Zuobai Zhang @Oxer22
Ph.D. student at @Mila_Quebec. Interested in graph representation learning, drug discovery and protein science. oxer11.github.io Montreal, Quebec Joined September 2021-
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ICML will be 🔥🔥🔥: Our workshop for ML for Life and Material Science: From Theory to Industry Applications is happening! Stay tuned for further announcements!
🤔 Can we teach LLMs to understand protein sequences? 🧬 Introducing ProtLLM, a versatile cross-modal LLM that bridges the gap between natural language and protein. Paper: arxiv.org/abs/2403.07920 Page: protllm.github.io/project/ 1/🧵
🚀Check our latest work on protein conformation generation!
🚀Check our latest work on protein conformation generation!
Excited to share our latest work with our Mila collaborators Yangtian Zhang (@IIAppleII6), Zuobai Zhang (@Oxer22), Bozitao Zhang and Jian Tang (@tangjianpku ) on predicting protein side-chain packing using autoregressive diffusion model that has been accepted at NeurIPS'23!
Excited to share our latest work with our Mila collaborators Yangtian Zhang (@IIAppleII6), Zuobai Zhang (@Oxer22), Bozitao Zhang and Jian Tang (@tangjianpku ) on predicting protein side-chain packing using autoregressive diffusion model that has been accepted at NeurIPS'23!
I’ll be attending #NeurIPS2023 next week to present our work SiamDiff and DiffPack. Please feel free to reach out if you want to chat about AI4Science, geometric deep learning, and generative models!
That's why we always love DeepMind🚀! Utilize those research skills in your hobby! Absolutely fantastic!😍 Though I'd rather like to see more analysis for @ManCity as a Citezen😜
That's why we always love DeepMind🚀! Utilize those research skills in your hobby! Absolutely fantastic!😍 Though I'd rather like to see more analysis for @ManCity as a Citezen😜
🔥Interested in Geometric Deep Learning and Generative Models for Drug Discovery? Join my research group at Mila, with opportunities collaborating with top researchers in both AI and Biological communities. Deadline: December, 1st.
🔥Interested in Geometric Deep Learning and Generative Models for Drug Discovery? Join my research group at Mila, with opportunities collaborating with top researchers in both AI and Biological communities. Deadline: December, 1st.
Another #NeurIPS2023 paper on protein side-chain packing🚀 Nice collaboration with Yangtian and Intel😍
Another #NeurIPS2023 paper on protein side-chain packing🚀 Nice collaboration with Yangtian and Intel😍
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✈️ Heading off to Vienna for #ICLR2024 for May 5th-10th (15h flight included). We'll be presenting ULTRA (the first foundation model for graph reasoning) with @zhu_zhaocheng on Wednesday. Reach out to talk about graph learning :)
Coming up on 3 years at Genentech and I continue to be impressed by the quality of science and engineering our team has cultivated. Lab-in-the-Loop as a conceptual framework for tethering the experimental to the computational sounds deceivingly simply but...
We're excited to have 4 papers accepted at #ICML2024! 1⃣ "Structure-based drug design by denoising voxel grids" @pedroopinheiro, @arian_jamasb, @omarnmahmood, @VishnuSresht, Saeed Saremi (Preprint coming soon!)
We're excited to have 4 papers accepted at #ICML2024! 1⃣ "Structure-based drug design by denoising voxel grids" @pedroopinheiro, @arian_jamasb, @omarnmahmood, @VishnuSresht, Saeed Saremi (Preprint coming soon!)
MLPs are so foundational, but are there alternatives? MLPs place activation functions on neurons, but can we instead place (learnable) activation functions on weights? Yes, we KAN! We propose Kolmogorov-Arnold Networks (KAN), which are more accurate and interpretable than MLPs.🧵
A new update to DiffDock-L with significantly reduced inference-time memory requirement is now live on GitHub and @huggingface! Credit for the update to Jacob Silterra! GitHub: github.com/gcorso/DiffDock HuggingFace Space: huggingface.co/spaces/reginab…
@arthurdeng0205 @nickpolizzi_ @BarzilayRegina Finally, thanks to the amazing help of Jacob Silterra and the grant from @huggingface (thx @_akhaliq!) you can now use the new version of DiffDock-L directly on Hugging Face for free! huggingface.co/spaces/reginab…
Accepted to #ICML. Why do ICLR and ICML have to both be in Vienna 🙃
Combining discrete and continuous data is an important capability for generative models. To address this for protein design, we introduce Multiflow, a generative model for structure and sequence generation. Preprint: arxiv.org/abs/2402.04997 Code: github.com/jasonkyuyim/mu… 1/8
Could agents driven by powerful language models perform machine learning experimentation effectively? Our MLAgentBench paper is updated on arxiv! arxiv.org/pdf/2310.03302 Now we include more results from claude v3 Opus, gpt4 turbo, mixtral and gemini pro! Try out MLAgentbench…
Thrilled to release 🌟STaRK 🌟 - A large-scale LLM retrieval benchmark on semi-structured knowledge bases. While LLMs excel at reasoning and semantic retrieval, they struggle with more complex tasks. Especially when real-world user queries require a combination of unstructured…
How to steer generative antibody design models to design antibodies satisfying user-desired preferences, such as rationality and functionality🤔? We are thrilled to introduce AbDPO, a general framework for antibody design via energy-based preference optimization. The preprint,…
Excited to present perturb-seq-in-the-loop in #RECOMB2024 next Tuesday at 2pm!! Looking forward to being back in Boston!
