iiinova — where your digital self keeps evolving

Anthony Costa @anthonybcosta.bsky.social · 10/05/2025

Just released BioNeMo Framework v2.6! Check it out here: github.com/NVIDIA/bione... Particularly notable include support for AMPLIFY, with a 70% speed over the existing xformers-based attention backend (+ validation), alpha LoRA ESM, and a ton of fixes and improvements.

github.com

Release NVIDIA BioNeMo Framework v2.6 · NVIDIA/bionemo-framework

New Features Adds support for AMPLIFY doi:10.1101/2024.09.23.614603 pre-training and inference, offering a 70% speedup over the xformers-based attention backend with similar final perplexity value...

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Anthony Costa @anthonybcosta.bsky.social · 04/05/2025

Still empty. Employees seem to be having a great time.

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Anthony Costa @anthonybcosta.bsky.social · 30/04/2025

Check out new work from NVIDIA Genomics and Genentech: transcriptome-guided genomic alignment with transformer-based splice junction scoring, delivering SOTA in splice junction detection, indel identification, and resolving complex splicing patterns www.biorxiv.org/content/10.1...

biorxiv.org

DeepSAP: Improved RNA-Seq Alignment by Integrating Transcriptome Guidance with Transformer-Based Splice Junction Scoring

Advancements in high-throughput sequencing have revolutionized the field of transcriptomics, pro-viding unprecedented insights into gene expression, splicing events, and fusions. Despite these advance...

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Anthony Costa @anthonybcosta.bsky.social · 28/04/2025

Goodbye Singapore! Thanks for everything.

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Anthony Costa @anthonybcosta.bsky.social · 28/04/2025

Congratulations to Peter Holderrieth @msalbergo.bsky.social and Tommi Jaakkola for winning the best paper award for their work entitled "LEAPS: A discrete neural sampler via locally equivariant networks" at this year's Frontiers in Probabilistic Inference workshop #ICLR2025!

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Anthony Costa @anthonybcosta.bsky.social · 28/04/2025

Finally reached the limit of capability for my M1 Pro MacBook: Lightroom editing of 17 stitched 60Mp L compressed RAW.

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Anthony Costa @anthonybcosta.bsky.social · 20/04/2025

Heading to 🇸🇬 for #ICLR2025! Amazing work from our NVIDIA digital biology teams the whole week, plus a great opportunity to visit our local colleagues. Come say hi!

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Anthony Costa @anthonybcosta.bsky.social · 12/04/2025

One of my favorite flight experiences descending into Newark right now. Smooth as silk air, snow up at 1K ft flying by the window lit up by our approach lights.

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Reposted by Anthony Costa

Andrew Dunn @andrewedunn.bsky.social · 21/03/2025

“It tackles the big next step after AlphaFold 3,” Luca Naef, VantAI’s CTO, told me. I talked with CEO Zach Carpenter, @lucanaef.bsky.social Luca, and @mmbronstein.bsky.social on VantAI's most substantive update since its 2019 start. My exclusive for @endpts.com: endpts.com/exclusive-va...

endpts.com

Exclusive: Roivant-backed VantAI debuts AI model Neo-1, taking ‘the big next step’ after AlphaFold 3

VantAI unveils Neo-1, an AI model that simultaneously predicts biomolecule structures and generates new molecular glues, claiming advancement beyond AlphaFold 3's capabilities.

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Anthony Costa @anthonybcosta.bsky.social · 19/03/2025

I finally did it, a picture with the great @mmbronstein.bsky.social!! Enjoying the talk so far at #GTC2025, “Advancing Molecular Design with Deep Learning”.

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Hannes Stark @hannes-stark.bsky.social · 10/03/2025

New paper (and #ICLR2025 Oral :)): ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids arxiv.org/abs/2503.05025 Condition on your 3D layout (of ellipsoids) to generate proteins like this or to get better designability/diversity/novelty tradeoffs. 1/6

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Hannes Stark @hannes-stark.bsky.social · 09/03/2025

The Evo 2 authors join us tomorrow in the reading group to discuss their paper: "Genome modeling and design across all domains of life with Evo 2" www.biorxiv.org/content/10.1... Join on zoom (Monday) at 9am PT / 12pm ET / 6pm CET: www.biorxiv.org/content/10.1...

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Anthony Costa @anthonybcosta.bsky.social · 09/03/2025

I prefer more light later in the day and would therefore like to see DST become permanent. But mostly I just want to stop the changes.

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Anthony Costa @anthonybcosta.bsky.social · 19/02/2025

By my count, I have four different Nature accounts, and there is absolutely no way to link them all up.

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Reposted by Anthony Costa

Andrew Beam @andrewlbeam.bsky.social · 04/12/2024

We at LilaSciences are excited to come out of stealth! Join us at #NeurIPS2024 for a happy hour co-hosted with Nvidia, featuring a discussion on AI in science with Max Welling and Chris Bishop. If you’ll be at NeurIPS this year, we’d love to see you! RSVP here: lu.ma/nt1c4vf4

lu.ma

Toward Scientific Superintelligence with Lila Sciences and NVIDIA · Luma

Join Lila Sciences at NeurIPS at an exclusive event cohosted with NVIDIA to explore the transformative potential of AI in scientific discovery. Featuring a…

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Reposted by Anthony Costa

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 03/12/2024

Three BioML starter packs now! Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc Pack 3: go.bsky.app/NAKYUok DM if you want to be included (or nominate people who should be!)

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Anthony Costa @anthonybcosta.bsky.social · 02/12/2024

If @nathanbenaich.bsky.social really digs in here I might really be able to make a majority platform switch. No pressure.

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Anthony Costa @anthonybcosta.bsky.social · 02/12/2024

So many great collaborators, friends, colleagues, and #techbio leaders will be here. Unfortunately I’m going to miss the conference this year, but come find all my awesome colleagues!

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Anthony Costa @anthonybcosta.bsky.social · 02/12/2024

I feel like I’ve put together a pretty informative network of folks in AI/ML for chem, bio, genomics, materials, physics, and science generally, at least on par with what I had on Twitter. Thanks to all of you for doing the hard work up front. Don’t understand the vibe yet, but it feels exciting!

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Reposted by Anthony Costa

Christian Dallago @machine.learning.bio · 18/11/2024

GPUs are *fast* at aligning protein sequences (and profiles!). 178x faster than JackHMMER! In ColabFold, 23x faster end-to-end compared to AlphaFold2 reaching the same accuracy! You get immediate speedups for all methods leveraging MSAs, from DCA, to PoET, and even AlphaFold3!

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Anthony Costa @anthonybcosta.bsky.social · 01/12/2024

You all have done some wonderful things curating a community while I’ve been lurking. There may be some phantom me accounts lying around in ways I can’t figure out to access anymore, but this is me for real, the one from NVIDIA interested in all things computing and digital bio!

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