annotating unknown MS/MS spectra of known compounds
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SEES Lab @seeslab.bsky.social · 14/07/2025
Here, we present #SingleFrag, a novel deep learning tool that predicts individual MS/MS fragments separately, rather than attempting to predict the entire fragmentation spectrum at once
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SEES Lab @seeslab.bsky.social · 14/07/2025
Identifying metabolites in MS/MS data often means matching experimental spectra with existing spectral libraries. But, with limited libraries, identifying unknowns remains a big hurdle in #metabolomics
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SEES Lab @seeslab.bsky.social · 14/07/2025
New paper out in Briefings in Bioinformatics 📰SingleFrag: a deep learning tool for MS/MS fragment and spectral prediction and metabolite annotation academic.oup.com/bib/article/...
academic.oup.com
SingleFrag: a deep learning tool for MS/MS fragment and spectral prediction and metabolite annotation
Abstract. Metabolite and small molecule identification via tandem mass spectrometry (MS/MS) involves matching experimental spectra with prerecorded spectra
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Reposted by SEES Lab
BioMassSpec @realbiomassspec.bsky.social · 11/07/2025
SingleFrag: a deep learning tool for MS/MS fragment and spectral prediction and metabolite annotation #BriedBioinform academic.oup.com/bib/article/...
academic.oup.com
SingleFrag: a deep learning tool for MS/MS fragment and spectral prediction and metabolite annotation
Abstract. Metabolite and small molecule identification via tandem mass spectrometry (MS/MS) involves matching experimental spectra with prerecorded spectra
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Reposted by SEES Lab
Manlio De Domenico @manlius.bsky.social · 05/07/2025
Thanks 🙏🙏 @martikagv.bsky.social @vcolizza.bsky.social @pessoabrain.bsky.social @asteixeira.bsky.social @gomezgardenes.bsky.social @seeslab.bsky.social (and all the speakers not in this platform) for their amazing contribution to make this edition a reference for young Network Scientists.
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Reposted by SEES Lab
Manlio De Domenico @manlius.bsky.social · 05/07/2025
@mscxnetworks.bsky.social ended. A week of cutting edge complexity science, from foundations to applications. Amazing speakers and great cohort of attendants. One of the best editions ever. 10 years of passion, love and network science. In an amazing piece of #Sicily youtu.be/Nh5vrEKheH0?...
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Reposted by SEES Lab
arXiv cs.LG Machine Learning @cslg-bot.bsky.social · 23/05/2025
Manuel Ruiz-Botella, Marta Sales-Pardo, Roger Guimer\`a: A collaborative constrained graph diffusion model for the generation of realistic synthetic molecules arxiv.org/abs/2505.16365 arxiv.org/pdf/2505.16365 arxiv.org/html/2505.16365
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SEES Lab @seeslab.bsky.social · 25/06/2025
Great work by first author Manuel Ruiz-Botella!
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SEES Lab @seeslab.bsky.social · 25/06/2025
Leveraging the model’s efficiency, we created a database of 8.2M synthetically generated molecules and conducted a Turing-like test with organic chemistry experts to further assess the plausibility of the generated molecules, and potential biases and limitations of #CoCoGraph
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SEES Lab @seeslab.bsky.social · 25/06/2025
#CoCoGraph outperforms state-of-the-art approaches on standard benchmarks while requiring up to an order of magnitude fewer parameters
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SEES Lab @seeslab.bsky.social · 25/06/2025
New preprint out in the arXiv! We introduce #CoCoGraph, a collaborative and constrained graph diffusion model capable of generating molecules that are guaranteed to be chemically valid www.arxiv.org/abs/2505.16365
arxiv.org
A collaborative constrained graph diffusion model for the generation of realistic synthetic molecules
Developing new molecular compounds is crucial to address pressing challenges, from health to environmental sustainability. However, exploring the molecular space to discover new molecules is difficult...
