Shakedown Social

Victoria Stuart 🇨🇦 🏳️‍⚧️GREmLN: A Cellular Regulatory Network-Aware Transcriptomics Foundation Model <a href="https://www.biorxiv.org/content/10.1101/2025.07.03.663009v1?rss=1" rel="nofollow noopener" translate="no" target="_blank">https://www.biorxiv.org/content/10.1101/2025.07.03.663009v1?rss=1</a>Comments * really brilliant work: LLM + neural transformer architecture * a molecular biologist, I long-thought (no time to learn / program) flux-based analysis / ODE models * this type of modeling is foundational to in silico modeling * huge proponent of graphs - add LLM, attention heads - brilliant! 😀 👍️ kudos<a href="https://mastodon.social/tags/BiologicalModeling" class="mention hashtag" rel="nofollow noopener" target="_blank">#BiologicalModeling</a> <a href="https://mastodon.social/tags/FoundationModels" class="mention hashtag" rel="nofollow noopener" target="_blank">#FoundationModels</a> <a href="https://mastodon.social/tags/LLM" class="mention hashtag" rel="nofollow noopener" target="_blank">#LLM</a> <a href="https://mastodon.social/tags/attention" class="mention hashtag" rel="nofollow noopener" target="_blank">#attention</a> <a href="https://mastodon.social/tags/GraphTheory" class="mention hashtag" rel="nofollow noopener" target="_blank">#GraphTheory</a> <a href="https://mastodon.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a>

Fractal KittyA friend showed me a leetcode problem yesterday at the Recurse Center:<a href="https://leetcode.com/problems/minimum-height-trees/description/?envType=problem-list-v2&envId=rab78cw1" rel="nofollow noopener" translate="no" target="_blank">https://leetcode.com/problems/minimum-height-trees/description/?envType=problem-list-v2&envId=rab78cw1</a>Which led me to play for a bit on paper, then drafted a rough a visual toy:<a href="https://codepen.io/fractalkitty/live/WbvJKgy" rel="nofollow noopener" translate="no" target="_blank">https://codepen.io/fractalkitty/live/WbvJKgy</a>(I haven't actually done any leetcode problems because I often end up on paper and down rabbit holes)<a href="https://mathstodon.xyz/tags/recurseCenter" class="mention hashtag" rel="nofollow noopener" target="_blank">#recurseCenter</a> <a href="https://mathstodon.xyz/tags/graphtheory" class="mention hashtag" rel="nofollow noopener" target="_blank">#graphtheory</a> <a href="https://mathstodon.xyz/tags/trees" class="mention hashtag" rel="nofollow noopener" target="_blank">#trees</a> <a href="https://mathstodon.xyz/tags/codepen" class="mention hashtag" rel="nofollow noopener" target="_blank">#codepen</a> <a href="https://mathstodon.xyz/tags/leetcode" class="mention hashtag" rel="nofollow noopener" target="_blank">#leetcode</a>

Fractal KittyI am starting a new series on the blog for inquiries in math. I posted the first one today:<a href="https://www.fractalkitty.com/inquiries-week-1-circle-shading/" rel="nofollow noopener" translate="no" target="_blank">https://www.fractalkitty.com/inquiries-week-1-circle-shading/</a><a href="https://mathstodon.xyz/tags/mtbos" class="mention hashtag" rel="nofollow noopener" target="_blank">#mtbos</a> <a href="https://mathstodon.xyz/tags/iteachmath" class="mention hashtag" rel="nofollow noopener" target="_blank">#iteachmath</a> <a href="https://mathstodon.xyz/tags/circles" class="mention hashtag" rel="nofollow noopener" target="_blank">#circles</a> <a href="https://mathstodon.xyz/tags/graphtheory" class="mention hashtag" rel="nofollow noopener" target="_blank">#graphtheory</a> <a href="https://mathstodon.xyz/tags/math" class="mention hashtag" rel="nofollow noopener" target="_blank">#math</a>

HoldMyType<a href="https://mathstodon.xyz/tags/git" class="mention hashtag" rel="nofollow noopener" target="_blank">#git</a> can be hard, like anything if you want to understand it So are DAGs Then again of you want to start with git and get to <a href="https://mathstodon.xyz/tags/graphtheory" class="mention hashtag" rel="nofollow noopener" target="_blank">#graphtheory</a> , which is fun in my view. It ll be after months of accidents No employer wants that on their payroll and no team or authority wants to be responsible for it or accepts it and it ll be a nightmare for the person after fun. So the society, the institution and the market collectively orient workforce not to have fun in learning things, including cubicles. Oh yes move fast and break thing , but at your expense, which clearly is hoarded. That explains a lot , including the rise of <a href="https://mathstodon.xyz/tags/ai" class="mention hashtag" rel="nofollow noopener" target="_blank">#ai</a> <a href="https://mathstodon.xyz/tags/git" class="mention hashtag" rel="nofollow noopener" target="_blank">#git</a> <a href="https://ohshitgit.com/" rel="nofollow noopener" translate="no" target="_blank">https://ohshitgit.com/</a>

