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MrG

@biomattrs.bsky.social
215 followers 300 following 85 posts

Matthew Robert Gruner (MrG). In Reno, NV. High school biology instructor. Python/informatics enthusiast. 🏳️‍🌈🏳️‍⚧️

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Reposted by MrG
mr. TIM @timkellogg.me · 25/01/2025
huggingface is doing a fully open source replication of R1 github.com/huggingface/...
github.com
GitHub - huggingface/open-r1: Fully open reproduction of DeepSeek-R1
Fully open reproduction of DeepSeek-R1. Contribute to huggingface/open-r1 development by creating an account on GitHub.
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Ming Tommy Tang @tommytang.bsky.social · 25/01/2025
Bioinformaticians: Before diving into data analysis, pause. Quality control (QC) can make or break your results. 🧵👇
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IAS - the International AIDS Society @iasociety.bsky.social · 25/01/2025
The immediate halting of funding to #PEPFAR places millions of lives in jeopardy. The IAS urgently calls on policy makers and stakeholders to restore the funding lifeline to this pivotal programme. Lives depend on it, right now. Read our full statement:
iasociety.org
IAS statement: PEPFAR freeze threatens millions of lives
25 January 2025 (
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Kelly @broadwaybabyto.bsky.social · 25/01/2025
It’s easy to feel helpless right now, but remember we have tremendous capacity to help one another Small acts of kindness like wearing a respirator, checking on someone who might be all alone, making a meal for someone in need, donating to mutual aid….These things have a huge impact Love over hate
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Ming Tommy Tang @tommytang.bsky.social · 25/01/2025
Everyone wants YOUR problems. Think about people in the war zone; Think about people who lost their homes in the LA fire; Think about researchers affected by the NIH stopping funding review; Your problem is tiny compared to theirs.
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Scott McGrath @smcgrath.phd · 23/01/2025
🧪 "Humanity's Last Exam" sets a new benchmark for AI: 3,000 expert-crafted questions spanning 100+ subjects. Current LLMs perform poorly, revealing a gap in expert-level knowledge and calibration, but it would be difficult to build a harder test. 🩺💻 #MLSky
lastexam.ai
Humanity's Last Exam
Benchmarks are important tools for tracking the rapid advancements in large language model (LLM) capabilities. However, benchmarks are not keeping pace in difficulty: LLMs now achieve over 90% accuracy on popular benchmarks like MMLU, limiting informed measurement of state-of-the-art LLM capabilities. In response, we introduce Humanity's Last Exam, a multi-modal benchmark at the frontier of human knowledge, designed to be the final closed-ended academic benchmark of its kind with broad subject coverage. The dataset consists of 3,000 challenging questions across over a hundred subjects. We publicly release these questions, while maintaining a private test set of held out questions to assess model overfitting.
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Sitting on a corn flake @grrlscientist.bsky.social · 24/01/2025
How Small Can You Get? Another New-To-Science Flea-Toad Wows Scientists "The smallest vertebrates so far discovered are the flea-toads, which live at the limit for how small any vertebrate can possibly get." by @grrlscientist via medium #vertebrate #evolution #SciComm🧪 medium.com/grrlscientis...
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Daniel Pomarède @pomarede.bsky.social · 24/01/2025
Positive vibes, perception that there are fewer “Nazis” on the platform than on X, Science starter packs, lists and feeds: roughly 6,000 readers answered @nature.com's poll, with many declaring that Bluesky was nicer, kinder and less antagonistic to science than X. 🧪 www.nature.com/articles/d41...
nature.com
Bluesky’s science takeover: 70% of Nature poll respondents use platform
Roughly 6,000 readers answered our poll, with many declaring that Bluesky was nicer, kinder and less antagonistic to science than X.