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SEES Lab @seeslab.bsky.social · 18/06/2025
💡Our paper on probabilistic alignment of networks has been highlighted by Nature Communications as one the 50 best papers recently published in the area of Applied physics and mathematics www.nature.com/collections/... 📰Read the paper www.nature.com/articles/s41...
nature.com
Applied physics and mathematics
The highlights include but are not limited to the research areas of electronics, optoelectronics, computing technologies and theories, soft matter physics, ...
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SEES Lab @seeslab.bsky.social · 02/06/2025
At #NetSci2025 @netsciconf.bsky.social today? Don't miss Gemma Bel's poster at the Network Neuroscience satellite 📰Model-based alignment of developing connectomes 📍FaSos GG76S 1.018 🕔5:30pm
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SEES Lab @seeslab.bsky.social · 02/06/2025
At #NetSci2025? Don't miss Teresa Lazaros's talk today at the Network Neuroscience satellite 📰 Probabilistic network alignment applied to brain connectomes 📍 FaSos GG76S 1.018 🕔 5pm 🔗 to paper: dx.doi.org/10.1038/s414...
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SEES Lab @seeslab.bsky.social · 02/06/2025
At #NetSci2025 today? Don't miss Manuel Ruiz-Botella's talk at the @netbiomed2025.bsky.social‬ satellite 📰 CoCoGraph: A collaborative constrained graph diffusion model for the generation of realistic synthetic molecules 📍 FaSos FaSoS GG76 1.02 🕒 3:30pm 🔗 to paper: doi.org/10.48550/arX...
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Reposted by SEES Lab
Yann Moalic @drym.bsky.social · 16/05/2025
#Networks www.nature.com/articles/s41...
nature.com
Probabilistic alignment of multiple networks - Nature Communications
Network alignment is a fundamental problem in several domains that aims at mapping nodes across networks. Here, the authors develop a probabilistic approach that assumes that observed networks are err...
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SEES Lab @seeslab.bsky.social · 12/05/2025
‘Data manipulations’ alleged in study that paved the way for Microsoft’s quantum chip | Science | AAAS www.science.org/content/arti...
science.org
‘Data manipulations’ alleged in study that paved the way for Microsoft’s quantum chip
Internal emails from 2021 reveal tensions among researchers hunting for elusive Majorana particle
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Reposted by SEES Lab
Artime @oriartime.bsky.social · 08/05/2025
So happy to share this one! Beautiful collaboration with @anduviera.bsky.social, @raissadsouza.bsky.social and Guram Mikaberidze on network flows: journals.aps.org/prx/abstract...
journals.aps.org
Multiscale Field Theory for Network Flows
A new theoretical framework reveals universal principles governing network flows, predicting a threshold where flow becomes unsustainable and uncovering how dissipation can enhance performance in cert...
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Reposted by SEES Lab
Leto Peel @piratepeel.bsky.social · 06/05/2025
We're looking for a new colleague to join us in Maastricht as an Assistant/Associate Professor in statistical learning in our Data Analytics and Digitalisation department. Deadline to apply: June 8th vacancies.maastrichtuniversity.nl/job/Maastric...
vacancies.maastrichtuniversity.nl
Assistant/Associate Professor in Statistical Learning
Assistant/Associate Professor in Statistical Learning
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Reposted by SEES Lab
Jorge Bravo Abad @bravo-abad.bsky.social · 03/05/2025
New substack post: I discuss a recent innovative method—ProbAlign, introduced by Lázaro, Guimerà, & Marta Sales-Pardo—which uses probabilistic modeling to achieve more accurate, transparent, and flexible network alignments. open.substack.com/pub/bravoaba...
open.substack.com
How probabilistic modeling transforms our approach to aligning complex networks
Networks are everywhere—from social connections among individuals, neural connections in brains, interactions among proteins in biological cells, to communication channels within large organizations.
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Reposted by SEES Lab
Climate, Ecology, War & More: Dr. Glen Barry BigEarthData.ai @bigearthdata.ai · 27/04/2025
Probabilistic alignment of multiple networks ->Nature | More info from EcoSearch
nature.com
Probabilistic alignment of multiple networks
Consider K network observations, with N nodes each and adjacency matrices {Ak; , k = 1, …, K }. We consider networks that are directed and with binary edges (that is, we just consider the presence or absence of connection...
