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Paul Sample

@paulsample.bsky.social
1.6K followers 865 following 45 posts

Biology x AI and other fun stuff.

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Paul Sample @paulsample.bsky.social · 12/02/2026
At what point do you decide to just not publish a paper because the models are so out of date? This paper was published yesterday but uses models that are ancient by today's standards (GPT 4, Gemini 2, Llama 2 & 3).
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Paul Sample @paulsample.bsky.social · 01/09/2025
I think these guys are based in the US and offer GLM-4.5 synthetic.new/landing/home
synthetic.new
Synthetic | Run LLMs, privately
Chat with open-source models privately
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Paul Sample @paulsample.bsky.social · 22/08/2025
openai.com/index/accele...
openai.com
Accelerating life sciences research
OpenAI and Retro Biosciences achieve 50x increase in expressing stem cell reprogramming markers.
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Paul Sample @paulsample.bsky.social · 21/08/2025
cloud.google.com/blog/product...
cloud.google.com
Measuring the environmental impact of AI inference | Google Cloud Blog
A methodology for measuring the energy, emissions, and water impact of Gemini prompts shines a light on the environmental impact of AI inference.
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Paul Sample @paulsample.bsky.social · 08/07/2025
Today would be a great day for the AI research community to leave X for good. In your own self interest and for the public perception of AI, take a stand. Unless you agree with using it as a misinformation and propaganda machine, I guess.
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Ai2 @ai2.bsky.social · 01/07/2025
Introducing SciArena, a platform for benchmarking models across scientific literature tasks. Inspired by Chatbot Arena, SciArena applies a crowdsourced LLM evaluation approach to the scientific domain. 🧵
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Paul Sample @paulsample.bsky.social · 12/06/2025
Anthropic's Claude Code Python SDK just released? Currently sitting at 1 star! github.com/anthropics/c...
github.com
GitHub - anthropics/claude-code-sdk-python
Contribute to anthropics/claude-code-sdk-python development by creating an account on GitHub.
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Paul Sample @paulsample.bsky.social · 22/05/2025
These are wonderfully weird.
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AI x Bio Discovery @aixbiobot.bsky.social · 20/05/2025
Robin: A multi-agent system for automating scientific discovery [new] Automating scientific discovery via a multi-agent system that integrates literature search and data analysis to propose/validate hypotheses.
Robin: A multi-agent system for automating scientific discoveryFigure 1Figure 2Figure 3
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Paul Sample @paulsample.bsky.social · 16/05/2025
The learning objective is next token prediction, but to do that well the models have to learn a deeper representation of “the world”. Compare the latest LLMs to a simple N gram model and tell me that they’re just “next word” predictors.
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Nicole Hennig @nic221.bsky.social · 14/05/2025
Power-Hungry Data Centers Are Warming Homes in the Nordics bloom.bg/4jYABDI #AI #DataCenters #climate
Text Shot: Now the biggest project with heat recovery technology anywhere in the world is underway just outside Helsinki. Microsoft Corp. is building a cluster of data centers that, when completed, should supply heating to 40% of Espoo, Finland’s second-largest city. That’s about 100,000 homes. A local coal-fired heating plant has already shut as it’s no longer needed.

More major Finnish data center projects using heat recovery have been announced in May and March; other examples are already running in Sweden.
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Paul Sample @paulsample.bsky.social · 14/05/2025
WhyTF would people use Grok when they do things like this? Not to mention the pollution they’re producing in Memphis.
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Paul Sample @paulsample.bsky.social · 13/05/2025
There is no bigger turn off to reading a paper than seeing the words “is all you need” in the title.
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Paul Sample @paulsample.bsky.social · 10/05/2025
Finally, the Twitter/X killer. Nothing quite as satisfying as operating in purely in a terminal. www.itter.sh
itter.sh
itter.sh - Social Media via SSH
itter.sh: Ironic, text-only, SSH-based social networking for terminal lovers. No browser, no js, just eets.
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Paul Sample @paulsample.bsky.social · 02/05/2025
I always look forward to FutureHouse releases. I had to do a little digging for API information so here it is for those who are interested. futurehouse.gitbook.io/futurehouse-...
futurehouse.gitbook.io
FutureHouse Platform API Documentation | FutureHouse Cookbook
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Angie Rasmussen @angierasmussen.bsky.social · 30/04/2025
I knew he would do this. I wrote a whole article about how he would do this. I am not surprised he’s undermining vaccination. I know he’s an anti-vaxxer & a predatory crank. And yet…you have got to be fucking kidding me. He’s promoting infant mortality.