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Derek Lowe @dereklowe.bsky.social · 23/01/2025
A terrifying new report by John Carreyrou illustrates why we have those pesky regulations and those irritating clinical trials:
science.org
Killing Cancer Patients (Once the Payments Clear)
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Prof Sam Illingworth @samillingworth.com · 24/01/2025
🧪 Are Biomedical Studies Reliable? A new survey reveals 72% of researchers believe there is a reproducibility crisis in biomedicine. The biggest issue? Pressure to publish, as most institutions value new discoveries over replicating studies. 🔗 journals.plos.org/plosbiology/... #SciComm
journals.plos.org
Biomedical researchers’ perspectives on the reproducibility of research
There is growing interest in the reproducibility of research and ways to enhance transparency. This study uses an international survey of more than 1900 biomedical researchers to reveal the perceived ...
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Maureen Barr @barrlab.bsky.social · 24/01/2025
🧪💡let's get our professional societies together and join forces to advocate for science @genetics-gsa.bsky.social @ascbiology.bsky.social @socdevbio.bsky.social @asm.org @marymunson4.bsky.social @copperbae.bsky.social @rburdine1.bsky.social @labonnelab.bsky.social @vscooper.micropopbio.org
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Liz Highleyman @lizhighleyman.bsky.social · 24/01/2025
For the first time in six decades, the CDC did not publish its Morbidity and Mortality Weekly Report on Thursday, just one effect of a flurry of executive orders & administrative moves after President Donald Trump’s January 20 inauguration. www.poz.com/article/trum...
poz.com
Trump Muzzles Federal Health Agencies, Withdraws from World Health Organization
CDC and other agencies were told to halt public communications, and the NIH grant process appears to be on hold.
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Dr. Or M. Bialik |📚|🔬|🌊|⚒️ @obialik.bsky.social · 23/01/2025
Not all planets are like ours. I don't just mean the water and life, I also mean the surface process. You look at a high resolution geological of Mars (like this one by Fawdon et al.), and you see stories you won't see on modern Earth. 🧪⚒️ www.tandfonline.com/doi/full/10....
The map of rock units and correlation of map units. The 1:150,000 scale map of bedrock units from the main map and the correlation of map units (Skinner et al., 2022). The timing of events is drawn from the contextual geological literature and the timing of other events in the region. Coloured bars represent the time in which these events are likely to have occurred, and not representative to their duration. We have not derived impact crater size frequency distribution model ages of for map units because, following the discussion in Sun and Stack (2020), these techniques is not an appropriate technique for units of this size and in this complex state of erosion/exhumation (e.g. Warner et al., 2015).
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Drug Monkey @drugmonkey.bsky.social · 23/01/2025
Interesting. Will the current chaos cause potential reviewers to refuse? I always think that if you are not in the right mind frame to be fair, you should always turn down review invitations.
to.you
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Alex Shevrin Venet @asv.bsky.social · 23/01/2025
When I train teachers about trauma-informed classrooms, I emphasize that you cannot simply declare that a person or a place is safe and make it so. People determine safety for themselves based on explicit and implicit cues of safety. (🧵 1/4)
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Richard Sever @richardsever.bsky.social · 23/01/2025
This is one of the reasons people were/are wary of science publishing 'solutions' that are basically "the government should run it"...
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George Takei @georgetakei.bsky.social · 23/01/2025
The joke is on us.
World map with all countries in green except for the United States, symbolizing U.S. withdrawal from the World Health Organization. Caption from '@IdiotBenevolent' says "The updated World Health Organization map is a sick joke."
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Eric Topol @erictopol.bsky.social · 21/01/2025
A systematic review involving >130 million people and 1 million dementia cases found that anti-inflammatory medications, vaccinations, and antibiotics were associated with reduced dementia, whereas vitamins and supplements linked to higher risk alz-journals.onlinelibrary.wiley.com/doi/10.1002/...
alz-journals.onlinelibrary.wiley.com
Data‐driven discovery of associations between prescribed drugs and dementia risk: A systematic review
Abstract Recent clinical trials on slowing dementia progression have led to renewed focus on finding safer, more effective treatments. One approach to identify plausible candidates is to assess whet...
