
Biomedical Data Science PhD student @Stanford
Joined September 2020
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Jake Silberg retweeted
Very excited to release ProVADA! It was so much fun working with the incredible @Xiaowei0402, @sluu_06, and the rest of the team. Check out Xiaowei's thread for more details!
Jake Silberg retweeted
We deimmunized a clinical CD19 CAR binder with experimentally detected HLA-I epitope depletion while retaining tumor killing, and rescued a secreted protease to function in the cytosol.
Both done with one unified design framework: ProVADA.
How it works and what we tested 🧵 (1/11)
Jake Silberg retweeted
Excited to see this work led by @sean_n_wu out.
In our lab with @james_y_zou, we have been interested in what the future of agent collaboration will need to be useful and safe. The first important step is understanding when and how models are good (or not!) as collaborators.
We take a step towards this with our Collaborative Intelligence benchmark:
Last month, 10,000 OpenAI agents cracked a $1M Millennium Prize problem together.
We found OpenAI models are also the best overall teammates.
Introducing 🐟 the Collaborative Intelligence Benchmark, measuring how well AI models work as teammates. 🧵
Jake Silberg retweeted
AI-generated scientific output is scaling beyond available human review capacity. Scaling scientific discovery requires scaling verification.
We introduce OSVerify, a framework for one-sided verification: rejecting as many invalid solutions as possible while preserving rare valid ones for expert review.
We used OSVerify to referee 11 recent OpenAI math preprints, identifying 5 major and 13 minor issues, all verified by human experts.
Our key insight: checking a proposed error can be easier than judging an entire solution. Instead of directly judging solution correctness, OSVerify decouples verification into error proposal (searching for potential errors) and error validation (checking whether they are real and substantial).
On competition and research mathematical benchmarks, OSVerify reduces invalid solutions requiring expert review by 46% on average compared to voting under the same low-FNR constraint, or 57% with an RL-trained validator.
Verification can also guide discovery. OSVerify can be integrated into existing scientific discovery workflows. Paired with an agentic math solver, it helped resolve 3 open conjectures in the Langlands program and contributed to resolving the Manin constant conjecture. All proofs were confirmed by mathematicians.
Our broader goal is to provide verification-based evaluation signals for scientific discovery, enabling test-time scaling and self-improvement even when reliable automatic evaluators are unavailable.
Project: osverify.github.io/
Paper: osverify.github.io/assets/pa…
GitHub: github.com/OSVerify
[1/n]
Jake Silberg retweeted
We created AI Sleep Co-Scientist to analyze 1M hours of rich, multimodal sleep recordings.
It discovered many new insights into human physiology:
🧠weaker brain–heart coupling predicts neurodegenerative diseases
🕑sleep "age" associated w/ health risks across multiple organs
😴distinct arousal characterizes comorbid insomnia/apnoea
+ more!
arxiv.org/abs/2607.25175
Awesome collaboration w/ Emmanuel Mignot’s group, led by @connect_thapa!
Jake Silberg retweeted
We had Qwen 3.8 study all of the docs in Harvey’s synthetic law firm - the more it studies, the fewer tokens it needs at inference time to respond to the queries
Jake Silberg retweeted
Very grateful for the opportunity to visit @broadinstitute and speak at @Schmidt_Center about our work on The Virtual Biotech. Many thanks to EWSC Director @CarolineUhler for the invitation to speak and @orrashenberg for organizing! And, always grateful to @james_y_zou for his support.
Rather than asking what a single AI agent can do, we’ve been asking a different question: What becomes possible when thousands of AI agents are organized into a scientific team — with distinct expertise, tools, review mechanisms, and leadership — much like a biotech R&D organization?
The talk covers our progress toward that vision and applications across therapeutic discovery and development. Recording below 👇
@StanfordDBDS @StanfordAILab @StanfordMed
New recording: our summer visitor @harrison_zhang (MD-PhD, @Stanford) on "The Virtual Biotech: A Multi-Agent AI Framework for Therapeutic Discovery and Development."
📺: youtu.be/jd3zHAw_S4Y
@broad_institute #AI #DrugDiscovery #Biotech
Jake Silberg retweeted
So what can you do with ENCODE GRAMMAR?
While we’ve shown the ability of one s2f model, ENCODE GRAMMAR brings a new dimension, layering multiple models across cell type & modality.
To illustrate, we showcase an example locus: MYC (also our main fig in the ENCODE 4 preprint) 1/
Jake Silberg retweeted
Finally… Excited to share what I’ve been working on for the first half of my PhD!
ENCODE GRAMMAR: One of the largest collections of regulatory DNA seq2func models to date (3,865 in total) trained across ENCODE, with full model interpretations and annotations tracks. 1/n
Jake Silberg retweeted
This week's feature in @CircAHA on agentic and generative AI for drug discovery is landing exactly how it should — real conversation, right out of the gate.
@james_y_zou and colleagues break down a genuinely complicated topic in clear terms. Extremely exciting, and extremely relevant to cardiovascular medicine.
