Seva Viliuga
@_ncyxx
PhD candidate in bioinformatics / Protein design / Protein structure prediction
1/6 One of the key features of functional proteins is their inherent structural flexibility. In our recent work at @icmlconf, we introduce flexibility to protein structure design. Our model FliPS generates protein structures with custom per-residue flexibilities as validated by…
finally!! did the alnTM-score mistake myself...
We have a pretty extensive discussion about this in our paper. We further recomputed a lot of the numbers reported in our prior work with the correct FoldSeek implementation. Have a read here: biorxiv.org/content/10.110…
The Geometric Deep Learning textbook: Chapter 5 - Graphs In multiple branches of science, from sociology to particle physics,graphs are a fundamental model of systems of relations and interactions. Graphs give rise to a basic type of symmetry modelled by the group…
ICML travel grants for PhD students in the US whose funding was cut: lnkd.in/e3PdJyuQ
I finally won a lottery and got the CA visa?! Something must be wrong.. Guess that means me + ICML 2025!
At 15, I left all my family and friends and came to the US , ALONE, seeking a country where MERIT and HARD WORK mattered-not politics. For 30 years, I worked tirelessly, even doing reseach at MIT the day my mother died, knowing she’d want me to keep pushing forward. Today, my…
What could Alphafold 4 look like? (Sergey Ovchinnikov, Ep #3) 2 hours listening time (links below) To those in the (machine-learning for protein design) space, Dr. Sergey Ovchinnikov (@sokrypton) is a very, very well-recognized name. A recent MIT professor (circa early…
Any billionaires with no idea what to do w/ their 💰 money? This could be your chance to stop the death of science, technically and innovation in America. Lots of PhD programs are being cancelled or reduced significantly in size across America... 🫣 wbur.org/news/2025/03/1…
When I open the news every morning I am getting the feeling I am watching a bad version of Star Wars. And there is are more than one Darth Vaders in this series. Still searching for Luke Skywalker.
What in the world have we been watching yesterday…
This is disgrace … this bullying, this arrogance of Vance and Trump attacking the most courageous man on earth …we can be happy that Roosevelt and not Trump was American President in 1941…otherwise we still lived in Europe under a Nazi regime…
Extending the RANGE of Graph Neural Networks: Relaying Attention Nodes for Global Encoding Virtual nodes introduced that pass information via attention; reduces oversquashing; improves GNN on molecules; MD22!! P: arxiv.org/abs/2502.13797
Sparse all-atom denoising models for protein backbone generation are fast and can generate designable structures up to 1000 residues. @MJendrusch
Can one model generalize to unseen graphs with arbitrary feature and label spaces? 📢 Introducing GraphAny #ICLR25: A fully-inductive model for node classification. 🚀 Trained on one graph, GraphAny generalizes to any unseen graph. 📎 Paper: openreview.net/pdf?id=1Qpt43c… 1/🧵
I'm super excited to share my recent work with @grocklin “Structural and energetic analysis of stabilizing indel mutations” biorxiv.org/content/10.110…. 1/8