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Alex Wellerstein @wellerstein.bsky.social · 21/01/2025
In the (great) first quarter of Neal Stephenson's (overall bad) 2019 novel "FALL," he has a scene set in a hypothetical American future in which the Red and Blue zones have become totally separate countries, essentially, and features a group of Blue denizens moving through the Red Ameristan...
Excerpt from Neal Stephenson's Fall; Or Dodge in Hell (William Morrow, 2019): 

“So, Martin Luther was running a false-flag operation for the Pope,” Phil said. “In that case—” But he broke off as he felt Sophia stepping on his toe, under the table.
He looked down at her. Having caught his eye, she panned her gaze across the entire scene, asking him to take it all in. Reminding him that this wasn’t Princeton. This was Ameristan. Facebooked to the molecular level. “Professor Long,” she muttered, “the Red Card.”Continued: 

It was a reference to one of their teachers at Princeton who had gone so far as to print up a wallet card for people to keep in front of them during conversations like this one. One side of the card was solid red, with no words or images, and was meant to be displayed outward as a nonverbal signal that you disagreed and that you weren’t going to be drawn into a fake argument. The other side, facing the user, was a list of little reminders as to what was really going on:Continued:

1.	Speech is aggression
2.	Every utterance has a winner and a loser
3.	Curiosity is feigned
4.	Lying is performative
5.	Stupidity is power
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Neil Shubin @neilshubin.bsky.social · 21/01/2025
Such a thrill…seeing a book you spent 2 years writing and over three decades living in print for the first time. ENDS OF THE EARTH. Onsale 2/4. 🧪 Hope to see you while I’m on tour!
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Kelly @broadwaybabyto.bsky.social · 21/01/2025
Today I’m thinking of Miep Gies, an ordinary person who risked her own life to protect the Frank family during WWII. Her quote reminds me that we all have the power to help others. To stand up against evil. To do the right thing even when it’s hard. We can all turn on a light.
Quote bubble which reads  don't like being called a hero because no one should ever think you have to be special to help others."
"I am afraid that if people feel that I am a very special person, a sort of heroine, they may doubt whether they will do the same I once did."
"But even an ordinary secretary or a housewife or a teenager can, within their own small ways, turn on a small light in a dark room."
"We did our duty as human beings: helping people in need."
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Pearl Freier @pearlf.bsky.social · 21/01/2025
Spravato is the 1st FDA approval 4 a monotherapy for major depressive disorder/MDD. Drug has been administered to >140,000 patients worldwide & they have nearly 6 yrs of real world data they said in the press release. Estimated 21 million US adults living w/ MDD www.jnj.com/media-center... #biosky
jnj.com
SPRAVATO® (esketamine) approved in the U.S. as the first and only monotherapy for adults with treatment-resistant depression
Following U.S. FDA Priority Review, approval is based on data demonstrating SPRAVATO® alone met its primary endpoint at 4 weeks and led to rapid and superior improvement in depressive symptoms compare...
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Ming Tommy Tang @tommytang.bsky.social · 21/01/2025
Why understanding biology matters in bioinformatics One big lesson: RNA and protein levels aren’t always correlated. If you don’t know this, you might draw the wrong conclusions. 🧵👇
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Stephen Turner @stephenturner.us · 17/01/2025
Exploring the Pathogen Profiles of Ancient Feces www.biorxiv.org/content/10.1101/202… 🧬🖥️🧪🦠💩
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Ming Tommy Tang @tommytang.bsky.social · 18/01/2025
What the heck is an object (Seurat object?) in object-oriented programming? 🤔 Let's break it down with bioinformatics examples👇
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Dr Simon Goodman @phoca-sapiens.bsky.social · 20/01/2025
Hey, I made a parasitology feed since there wasn't one... It collates posts including 'parasitology', 'parasitological' , and 'parasitologist', but NOT 'parasite' as this is frequently used outside of science contexts and pulls in all sorts of wierd stuff. Enjoy... bsky.app/profile/did:... 🧪🪱🌍🧬🖥️
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Ensembl @ensembl.org · 20/01/2025
Did you know our colleagues have been working tirelessly on a new #Ensembl genome browser? 🥳 Join us at this @ebi.embl.org webinar to learn more about the new browser and how to navigate it 🧬 💻 Registration is free but essential 📆 Wed, 29 Jan 2025 🕞 15:30 – 16:30 GMT 📍 Virtual ℹ bit.ly/EnsBeta
Webinar advertisement.