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Paul Sample @paulsample.bsky.social · 30/04/2025
We have to be reaching the sycophancy floor soon.. right?
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Paul Sample @paulsample.bsky.social · 29/04/2025
I had no idea. Very useful — thanks for sharing.
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Paul Sample @paulsample.bsky.social · 19/04/2025
I’m curious about what your thoughts are on the odds of Trump et al putting a finger on the scale if Tesla shares tank. And ultimately, what could they reasonably do to give it some juice.
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AI x Bio Discovery @aixbiobot.bsky.social · 24/02/2025
Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling [new] Atlas maps 50 cancer lines' trancriptomic response to 1.1k mols, aiding AI modeling.
Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular ModelingFigure 1Figure 2Figure 3
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AI x Bio Discovery @aixbiobot.bsky.social · 22/02/2025
Genome modeling and design across all domains of life with Evo 2 [new] Evo 2: Learns genomic features across life's domains from DNA alone and generates coherent, controllable genome sequences at scale.
Genome modeling and design across all domains of life with Evo 2Figure 2Figure 3Figure 4
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Paul Sample @paulsample.bsky.social · 21/02/2025
"Most baffling to many were the firings of hundreds whose jobs were not funded by taxpayers. Their positions were financed through congressionally approved agreements that routed fees from the drug, medical device and tobacco industries to the agency." 🤡 www.nytimes.com/live/2025/02...
nytimes.com
Trump Live Updates: Layoffs, Ukraine War and Deportation News
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Karen Hao @karenhao.bsky.social · 21/02/2025
For decades, the US government has painstakingly kept American science #1 globally—and every facet of American life has improved because of it. The internet? Flu shot? Ozempic? All grew out of federally-funded research. Now all that's being dismantled. 1/ www.technologyreview.com/2025/02/21/1...
technologyreview.com
The foundations of America’s prosperity are being dismantled
Federal scientists warn that Americans could feel the effects of the new administration's devastating cuts for decades to come
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Paul Sample @paulsample.bsky.social · 16/02/2025
🤮
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Paul Sample @paulsample.bsky.social · 04/02/2025
Has anyone tried this? Struggling to find an information retrieval system I like. www.perplexity.ai/help-center/...
perplexity.ai
What is Internal Knowledge Search | Perplexity Help Center
Internal Knowledge Search allows both Perplexity Pro and Enterprise Pro users to search across internal files alongside the web.
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Paul Sample @paulsample.bsky.social · 02/02/2025
www.openbioml.org has a discord.
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Simon Willison @simonwillison.net · 31/01/2025
Severance obsessives like myself may be interested to hear that the first 8 chapters of The You You Are by Dr. Ricken Lazlo Hale, PhD are now available for free as both text and an audiobook read by Ricken himself: books.apple.com/us/book/the-...
books.apple.com
‎The You You Are
‎Health, Mind & Body · 2025
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Paul Sample @paulsample.bsky.social · 27/01/2025
Avoidance is better for mental health but not for decision making in an increasingly complex and unpredictable world.
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Sung Kim @sungkim.bsky.social · 24/01/2025
Aider reports that R1+Sonnet (R1 Thinking + Sonnet) set a new SOTA on the aider polyglot benchmark at 14X less cost compared to o1. 64% R1+Sonnet 62% o1 57% R1 52% Sonnet 48% DeepSeek V3 aider.chat/2025/01/24/r...
aider.chat
R1+Sonnet set SOTA on aider’s polyglot benchmark
R1+Sonnet has set a new SOTA on the aider polyglot benchmark. At 14X less cost compared to o1.
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Paul Sample @paulsample.bsky.social · 21/01/2025
I tried a few biology-related queries and was impressed with the results. Researchers should check this out.
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Paul Sample @paulsample.bsky.social · 18/01/2025
How have I been coding with Python for 10 years and just learned today that you can update the same line in a terminal using '\r' and end=''? print(f"\rDownload progress: {percent}%", end='') Thanks Claude.
