#Data scientist, #Researcher, Bioinformatician, Photographer, Geek & Bookworm. PhD #AI #LLM @HebrewU @HyadataLab @liniallab @shebaARC
Israel
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1/ Our paper “Protein Language Models Expose Viral Immune Mimicry” is now published in Viruses!
We show that protein Language Models can identify viral proteins, and those that fool our immune system.
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Sometimes you realize you're doing medical science and unironically opening a PR like "AI rips up the blood locus faster, missed an end of the gene"
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Our diploid aware genomic language model is out!
The genomes we train AI models on do not exist. Most genomic language models read a single haploid sequence, but human genomes are diploid.
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We introduced Contrastive Phase Loss (CPL) to make phase survive pretraining. At 100M parameters, frozen-probe cis/trans AUROC rose from 0.54 to 0.62.
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Thanks to our team across Sheba Medical Center, NVIDIA and Mount Sinai.
Want to see how we made a Nucleotide Transformer diploid? Check out our preprint: DNT: Diploid Genomic Foundation Model
biorxiv.org/content/10.64898…
Models: huggingface.co/collections/s…
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Ongoing good life habits:
1. Stop and smell the roses (other flowers border on acceptable)
2. Smile in the mirror at yourself. (Idiotic but it hacks the brain by +0.001).
3. Send a thank you after someone cites or dates or feeds you
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Dan Ofer (✈️ ICML-26 Was @Worldcon) retweeted
There is a child with a rare disease who is currently suffering and struggling to manage his symptoms. Rare as this is, you can directly help him.
Today we are launching the "Rare Disease, Real Kid" Hackathon, and there are $50,000 in prizes from @AnthropicAI and @awscloud.
We (@huggingface & @Sagebio) are helping this child open his genome and clinical data to the community, so that we can find what's caused his disease and what currently-approved drugs could help him.
I doubt I need to motivate this much further or explain how rare it is for a family to share their child's genome and clinical data, but if you're not sure, consider this:
Until very recently, it wasn't feasible for patients like this to get treatment because their disease was so rare that the economics could never justify the investment. Now, as we've seen, people with rare diseases are starting to be able to find the answers themselves (with the help of AI tools, cheaper sequencing, etc). This kid is not able to do that for himself and neither are his parents, so we're asking you for help. Both for this kid and to prove that it's possible for everyone else suffering from a rare disease.
More details in 🧵.
sagebio-rare-disease-real-ki…
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Ink spilled over #Neurips 3 reviews/rebuttals for my papers:
Characters 104,862 words 15,123
Characters 44,386 words 6,972
Characters 78,142 words 1,1861
(Fuzzed slightly for anonymity).
Doesn't count the reviews I did :)
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Pop Quiz: Is a Gene the same thing as a drug?
64%
No, Bio/med background
9%
Yes, Bio/med background
27%
No
0%
Yes
11 votes • Final results
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Dan Ofer (✈️ ICML-26 Was @Worldcon) retweeted
idk how i’m down this rabbit hole now, but do people realize this??
muslims literally don’t believe 9/11 was conducted by arab muslims. TO THIS DAY.
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Our newest paper is out!
InterFeat: An Automated Pipeline for Finding Interesting Hypotheses in Structured Biomedical Data
tl;dr: It's an automated method using AI/LLMs to find interesting features in data. Doctors reviewed them on different diseases and the UK BioBank.
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Paper: arxiv.org/abs/2505.13534
Code: github.com/LinialLab/InterFe…
This is part of my PhD in finding interesting things in Data
#science #phd #AI #huji #interfeat
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Interfeat is now published in Nature Scientific Reports (2026). doi.org/10.1038/s41598-026-4…
and got the top broad-applicability score in the ISBCB paper award (Israel's national bioinformatics society)! @michalinial @HyadataLab
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InterFeat just got the top broad-applicability score in the ISBCB paper award (Israel's national bioinformatics society)! @michalinial @HyadataLab
InterFeat helps researchers find the interesting findings in data: ones that are novel, make sense and actually useful.
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Conference and poster pics from icml @icmlconf :
You're all welcome to use my photos. I request is that you give credit/cite (Dan Ofer / @ddofer ddofer@gmail.com)
drive.google.com/drive/folde…
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Fare thee well Korea, it's been 🔥
Ps #Icml peeps, ping if I forgot to reach out or send papers, cites or pics
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