Ross KangA post of <a href="https://mathstodon.xyz/@11011110" class="u-url mention" rel="nofollow noopener" target="_blank">@11011110</a> has reminded me that (after a year and a half lurking here) it's never too late for me to toot and pin an intro here.I am a Canadian mathematician in the Netherlands, and I have been based at the University of Amsterdam since 2022. I also have some rich and longstanding ties to the UK, France, and Japan.My interests are somewhere in the nexus of Combinatorics, Probability, and Algorithms. Specifically, I like graph colouring, random graphs, and probabilistic/extremal combinatorics. I have an appreciation for randomised algorithms, graph structure theory, and discrete geometry.Around 2020, I began taking a more active role in the community, especially in efforts towards improved fairness and openness in science. I am proud to be part of a team that founded the journal, Innovations in Graph Theory (<a href="https://igt.centre-mersenne.org/" rel="nofollow noopener" translate="no" target="_blank">https://igt.centre-mersenne.org/</a>), that launched in 2023. (That is probably the main reason I joined mathstodon!) I have also been a coordinator since 2020 of the informal research network, A Sparse (Graphs) Coalition (<a href="https://sparse-graphs.mimuw.edu.pl/" rel="nofollow noopener" translate="no" target="_blank">https://sparse-graphs.mimuw.edu.pl/</a>), devoted to online collaborative workshops. In 2024, I helped spearhead the MathOA Diamond Open Access Stimulus Fund (<a href="https://www.mathoa.org/diamond-open-access-stimulus-fund/" rel="nofollow noopener" translate="no" target="_blank">https://www.mathoa.org/diamond-open-access-stimulus-fund/</a>).Until now, my posts have mostly been about scientific publishing and combinatorics.<a href="https://mathstodon.xyz/tags/introduction" class="mention hashtag" rel="nofollow noopener" target="_blank">#introduction</a> <a href="https://mathstodon.xyz/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#openscience</a> <a href="https://mathstodon.xyz/tags/diamondopenaccess" class="mention hashtag" rel="nofollow noopener" target="_blank">#diamondopenaccess</a> <a href="https://mathstodon.xyz/tags/scientificpublishing" class="mention hashtag" rel="nofollow noopener" target="_blank">#scientificpublishing</a> <a href="https://mathstodon.xyz/tags/openaccess" class="mention hashtag" rel="nofollow noopener" target="_blank">#openaccess</a> <a href="https://mathstodon.xyz/tags/RemoteConferences" class="mention hashtag" rel="nofollow noopener" target="_blank">#RemoteConferences</a> <a href="https://mathstodon.xyz/tags/combinatorics" class="mention hashtag" rel="nofollow noopener" target="_blank">#combinatorics</a> <a href="https://mathstodon.xyz/tags/graphtheory" class="mention hashtag" rel="nofollow noopener" target="_blank">#graphtheory</a> <a href="https://mathstodon.xyz/tags/ExtremalCombinatorics" class="mention hashtag" rel="nofollow noopener" target="_blank">#ExtremalCombinatorics</a> <a href="https://mathstodon.xyz/tags/probability" class="mention hashtag" rel="nofollow noopener" target="_blank">#probability</a>

OblomovAnyway, I wanted you to know that there's a kind of graph in <a href="https://sociale.network/tags/mathematics" class="mention hashtag" rel="nofollow noopener" target="_blank">#mathematics</a> <a href="https://sociale.network/tags/graphTheory" class="mention hashtag" rel="nofollow noopener" target="_blank">#graphTheory</a> that is called «dessin d'enfant» (child's drawing).<a href="https://en.wikipedia.org/wiki/Dessin_d%27enfant" rel="nofollow noopener" target="_blank">https://en.wikipedia.org/wiki/Dessin_d%27enfant</a><a href="https://sociale.network/tags/TheMoreYouKnow" class="mention hashtag" rel="nofollow noopener" target="_blank">#TheMoreYouKnow</a>