Congrats to the whole team. This is what translational science should look like. 🫀
@JakeSilberg @American_Heart | #Circulation #AIinMedicine

ALT Circulation journal cover beside a graphic reading 'This Week in Circulation: Agentic & Generative AI for Drug Discovery' by Jake Silberg, Peter Eckmann, Joseph Boen, and James Zou, with a three-panel diagram illustrating AI-assisted drug target selection, therapeutic design, and clinical trial recruitment.
Happy to share our new @CircAHA article discussing agentic and generative AI for drug discovery💊 ahajournals.org/doi/full/10.…
Great job @JakeSilberg Peter Eckmann, Joseph Boen! Also thanks to @bradleymaronmd for helpful guidance.
Jake Silberg retweeted
Happy to share our new @CircAHA article discussing agentic and generative AI for drug discovery💊 ahajournals.org/doi/full/10.…
Great job @JakeSilberg Peter Eckmann, Joseph Boen! Also thanks to @bradleymaronmd for helpful guidance.
Jake Silberg retweeted
They died serving our country. They should be honored, not erased.
Lt. Tyler James Feehan, 25, of Hawaii
Pvt. Isabella Gonzales, 19, of Texas
Sgt. Angel Rampersad, 28, of New York
Sgt. Michael Emmanuel Swinton, 30, of North Carolina
Adding 70 units of housing in 3 weeks!
Jake Silberg retweeted
Really cool to see SynthMol-RL featured on the cover of @MolSystBiol!
Reinforcement learning makes small-molecule drug discovery more effective and easier to synthesize.
Paper: link.springer.com/article/10…
Code: github.com/swansonk14/Synthe…
Awesome collaboration w/ @ItsJonStokes lab led by @KyleWSwanson and Gary Liu
Congrats @bviggiano_13 and the Proto team on the launch of this amazing project for making bio models much easier to use and deploy!
Performing bioinformatics analysis and building biological design pipelines can mean a lot of infrastructure fighting: fragmented tools, idiosyncratic formats, and APIs that are hard to compose. That friction slows researchers down, and as this Anthropic blog post lays out, it's now a major bottleneck for modern agents as well.
Today, we're releasing Proto, a design platform for generative biology. This thread is on the layer that makes it work: proto-tools, a universal open-source infrastructure layer for biological models and tools.
Jake Silberg retweeted
Our lab is looking for a (junior) research technician to help accelerate several exciting projects in the lab, including our preclinical assessment of AI-designed biologics, single-cell technology development, and structure/function of viral proteins. jobrxiv.org/job/memorial-slo…
Super cool SAE work by @ElanaPearl! Excited to see how this enables more interp research in bio models
Jake Silberg retweeted
🚀 Today, we’re excited to introduce SimpleTES for scaling the scientific discovery loop.
🧵 I always ask myself: what are we actually scaling in scientific discovery?
Most LLM discovery methods focus on test-time scaling generation — more tokens, more agents, more turns.
But science advances through the evaluation-driven loops: propose → evaluate → refine → repeat.
SimleTES captures this idea, discovering SOTA solutions across 21 scientific problems!
Key discoveries:
🏎️ 2.17x faster lasso solver than glmnet — the gold-standard LASSO solver, engineered for decades.
⚛️ 24.5% fewer quantum routing overhead on IBM Q20 — superior than previous standard library LightSABRE.
📐 0.380868 on Erdős Minimum Overlap — outperforming previous solutions from mixed-frontier ensembles or humans.
🧬 0.74 on Tabula Muris (scRNA-seq denoising) — new SOTA, generalizing to unseen tissue types without retraining.
#LLM #AI4Science #ScalingLaws #SimpleTES #MachineLearning
Jake Silberg retweeted
In AI for scientific discovery, the bottleneck isn't always generation — it's quite often evaluation. How do you design evaluators close to gold? Prevent reward hacking? And critically, how do you scale the evaluation-driven loop to reach genuinely novel discoveries?
🚀 Today, we’re excited to introduce SimpleTES for scaling the scientific discovery loop.
🧵 I always ask myself: what are we actually scaling in scientific discovery?
Most LLM discovery methods focus on test-time scaling generation — more tokens, more agents, more turns.
But science advances through the evaluation-driven loops: propose → evaluate → refine → repeat.
SimleTES captures this idea, discovering SOTA solutions across 21 scientific problems!
Key discoveries:
🏎️ 2.17x faster lasso solver than glmnet — the gold-standard LASSO solver, engineered for decades.
⚛️ 24.5% fewer quantum routing overhead on IBM Q20 — superior than previous standard library LightSABRE.
📐 0.380868 on Erdős Minimum Overlap — outperforming previous solutions from mixed-frontier ensembles or humans.
🧬 0.74 on Tabula Muris (scRNA-seq denoising) — new SOTA, generalizing to unseen tissue types without retraining.
#LLM #AI4Science #ScalingLaws #SimpleTES #MachineLearning
Jake Silberg retweeted
Extremely excited about the results of @adaptyvbio RBX1 binder design competition! 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕2 performed very well, with 3 out of 7 designs binding to the disordered tail. Overall, only 9 binders worked out of 322 tested, 2.8% hit rate! Proud of the BC2 team ♥️




