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Eric Topol @erictopol.bsky.social · 16/01/2025
98% of microplastic particles (MP) in bottled water are smaller than 20 μm, which are much more likely to get thru the GI tract to blood and organ tissue. Municipal tap water was higher in MP than 8 of 10 bottled water brands journals.plos.org/water/articl...
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Vikram Agarwal @vagar.bsky.social · 15/01/2025
Super excited to announce our latest work. On a personal note, it's not an exaggeration to say that blood, sweat, and tears got us to the finish line on this: working w/ an outstanding global team of scientists in Germany, Japan, Russia, and USA responding in >100 pages of complex reviewer comments.
nature.com
Massively parallel characterization of transcriptional regulatory elements - Nature
Lentivirus-based reporter assays for 680,000 regulatory sequences from three cell lines coupled to machine-learning models lead to insights into the grammar of cis-regulatory elements.
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Paul Sample @paulsample.bsky.social · 09/01/2025
temperature = 0
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Paul Sample @paulsample.bsky.social · 09/01/2025
Gemini 2.0 Flash gets straight to the point with "peanut".
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Paul Sample @paulsample.bsky.social · 08/01/2025
Not to brag but apparently I'm "on a roll!" over at LinkedIn. Blessed 🙏.
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Jeremy Howard @howard.fm · 19/12/2024
I'll get straight to the point. We trained 2 new models. Like BERT, but modern. ModernBERT. Not some hypey GenAI thing, but a proper workhorse model, for retrieval, classification, etc. Real practical stuff. It's much faster, more accurate, longer context, and more useful. 🧵
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David Bikard @dbikard.bsky.social · 13/12/2024
Excited to share that we have just released genomenotebook 1.0 together with @trichomedoctor.bsky.social ! If you like to analyze genomics data in Jupyter notebooks this is for you. You can get beautiful genome browsers directly in your notebooks: dbikard.github.io/genomenotebo...
dbikard.github.io
genomenotebook
A genome browser in your Jupyter notebook
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Paul Sample @paulsample.bsky.social · 11/12/2024
I know this store. It's in the well-to-do Magnolia neighborhood of Seattle. It's a little rundown but otherwise fine.The sign describes a plan to demolish it in order to build apartments (or something) but there has been no movement on it in years.
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Paul Sample @paulsample.bsky.social · 08/12/2024
Nice tool and the UI is great. It would be helpful if you could filter for specific file types. For example, ingesting github.com/google-gemin... pulls out tons of stuff you wouldn't actually need for an LM.
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Rom2 @yasbaltrine.bsky.social · 07/12/2024
I made this free and open source dev tool: gitingest.com Replace "hub" with "ingest" in any github URL to get a text digest that you can feed into any LLM
home screen for gitingest.com
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Paul Sample @paulsample.bsky.social · 08/12/2024
Great, and for the pay-as-you-go tier the experimental 1.5 models are charged at the rates of 1.5 pro?
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Paul Sample @paulsample.bsky.social · 08/12/2024
Very cool. I know that the experimental models are free of charge in AI Studio, but do you know if that’s true when using the API? I can’t seem to find a clear answer.
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Paul Sample @paulsample.bsky.social · 05/12/2024
Once again reminded of the amazing storytelling through data visualization that W.E.B Du Bois was doing in 1899!
Infographic by WEB Du Bois.
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Diego del Alamo @delalamo.xyz · 04/12/2024
New ESM models! Unlike ESM3 these seem to be classic sequence-only PLMs. The 300M and 600M param models are open source and available for commercial use, while the 6B param model is academic use only www.evolutionaryscale.ai/blog/esm-cam...
ESM C establishes a new state of the art. ESM has consistently set the state of the art for protein language models. Now ESM C unlocks a new frontier of performance with scaling up to 6 billion parameters. The ESM C family delivers significant inference time performance gains, matching and even exceeding the capabilities of far larger previous generation models. Contact precision (P@L) is computed on CASP15.
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Paul Sample @paulsample.bsky.social · 01/12/2024
However it is not deterministic! I've rerun the same abstracts and noticed some borderline papers get classified differently with each run.
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Paul Sample @paulsample.bsky.social · 01/12/2024
I'm really enjoying the structured output ability of Gemini for this zero shot classification problem. I'm trying to categorize bioRxiv papers to focus on the ones most relevant to my interests and it's working with very little fiddling.
Code example using Gemini for zeroshot classification of bioRxiv papers.
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