IT NewsWhere Graph Theory Meets The Road: The Algorithms Behind Route Planning - Back in the hazy olden days of the pre-2000s, navigating between two locations gen... - <a href="https://hackaday.com/2024/04/04/where-graph-theory-meets-the-road-the-algorithms-behind-route-planning/" rel="nofollow noopener" translate="no" target="_blank">https://hackaday.com/2024/04/04/where-graph-theory-meets-the-road-the-algorithms-behind-route-planning/</a> <a href="https://schleuss.online/tags/transportationhacks" class="mention hashtag" rel="nofollow noopener" target="_blank">#transportationhacks</a> <a href="https://schleuss.online/tags/routeplanning" class="mention hashtag" rel="nofollow noopener" target="_blank">#routeplanning</a> <a href="https://schleuss.online/tags/graphtheory" class="mention hashtag" rel="nofollow noopener" target="_blank">#graphtheory</a> <a href="https://schleuss.online/tags/featured" class="mention hashtag" rel="nofollow noopener" target="_blank">#featured</a> <a href="https://schleuss.online/tags/interest" class="mention hashtag" rel="nofollow noopener" target="_blank">#interest</a> <a href="https://schleuss.online/tags/history" class="mention hashtag" rel="nofollow noopener" target="_blank">#history</a>

Vis Lab @ Khoury, NortheasternHey Mastodon! 👋 Here is our <a href="https://vis.social/tags/introduction" class="mention hashtag" rel="nofollow noopener" target="_blank">#introduction</a> post: We are the Data Visualization Lab at Khoury College of Computer Sciences at Northeastern University. You can find more about our work here: <a href="https://vis.khoury.northeastern.edu/" rel="nofollow noopener" translate="no" target="_blank">https://vis.khoury.northeastern.edu/</a>We'd love to be connected to more folks and labs in the realms of <a href="https://vis.social/tags/DataVisualization" class="mention hashtag" rel="nofollow noopener" target="_blank">#DataVisualization</a> <a href="https://vis.social/tags/HCI" class="mention hashtag" rel="nofollow noopener" target="_blank">#HCI</a> <a href="https://vis.social/tags/xAI" class="mention hashtag" rel="nofollow noopener" target="_blank">#xAI</a> <a href="https://vis.social/tags/AR" class="mention hashtag" rel="nofollow noopener" target="_blank">#AR</a> <a href="https://vis.social/tags/VR" class="mention hashtag" rel="nofollow noopener" target="_blank">#VR</a> <a href="https://vis.social/tags/VisualAnalytics" class="mention hashtag" rel="nofollow noopener" target="_blank">#VisualAnalytics</a> <a href="https://vis.social/tags/PhD" class="mention hashtag" rel="nofollow noopener" target="_blank">#PhD</a> <a href="https://vis.social/tags/Research" class="mention hashtag" rel="nofollow noopener" target="_blank">#Research</a> Our lab has been applying visualization to domain areas like <a href="https://vis.social/tags/accessibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#accessibility</a> <a href="https://vis.social/tags/UAVs" class="mention hashtag" rel="nofollow noopener" target="_blank">#UAVs</a> <a href="https://vis.social/tags/Genetics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Genetics</a> <a href="https://vis.social/tags/Privacy" class="mention hashtag" rel="nofollow noopener" target="_blank">#Privacy</a> <a href="https://vis.social/tags/Pedagogy" class="mention hashtag" rel="nofollow noopener" target="_blank">#Pedagogy</a> <a href="https://vis.social/tags/Networks" class="mention hashtag" rel="nofollow noopener" target="_blank">#Networks</a> <a href="https://vis.social/tags/GraphTheory" class="mention hashtag" rel="nofollow noopener" target="_blank">#GraphTheory</a> Say hi!

David AmosI still need to add some short blurbs about each chapter, but here's the website for Exploring Graph Theory With Julia, complete with my lazily-designed temporary cover "art": <a href="https://leanpub.com/exploring-graph-theory-with-julia" rel="nofollow noopener" target="_blank">https://leanpub.com/exploring-graph-theory-with-julia</a>I would love to know if this book sounds interesting to you!(Boosts welcome 🙏 )<a href="https://hachyderm.io/tags/JuliaLang" class="mention hashtag" rel="nofollow noopener" target="_blank">#JuliaLang</a> <a href="https://hachyderm.io/tags/GraphTheory" class="mention hashtag" rel="nofollow noopener" target="_blank">#GraphTheory</a> <a href="https://hachyderm.io/tags/Books" class="mention hashtag" rel="nofollow noopener" target="_blank">#Books</a>

