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Hamed Shirzad

@hamedshirzad.bsky.social
851 followers 432 following 40 posts

PhD student in Computer Science at UBC | Exploring Machine Learning on Graphs www.hamedshirzad.com

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Hamed Shirzad @hamedshirzad.bsky.social · 31/08/2025
Enjoyed giving our tutorial on Geometric & Topological Deep Learning at IEEE MLSP 2025 alongside @semihcanturk.bsky.social. Loving the Istanbul vibes and the amazing food here! ✅
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Valence Labs @valenceai.bsky.social · 22/05/2025
1/ Introducing TxPert: a new model that predicts transcriptional responses across diverse biological contexts It’s designed to generalize across unseen single-gene perturbations, novel combinations of gene perturbations, and even new cell types 🧵 www.valencelabs.com/txpert-predi...
valencelabs.com
TxPert: Predicting Cellular Responses to Unseen Genetic Perturbations - Valence Labs
We introduce TxPert: a state-of-the-art model that leverages multiple biological knowledge networks to accurately predict transcriptional responses under OOD scenarios.
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Valence Labs @valenceai.bsky.social · 20/05/2025
1/ At Valence Labs, @recursionpharma.bsky.social's AI research engine, we’re focused on advancing drug discovery outcomes through cutting-edge computational methods Today, we're excited to share our vision for building virtual cells, guided by the predict-explain-discover framework 🧵
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Hamed Shirzad @hamedshirzad.bsky.social · 21/05/2025
Loved working on the TxPert project! It's also exciting to see my PhD work on Graph Transformers (Exphormer model) finding such meaningful application in a critical real-world task.
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Hamed Shirzad @hamedshirzad.bsky.social · 23/04/2025
Huge congrats to my labmate @joshuaren.bsky.social and my supervisor @djsutherland.ml for receiving an Outstanding Paper Award at @iclr-conf.bsky.social for their work: "Learning Dynamics of LLM Finetuning" 🏆 So proud to see their amazing research recognized! 👏🔥 blog.iclr.cc/2025/04/22/a...
blog.iclr.cc
Announcing the Outstanding Paper Awards at ICLR 2025 – ICLR Blog
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Hamed Shirzad @hamedshirzad.bsky.social · 12/12/2024
As a reminder, we will have our poster session tomorrow: 📍 East Exhibit Hall, Poster #3010 📄 arxiv.org/abs/2411.16278 💻 github.com/hamed1375/Sp... To motivate you further, we have some insights gained from the attention score analysis of this work, which I'll share in this thread:
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Michael Bronstein @mmbronstein.bsky.social · 09/12/2024
After two years, our paper on generative models for structure-based drug design is finally out in @natcomputsci.bsky.social www.nature.com/articles/s43...
nature.com
Structure-based drug design with equivariant diffusion models - Nature Computational Science
This work applies diffusion models to conditional molecule generation and shows how they can be used to tackle various structure-based drug design problems
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Hamed Shirzad @hamedshirzad.bsky.social · 05/12/2024
Graph Transformers (GTs) can handle long-range dependencies and resolve information bottlenecks, but they’re computationally expensive. Our new model, Spexphormer, helps scale them to much larger graphs – check it out at NeurIPS next week, or the preview here! [1/13] #NeurIPS2024
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logconference.bsky.social @logconference.bsky.social · 29/11/2024
✨ Top Reviewers of LoG 2024 ✨ Thank you to our incredible reviewers who went above and beyond to provide thoughtful and constructive feedback! 🙏 👏 Your efforts are the backbone of LoG’s success!
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Hamed Shirzad @hamedshirzad.bsky.social · 28/11/2024
Had a great time attending the @logconference.bsky.social meetup in Vancouver! Big thanks to the organizers, Renjie Liao and Oliver Schulte!
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NeurIPS Conference @neuripsconf.bsky.social · 22/11/2024
NeurIPS Conference is now Live on Bluesky! -NeurIPS2024 Communication Chairs
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Hamed Shirzad @hamedshirzad.bsky.social · 21/11/2024
Our new preprint is out! 🚀 I’ll be presenting this work at the Machine Learning and Compression Workshop @ NeurIPS 2024. The research is still ongoing, and we’re working on deeper theoretical results. Stay tuned for a thread on our findings so far—coming soon! arxiv.org/abs/2411.13028
arxiv.org
A Theory for Compressibility of Graph Transformers for Transductive Learning
Transductive tasks on graphs differ fundamentally from typical supervised machine learning tasks, as the independent and identically distributed (i.i.d.) assumption does not hold among samples. Instea...
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 18/11/2024
Two BioML starter packs now: Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc DM if you want to be included (or nominate people who should be!)
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Clément Canonne @ccanonne.github.io · 18/11/2024
Periodic reminder: submitting on #arXiv is great! But the source is available: good per se, but remember to remove LaTeX comments you don't want to be made public. Thankfully, there are tools that do that (and more) easily and automatically for you! E.g., arXiv-collector: github.com/djsutherland...
github.com
GitHub - djsutherland/arxiv-collector: A little Python script to collect LaTeX sources for upload to the arXiv.
A little Python script to collect LaTeX sources for upload to the arXiv. - djsutherland/arxiv-collector
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ICLR Conference @iclr-conf.bsky.social · 16/11/2024
Hello World!
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Hamed Shirzad @hamedshirzad.bsky.social · 16/11/2024
Bluesky feels just like the good old days of Twitter!
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Kimon Fountoulakis @kfountou.bsky.social · 16/11/2024
Here is an initial starter pack list on Machine Learning on Graphs: go.bsky.app/HN2MTzp
go.bsky.app
Machine Learning on Graphs
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