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Mike Brown @plutokiller.com · 17/01/2025
Just had a sample of the Eaton Fire ash that is in my driveway run on the department XRF. Is there titanium (new house paint)? Yup. Lead (old house paint)? You betcha. Heavy metals? Check. Treat that ash like it's toxic folks (because it is)
A computer screen with a display showing output from an xray diffraction spectrometer. Close up view showing fraction of metals. Fun stuff.
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Eric Topol @erictopol.bsky.social · 19/01/2025
Two new studies provide some insights on red meat intake, with respect to both potential risks and how they can be mitigated. erictopol.substack.com/p/the-update...
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Kate Watson @loreandordure.com · 19/01/2025
Accidental archive finds are The Greatest Joy.
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Ming Tommy Tang @tommytang.bsky.social · 19/01/2025
pipemake: A pipeline creation tool using Snakemake for reproducible analysis of biological datasets www.biorxiv.org/content/10....
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Pearl Freier @pearlf.bsky.social · 16/01/2025
GSK's SVP Global Head Oncology Hesham Abdullah announced a 2nd acquisition this wk—German biotech CELLphenomics. He said they're a leader in patient-derived organoids.#JPM25 #biosky www.linkedin.com/posts/hesham... "PDOs can enable the generation of 3D models that recreate a patient’s tumor 1/n
linkedin.com
Hesham A. Abdullah, MD, MSc on LinkedIn: #aheadtogether #jpm2025
At GSK, we are driven by our ambition to accelerate the discovery and development of new treatments for patients. Today, I’m pleased to announce another…
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Ming Tommy Tang @tommytang.bsky.social · 16/01/2025
Want to assign unique IDs to combinations of multiple columns in an R dataframe? Here's a quick R trick you can’t miss! 👇
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An argument for the LORD OF THE pit @jeblucas.bsky.social · 15/01/2025
Reading Midnight in Chernobyl and the best part is the discussion of what happened in the reactor and core during the active phase. The author thanks a PhD dissertation for most of this in the acknowledgments and here it is as a 60MB PDF: dspace.mit.edu/handle/1721....
dspace.mit.edu
The Chornobyl [sic] accident revisited--source term analysis and reconstruction of events during the active phase
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Nature Portfolio @natureportfolio.nature.com · 15/01/2025
A paper in Nature Medicine reports that large language models can be manipulated to generate misinformation by poisoning a small percentage of data on which they are trained and presents a harm mitigation strategy that can offer a method to address this vulnerability. #Medsky 🧪
go.nature.com
Medical large language models are vulnerable to data-poisoning attacks - Nature Medicine
Large language models can be manipulated to generate misinformation by poisoning of a very small percentage of the data on which they are trained, but a harm mitigation strategy using biomedical knowledge graphs can offer a method for addressing this vulnerability.
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Heather Shearer @heather-sea55.bsky.social · 15/01/2025
🧪 All aspects of this research are absolutely fascinating and highlights just how complex human/nature interactions can be. theconversation.com/lightning-st...
theconversation.com
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Jay Alammar @jayalammar.bsky.social · 15/01/2025
Alphaxiv is an awesome way to discuss ML papers -- often with the authors themselves. Here's an intro and demo by @rajpalleti.bsky.social we shot at #Neurips2024 www.youtube.com/watch?v=-Kwl...