1/🧵Introducing Perturb-seq-in-the-loop: a sequential experimental design strategy for perturbation screens guided by multimodal priors, with 3X speedup over state-of-the-art active learning methods! With amazing @_romain_lopez_ @jchuetter Taka Kudo @antonio_science Aviv Regev
Foldseek-Multimer is a protein complex aligner that is up to 10,000x times faster than SOTA methods without sacrificing quality, enabling the comparison of billions of complex pairs per day. 1/5 📄 biorxiv.org/content/10.110… 💾 github.com/steineggerlab/… 🌐 search.foldseek.com
Not a lie: this was said about me today. I feel so seen, for the first time in my messy italian 🤌🏻🤌🏻 existence. And yes, the ML4LMS workshop stuff's coming about nicely. Website to go live in 3, 2,... Prepare your typewriters, or whatever people use to write papers nowadays!
🚨Excited to introduce ConfDiff for protein conformation generation! Background: Protein folding can be likened to text-to-image generation, while protein conformation generation is akin to text-to-video generation. For protein folding, notable methods include AlphaFold,…
1/ Proteins exhibit a dynamic nature. We stand by the belief that steering with physical knowledge is vital in real-world dynamic structure prediction, and we're delighted to introduce our force-guided diffusion model for generating protein conformations. arxiv.org/abs/2403.14088
New review on diffusion models for protein structures and docking! It has been crazy to see this field develop in the past 2 years, we tried to shed light on the different ideas and design choices that have emerged!
Our review on diffusion models for protein structures and docking is out @HannesStaerk @GabriCorso Bowen Jing @BarzilayRegina Tommi Jaakkola. This summarize the advancements up to 2023. There have been lots of exciting new works since! wires.onlinelibrary.wiley.com/doi/10.1002/wc…
Our review on diffusion models for protein structures and docking is out @HannesStaerk @GabriCorso Bowen Jing @BarzilayRegina Tommi Jaakkola. This summarize the advancements up to 2023. There have been lots of exciting new works since! wires.onlinelibrary.wiley.com/doi/10.1002/wc…
I'm delighted to share that our TacticAI paper has been featured as a highlighted paper by the Editors of @NatureComms 🎉🥳⚽🌐 nature.com/collections/hj… @zhexwang @weballergy @yorambac @demishassabis @karl_tuyls
What makes a good cell embedding🧬? Is a higher score always better? Not quite! In this new preprint with @jure & #Aviv, we ... [1/3] biorxiv.org/content/10.110…
The US immigration system makes it incredibly hard for international scientists to stay and thrive. People often mention the existence of visas like EB-1 for talented individuals, but as a PhD student, I would have to spend 12-18 months without leaving the US for the process...
I strongly believe that the U.S. is at its best when it brings in talented scientists and engineers from all over the world to study, to be hired into companies to push forward our most advanced science and engineering efforts, and to start new U.S.-based companies. We should…
And'Pivotal', 'intricate', 'realm', 'showcasing' ... on arXiv preprints too🚨 🚨 New paper alert! 🚨 📊🔬Mapping the Increasing Use of LLMs in Scientific Papers 🤖📝 Check it out ➡️ arxiv.org/pdf/2404.01268… #Science #AI #ChatGPT #arXiv #LLM
Are medical studies being written with ChatGPT? Well, we all know ChatGPT overuses the word "delve". Look below at how often the word 'delve' is used in papers on PubMed (2023 was the first full year of ChatGPT).
Single Cell Genomics Day starts tomorrow at 10AM ET! Come for the awesome keynotes (@JD_Buenrostro , Xiaowei Zhuang, @IdoAmitLab) and to learn about our favorite new methods and trends for the field in the last year. All talks streamed on Youtube and satijalab.org/scgd
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