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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
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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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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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
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
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
📰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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Reposted by SEES Lab
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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Reposted by SEES Lab
Oscar Yanes @oyanes.bsky.social · 11/02/2025
5/ Want to learn more? 📄 Read our full paper on #bioRxiv: www.biorxiv.org/content/10.1... #Metabolomics #MachineLearning #DeepLearning #MSMS We’d love to hear your thoughts! This is another successful collaboration with @seeslab.bsky.social at @urv.cat
biorxiv.org
ChemEmbed: A deep learning framework for metabolite identification using enhanced MS/MS data and multidimensional molecular embeddings
Machine learning tools have become essential for annotating the vast number of unidentified MS/MS spectra in metabolomics, addressing the limitations of current reference spectral libraries. However, ...
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Reposted by SEES Lab
Oscar Yanes @oyanes.bsky.social · 11/02/2025
4/ The results: ✅ ChemEmbed ranks the correct metabolite #1 in 42% of cases in a test dataset. ✅ Finds the correct compound in the top 5 in 76% of cases ✅ Against external benchmarks CASMI 2016 and 2022, and ARUS dataset (unidentified spectra from human plasma & urine), ChemEmbed outperforms #SIRIUS
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Oscar Yanes @oyanes.bsky.social · 11/02/2025
3/ We enhance MS/MS data by: ✅ Merging spectra from multiple collision energies ✅ Incorporating calculated neutral losses ✅ Training a CNN on a dataset of 38,472 unique compounds from NIST20, MSDIAL, GNPS, and Agilent METLIN metabolomic libraries
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Oscar Yanes @oyanes.bsky.social · 11/02/2025
2/ Our solution to reduce this problem: #ChemEmbed We combine enhanced MS/MS spectra with continuous vector representations of molecular structures (300-dimensional embeddings aligned with Mol2vec representations). This gives our CNN-based model richer input, improving annotation accuracy.
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Oscar Yanes @oyanes.bsky.social · 11/02/2025
1/ The problem: #Metabolomics relies on MS/MS spectral databases, but most spectra remain unidentified due to limited reference libraries. Computational methods help, but they struggle with high-dimensional and sparse spectral and structural data.
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Oscar Yanes @oyanes.bsky.social · 11/02/2025
🚀 New paper alert! 🚀 Happy to introduce #ChemEmbed, a deep learning framework for metabolite identification that enhances MS/MS data and leverages multidimensional molecular embeddings. A 🧵 on how it works and why it matters! ⬇️ #metabolomics #MachineLearning #DeepLearning
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SEES Lab @seeslab.bsky.social · 05/02/2025
Can simple closed-form mathematical models predict human mobility as well as deep learning? In a new paper in @naturecomms.bsky.social we show that the answer is YES Human mobility is well described by closed-form gravity-like models learned automatically from data www.nature.com/articles/s41...
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Manlio De Domenico @manlius.bsky.social · 09/01/2025
Deadline is approaching, still some seats available 🏃🏃🏃
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SEES Lab @seeslab.bsky.social · 08/01/2025
During a pandemic such as COVID19, we hope (but fail) to accurately estimate the incidence of the disease. In this paper, we propose a new approach to machine-learn models of the real incidence from readily available information (tests and detected cases) dx.doi.org/10.1371/jour...
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estebanmoro @estebanmoro.bsky.social · 23/12/2024
📣 New paper in Nature Human Behavior @natureportfolio.bsky.social! Using large-scale mobility data, we find how businesses, amenities, and other urban places depend on each other. It reveals connections that aren’t always visible but have substantial economic impacts. www.nature.com/articles/s41...
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Manlio De Domenico @manlius.bsky.social · 04/12/2024
The call for the very special 10th Mediterranean School of Complex Networks is out! @mscxnetworks.bsky.social This year, it will take place in Ortigia, a beautiful small island in Syracuse, Italy. The lineup of lecturers is outstanding! All info in the website: mediterraneanschoolcomplex.net
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Tiago Peixoto @tiago.skewed.de · 25/11/2024
🚨Job alert!🚨 Come join us at the Inverse Complexity Lab @invcomplexity.skewed.de We’re hiring a post-doctoral researcher to join our group at IT:U, Linz, Austria. skewed.de/lab/call.html Deadline is 30 Nov 2024. (Next Saturday!) Spread the word. #networkscience #complexsystems
skewed.de
Open post-doc position at the Inverse Complexity Lab – Tiago P. Peixoto
Inverse Complexity Lab
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Chiara Poletto @chpoletto.bsky.social · 27/11/2024
@chpoletto.bsky.social @manlius.bsky.social @vcolizza.bsky.social @netscience.bsky.social @seeslab.bsky.social @bansallab.bsky.social @giuliapullano.bsky.social @giuliacencetti.bsky.social @tiago.skewed.de
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Sergi Valverde @svalver.bsky.social · 12/11/2024
A starter pack for researchers interested in #ComplexSystems. Complex system science investigates how interactions among multiple parts lead to collective behaviour, as well as how the system interacts and forms links with its environment - please add your name! go.bsky.app/FNYZ61y
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Manlio De Domenico @manlius.bsky.social · 22/11/2024
The Mediterranean School of Complex Networks is now on @bsky.app too! It's one of the oldest (if not the oldest?) school on #NetworkScience and this year we will celebrate its 10th edition! Follow it, since important announcements will follow in the next days: @mscxnetworks.bsky.social
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estebanmoro @estebanmoro.bsky.social · 20/11/2024
Great move! Foursquare just open-sourced their 100M+ place point of interest dataset. location.foursquare.com/resources/bl...
location.foursquare.com
Foursquare Open Source Places: A new foundational dataset for the geospatial community
Stay up to date with the latest from Foursquare! Learn more about Foursquare Open Source Places: A new foundational dataset for the geospatial community
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