youtube.com
AlphaXiv - a great place to discuss ML papers
YouTube video by Jay Alammar
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CSML IIT Lab @pontilgroup.bsky.social · 15/01/2025
1/ 🚀 Over the past two years, our team, CSML, at IIT, has made significant strides in the data-driven modeling of dynamical systems. Curious about how we use advanced operator-based techniques to tackle real-world challenges? Let’s dive in! 🧵👇
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Måns Thulin @mansthulin.bsky.social · 10/01/2025
TabPFN, published two days ago in Nature, looks like it may be the new state-of-the-art for machine learning models. It's not available in #RStats yet, but I wrote a short tutorial about how you can run it using the reticulate package: mansthulin.se/tabpfn/
mansthulin.se
Fitting TabPFN models in R using reticulate
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Francesca Grisoni @fragrisoni.bsky.social · 14/01/2025
If you use generative #DeepLearning for molecule design, check out our latest work, where we perform a large scale analysis (~1 B designs!) and find ‘traps’, ‘treasures’ and ‘ways out’ in the jungle of generative drug discovery. 🌴 🐒 Paper: arxiv.org/abs/2501.05457 Code: github.com/molML/jungle...
arxiv.org
The Jungle of Generative Drug Discovery: Traps, Treasures, and Ways Out
"How to evaluate de novo designs proposed by a generative model?" Despite the transformative potential of generative deep learning in drug discovery, this seemingly simple question has no clear answer...
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Colin Carlson @colincarlson.bsky.social · 15/01/2025
🚨😷🧪 NEW: A growing body of evidence shows that pandemics, biodiversity loss, and climate change are part of a broader polycrisis - but there are no simple solutions. A sweeping overview of "Pathogens and planetary change" for the first issue of @natrevbiodiv.bsky.social, out now 🔓 rdcu.be/d6lHl
Top panels: graphs showing increases in spillover events, extinction rates, and temperature anomalies over the last few centuries. Bottom panel: a map of 10 pandemics since the year 1900. Four were linked to agriculture, two to wildlife use, and one to climate change.
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Stephen Turner @stephenturner.us · 15/01/2025
Hard to fathom. $200M series C puts us at a $10B valuation 🦣 news.crunchbase.com/venture/de-e...
news.crunchbase.com
De-Extinction Startup Colossal Biosciences Hits Decacorn Status After $200M Raise
Colossal Biosciences, a de-extinction startup looking at ways to bring back the dodo bird and the woolly mammoth, raised a $200 million Series C at a $10.2 billion valuation.
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Christoph Fischer Photography @beautysurroundsyou.com · 15/01/2025
In a wilderness where gale force winds & furious weather reign supreme, Patagonia's mount Cerro Torre is bathed in the warm light of the rising moon, while the stars reflect beautifully in it's still waters. #photography #travel #nature #bluesky #landscape #landscapephotography #naturephotography
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Ming Tommy Tang @tommytang.bsky.social · 15/01/2025
Why every bioinformatician should master Unix commands Hint: Bioinformatics is all about text files, and Unix tools are perfect for wrangling them! Here's a quick thread on some super useful tricks 🧵👇
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Eric Topol @erictopol.bsky.social · 15/01/2025
Putting the alcohol advisory in context gift link www.nytimes.com/2025/01/13/o...
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Ming Tommy Tang @tommytang.bsky.social · 15/01/2025
A popular course on Bash scripting on Linux www.youtube.com/playlist?ap... #unix #bioinformatics
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Nick Timiraos @nicktimiraos.bsky.social · 15/01/2025
The CBO forecast sharply lower population growth in the U.S. over the next three decades than it projected one year ago, reflecting lower rates of immigration and fertility.  Deaths are expected to exceed births in 2033, seven years earlier than projected a year ago www.wsj.com/us-news/u-s-...
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Scott Hamilton @sdhamiltonvic.bsky.social · 13/01/2025
The world has been at its hottest for the past 10 years, with 2024 now declared the official record-holder. !!! #ClimateCrisis This is what 1.5 looks like. It is going to get worse!! Stop subsidising & burning fossil fuels ASAP. You too, AUS !!
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Infectious Disease Tracker @hmpxvt.bsky.social · 14/01/2025
Three more cats have been infected with H5N1 bird flu in Los Angeles, according to L.A. County Public Health. A total of 10 cats have been infected in the county, five from raw pet food and five from raw milk.
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