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Reposted by SEES Lab
Kleroterion @kleroterion.bsky.social · 28/04/2025
www.nature.com/articles/s41...
nature.com
Probabilistic alignment of multiple networks - Nature Communications
Network alignment is a fundamental problem in several domains that aims at mapping nodes across networks. Here, the authors develop a probabilistic approach that assumes that observed networks are err...
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Reposted by SEES Lab
Basti Kusch @bastikusch.bsky.social · 29/04/2025
This is such a cool paper! Everyone interested in aligning (multiple, possibly unlabelled) graphs, give it a read!
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SEES Lab @seeslab.bsky.social · 30/04/2025
Thank you! Glad you found it interesting!!
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SEES Lab @seeslab.bsky.social · 30/04/2025
🧠Our work was inspired by the need to align brain connectomes at the neuron level 💡But we show that our approach is also valid for other applications in computational social science and complex systems, and opens the door for further context-specific developments
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SEES Lab @seeslab.bsky.social · 30/04/2025
As a consequence of these, our approach leads to better alignment than the state of the art on synthetic and real networks
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SEES Lab @seeslab.bsky.social · 30/04/2025
With respect to existing methods for "graph matching": 1️⃣ Our approach naturally allows for the alignment of many networks 2️⃣ All assumptions are explicit and can be adapted to specific scenarios 3️⃣ It results in a posterior over alignments, rather than a single alignment
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SEES Lab @seeslab.bsky.social · 30/04/2025
📰New paper out in @natcomms.nature.com! We have developed a probabilistic approach that allows for the accurate alignment of multiple networks www.nature.com/articles/s41... Great work by Teresa Lázaro on her first article (of many to come)! Some highlights 👇🏽🧵
nature.com
Probabilistic alignment of multiple networks - Nature Communications
Network alignment is a fundamental problem in several domains that aims at mapping nodes across networks. Here, the authors develop a probabilistic approach that assumes that observed networks are err...
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Reposted by SEES Lab
NetScience @netscience.bsky.social · 28/04/2025
Probabilistic alignment of multiple networks www.nature.com/articles/s41...
nature.com
Probabilistic alignment of multiple networks - Nature Communications
Network alignment is a fundamental problem in several domains that aims at mapping nodes across networks. Here, the authors develop a probabilistic approach that assumes that observed networks are err...
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New papers in Network Science @networkspapers.bsky.social · 28/04/2025
Nat. Commun.: Probabilistic alignment of multiple networks www.nature.com/articles/s41467-025-…
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Communications Psychology @commspsychol.nature.com · 21/03/2025
Children's cognitive abilities and social preferences separate in the later school years, indicating that older students likely use differentiated social strategies for academic and recreational interactions. @ecorreig.bsky.social www.nature.com/articles/s44...
nature.com
Interplay between children’s cognitive profiles and within-school social interactions is nuanced and differs across ages - Communications Psychology
Children’s cognitive abilities and social preferences separate in the later school years, with work-related and leisure-related peer choices diverging at older ages, indicating that older students lik...
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Reposted by SEES Lab
estebanmoro @estebanmoro.bsky.social · 20/02/2025
New work in @naturecomms.bsky.social 🚀! Instead of black-box deep learning with 100's of parameters, what if we use large-scale data to discover simple, interpretable models that accurately describe human mobility? It works: Accuracy + insights for urban planning & beyond!
doi.org
Human mobility is well described by closed-form gravity-like models learned automatically from data - Nature Communications
Modeling human mobility is key for urban planning, sustainability, public health, and economic development. The authors show that simple machine-learned closed-form models are as predictive of mobilit...
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SEES Lab @seeslab.bsky.social · 14/02/2025
Our recent article on machine learning mathematical models for incidence estimation during pandemics, featured in today's edition of @manlius.bsky.social's Complexity Thoughts!
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