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Arcadia Science

@arcadiascience.com
1.6K followers 16 following 74 posts

Research and development company leveraging the biology of diverse organisms. Read about our science: research.arcadiascience.com

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Arcadia Science @arcadiascience.com · 30/01/2026
5/6 We traced this to layers 5-11, which integrate sequence weights blindly, regardless of whether they help or hurt. When they hurt prediction, we could progressively rescue performance by shuffling weights at earlier layers, saving the model from its own bad intuition.
Box plot of normalized P@L delta across shuffling start layers showing positive cohort recovers performance as shuffling stops while negative cohort degrades.
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Arcadia Science @arcadiascience.com · 30/01/2026
4/6 But surprisingly, encoding phylogeny ≠ leveraging it. Comparing learned weights against uniform averaging for contact prediction, the aggregate improvement was marginal. Per-MSA, uniform averaging outperformed learned weights about half the time, sometimes by a large margin.
Histogram of delta P@L showing roughly symmetric distribution around zero with slight positive mean.
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Arcadia Science @arcadiascience.com · 30/01/2026
3/6 The model consistently upweights evolutionarily close sequences and downweights distant ones, despite never being trained on this. There's also a division of labor across layers: layer 11 acts as a strong phylogenetic filter, while others contribute more modestly.
Unrooted tree for LytTR query with leaves colored by median sequence weight showing gradient of attention from query.
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Arcadia Science @arcadiascience.com · 30/01/2026
1/6 What does MSA Pairformer learns about evolutionary relationships? @yoakiyama.bsky.social et al achieved impressive contact & variant-fitness predictions w a fraction of ESM2's parameters; we wanted to better understand the mechanism arcadia-science.github.io/2025-phyloge... 🧪🧬 🖥️
Screenshot of pub title, "MSA-based pLMs encode evolutionary distance but don't reliably exploit it"
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Arcadia Science @arcadiascience.com · 16/09/2025
We demonstrated AutoOpenRaman's capabilities by automatically collecting 200 Raman spectra from Chlamydomonas reinhardtii colonies in 68 minutes across a 96-well plate format. The system successfully detected β-carotene signatures in the algae. [6/8]
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Arcadia Science @arcadiascience.com · 16/09/2025
The software is designed for non-programmers to install and use, built on µManager (micro-manager.org) for broad device support. Users can swap hardware components as long as µManager supports them — no code changes needed [5/8]
Diagram of AutoOpenRaman software flow and user interface
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Arcadia Science @arcadiascience.com · 16/09/2025
Our solution: AutoOpenRaman adds automation to OpenRAMAN while keeping it open-source and relatively inexpensive (~$8k in total). [3/8]
Diagrams of the AutoOpenRaman spectrometer setup
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Arcadia Science @arcadiascience.com · 22/06/2025
As #Evol2025 talks wrap up for the day, our mixer begins! Come upstairs at The Globe any time til 7:30 to learn about opportunities at Arcadia over charcuterie & drinks 🍷🧀 We’re looking for a Computational Evolutionary Biologist, Evolutionary Cell Biologist, and more…
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Arcadia Science @arcadiascience.com · 22/06/2025
📢 Hey #Evol2025 attendees, we’re hiring! If you’re interested in #careers at Arcadia, swing by our free mixer upstairs at The Globe today from 5:30 to 7:30. It’s a 7-minute walk from the Classic Center and drinks are free 🍻 jobs.lever.co/arcadiascience
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Arcadia Science @arcadiascience.com · 18/03/2025
We're trying a new publication format — the notebook pub! By turning our Jupyter Notebooks into publishable artifacts, we hope to share faster, reduce the effort to convert analysis ➡️ pub, and make our work more reproducible. Weigh in on our commentary: research.arcadiascience.com/pub/perspect...
Diagram comparing processes for creating standard vs. notebook pubs where notebook pubs cut out significant manual, irreproducible editing steps.
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Arcadia Science @arcadiascience.com · 17/12/2024
We 🖤 #OpenRAMAN!
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Arcadia Science @arcadiascience.com · 14/12/2024
Come find us at #CellBio24! Our CSO @pracheeac.bsky.social is giving a talk today, and then we've got another talk and a bunch of posters during the rest of the conference. Come say hey!
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Arcadia Science @arcadiascience.com · 22/11/2024
We curate a list of biology-focused preprints for which authors have requested comments: bit.ly/preprintrequests We pull @prereview.bsky.social requests, preprints ppl have requested feedback for on X/Bluesky, and sometimes our own work from PubPub. Add yours! bit.ly/submitpreprint 🧪🧬 🖥️ #evobio
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Arcadia Science @arcadiascience.com · 01/03/2024
Interested in commenting on 🧪 preprints but unsure of how to get started? Check out our how-to guide so you can contribute to the open science community ASAP! 👉 arcadia-web-assets.s3.us-west-1.amazonaws.com/publishing/a...
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Arcadia Science @arcadiascience.com · 03/12/2023
We’re at #cellbio2023! Visit us at booth #434 or check out ascb2023.arcadiascience.com to see posters we’re presenting and more!
Two Arcadia employees posing at our booth, which has two high-top tables, a monitor showing microscopy images, and various giveaway items
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Arcadia Science @arcadiascience.com · 17/10/2023
Back in May 2022 (one of our first pubs!), we developed a short bioinformatics workflow to to design MERFISH probes for C. reinhardtii. Check out the pub, with executable GoogleColab notebooks you can use to probe any genome of interest. Feedback is welcome! buff.ly/3FkH3SP
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Arcadia Science @arcadiascience.com · 12/10/2023
“Summer of Pubs” is part of our experiment in open publishing. It's all 🆓 to read, we put key links to code/data at the top, figures can be interactive, and we list authors A–Z with defined roles. You can do it too w your own PubPub community! www.pubpub.org
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Arcadia Science @arcadiascience.com · 06/10/2023
We're so delighted to be supporting open source science today with our mini-hackathon for Hacktoberfest 2023! Great conversations and even greater collaborations + a swag bag to take home 😎 🖥️
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Arcadia Science @arcadiascience.com · 04/10/2023
Our CEO @seemaychou.bsky.social recently spoke with Alok Tayi on the Biotech2050 podcast. Tune in to learn what we're up to! 🎧 podcasts.apple.com/us/podcast/u...
Quote from Seemay Chou (co-founder & CEO of Arcadia Science): My best piece of advice is just take the first step. Don't overthink it. Usually the first step is not your final step, or even a very long step, but it's the hardest one, ironically. But it opens up so many more opportunities.
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