Danny GarsideAre there any good tools for analysing your Mastodon network in a <a href="https://social.coop/tags/GraphTheory" class="mention hashtag" rel="nofollow noopener" target="_blank">#GraphTheory</a> / <a href="https://social.coop/tags/NetworkAnalysis" class="mention hashtag" rel="nofollow noopener" target="_blank">#NetworkAnalysis</a> kind of way?I'd love to: - visualise the different groups of people that I follow: what are the connections between the people that I follow? - see which accounts post a lot, or not at all - see which accounts I interact with the most (are there people that I followed but it turns out I'm not actually interested in what they post now?) - see what hours I and others post<a href="https://social.coop/tags/Mastodon" class="mention hashtag" rel="nofollow noopener" target="_blank">#Mastodon</a>

Dr Emily Jennings (she/her)💖💜💙Hi folks, I have somebody who is <a href="https://genomic.social/tags/lookingforajob" class="mention hashtag" rel="nofollow noopener" target="_blank">#lookingforajob</a> in the greater <a href="https://genomic.social/tags/boston" class="mention hashtag" rel="nofollow noopener" target="_blank">#boston</a> area. He’s a PhD in <a href="https://genomic.social/tags/math" class="mention hashtag" rel="nofollow noopener" target="_blank">#math</a> with experience doing <a href="https://genomic.social/tags/graphtheory" class="mention hashtag" rel="nofollow noopener" target="_blank">#graphtheory</a> as well as <a href="https://genomic.social/tags/quantumcomputing" class="mention hashtag" rel="nofollow noopener" target="_blank">#quantumcomputing</a> <a href="https://genomic.social/tags/quantumcompilation" class="mention hashtag" rel="nofollow noopener" target="_blank">#quantumcompilation</a>. Several yrs of post phd experience in govt looking to get back to <a href="https://genomic.social/tags/academia" class="mention hashtag" rel="nofollow noopener" target="_blank">#academia</a> and is open to <a href="https://genomic.social/tags/postdoc" class="mention hashtag" rel="nofollow noopener" target="_blank">#postdoc</a> or other roles in <a href="https://genomic.social/tags/research" class="mention hashtag" rel="nofollow noopener" target="_blank">#research</a>

Seth CookeLots of new people migrating to Mastodon from Twitter! Given that the crowd is very different here, I thought I'd reintroduce myself by being more open than usual about my recent art.'⦵ (pour Isidore)' is series of works (including speech synthesis, photography, graph analysis, found artefacts and text) presented across a wav and a pdf. There is no streaming preview.<a href="https://sethcooke.bandcamp.com/album/pour-isidore" rel="nofollow noopener" target="_blank">https://sethcooke.bandcamp.com/album/pour-isidore</a><a href="https://mastodon.art/tags/graphtheory" class="mention hashtag" rel="nofollow noopener" target="_blank">#graphtheory</a> <a href="https://mastodon.art/tags/soundpoetry" class="mention hashtag" rel="nofollow noopener" target="_blank">#soundpoetry</a> <a href="https://mastodon.art/tags/photography" class="mention hashtag" rel="nofollow noopener" target="_blank">#photography</a> <a href="https://mastodon.art/tags/speechsynthesis" class="mention hashtag" rel="nofollow noopener" target="_blank">#speechsynthesis</a>

Tanguy FardetWhat kind of <a href="https://fediscience.org/tags/network" class="mention hashtag" rel="nofollow noopener" target="_blank">#network</a> do we want for <a href="https://fediscience.org/tags/Mastodon" class="mention hashtag" rel="nofollow noopener" target="_blank">#Mastodon</a> (and <a href="https://fediscience.org/tags/Fediverse" class="mention hashtag" rel="nofollow noopener" target="_blank">#Fediverse</a> in general)?The answer may vary depending on users and communities, but let's discuss where the new follow-recommendation tool of Mastodon 3.5 leads us (<a href="https://github.com/mastodon/mastodon/pull/15945" rel="nofollow noopener" translate="no" target="_blank">https://github.com/mastodon/mastodon/pull/15945</a>).The evolution of a network where new users preferentially follow existing influencers can be modeled as a Price/BA network.<a href="https://en.wikipedia.org/wiki/Barab%C3%A1si%E2%80%93Albert_model" rel="nofollow noopener" translate="no" target="_blank">https://en.wikipedia.org/wiki/Barab%C3%A1si%E2%80%93Albert_model</a>You end up with few large influencers. Honestly, I'm not a fan...<a href="https://fediscience.org/tags/graphTheory" class="mention hashtag" rel="nofollow noopener" target="_blank">#graphTheory</a>

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