Rishal Aggarwal
@rishalchich.bsky.social
Machine Learning, Statistical Mechanics, Structural Biology. F1 and Football ⚽. PhD Student CMU-Pitt Comp Bio | IIITH | BITS Pilani
Pinned
Rishal Aggarwal
@rishalchich.bsky.social
· Mar 31
New "blogpost" from our lab, that got accepted at ICLR 2025! We compare an old MCMC method known as Sequential Monte Carlo to generative models trained on energy functions (iDEM/iEFM) and show that MCMC does better. Check it out here: rishalaggarwal.github.io/ebmvsmcmc/
Reposted by Rishal Aggarwal
Our new preprint PharmacoForge: Pharmacophore Generation with Diffusion Models is out now! PharmacoForge quickly generates pharmacophores for a given protein pocket that identify key binding features and find useful compounds in a pharmacophore search. Check it out! 🧪 doi.org/10.26434/che...
May 27, 2025 at 7:11 PM
Our new preprint PharmacoForge: Pharmacophore Generation with Diffusion Models is out now! PharmacoForge quickly generates pharmacophores for a given protein pocket that identify key binding features and find useful compounds in a pharmacophore search. Check it out! 🧪 doi.org/10.26434/che...
Reposted by Rishal Aggarwal
Happy to introduce 🔥LaM-SLidE🔥!
We show how trajectories of spatial dynamical systems can be modeled in latent space by
--> leveraging IDENTIFIERS.
📚Paper: arxiv.org/abs/2502.12128
💻Code: github.com/ml-jku/LaM-S...
📝Blog: ml-jku.github.io/LaM-SLidE/
1/n
We show how trajectories of spatial dynamical systems can be modeled in latent space by
--> leveraging IDENTIFIERS.
📚Paper: arxiv.org/abs/2502.12128
💻Code: github.com/ml-jku/LaM-S...
📝Blog: ml-jku.github.io/LaM-SLidE/
1/n
May 22, 2025 at 12:24 PM
Happy to introduce 🔥LaM-SLidE🔥!
We show how trajectories of spatial dynamical systems can be modeled in latent space by
--> leveraging IDENTIFIERS.
📚Paper: arxiv.org/abs/2502.12128
💻Code: github.com/ml-jku/LaM-S...
📝Blog: ml-jku.github.io/LaM-SLidE/
1/n
We show how trajectories of spatial dynamical systems can be modeled in latent space by
--> leveraging IDENTIFIERS.
📚Paper: arxiv.org/abs/2502.12128
💻Code: github.com/ml-jku/LaM-S...
📝Blog: ml-jku.github.io/LaM-SLidE/
1/n
Reposted by Rishal Aggarwal
Long & windy road of academic publishing! Few journal rejections and two years (!!!) after preprint, AIMNet2 paper was just published @chemsocrev.rsc.org With 69 citations to it as of now, it's immediately part of 2025 HOT🌶️ Article collection. pubs.rsc.org/en/content/a... #chemsky #compchem
April 29, 2025 at 5:54 PM
Long & windy road of academic publishing! Few journal rejections and two years (!!!) after preprint, AIMNet2 paper was just published @chemsocrev.rsc.org With 69 citations to it as of now, it's immediately part of 2025 HOT🌶️ Article collection. pubs.rsc.org/en/content/a... #chemsky #compchem
Reposted by Rishal Aggarwal
Thanks to everyone for helping make #ICLR2025 successful. 🥳 It was an honor to serve as General Chair.
The best part was using @iclr-conf.bsky.social as my personal meme account the past two years (first as Senior Program Chair). I hope that future ICLR organizers continue the tradition. 🤪
The best part was using @iclr-conf.bsky.social as my personal meme account the past two years (first as Senior Program Chair). I hope that future ICLR organizers continue the tradition. 🤪
April 28, 2025 at 10:32 AM
Thanks to everyone for helping make #ICLR2025 successful. 🥳 It was an honor to serve as General Chair.
The best part was using @iclr-conf.bsky.social as my personal meme account the past two years (first as Senior Program Chair). I hope that future ICLR organizers continue the tradition. 🤪
The best part was using @iclr-conf.bsky.social as my personal meme account the past two years (first as Senior Program Chair). I hope that future ICLR organizers continue the tradition. 🤪
Reposted by Rishal Aggarwal
Please welcome AITHYRA, the Research Institute for Artificial Intelligence of the Austrian Academy of Science on social media. Follow us and connect via Bluesky and LinkedIn 👋
April 28, 2025 at 7:44 AM
Please welcome AITHYRA, the Research Institute for Artificial Intelligence of the Austrian Academy of Science on social media. Follow us and connect via Bluesky and LinkedIn 👋
Reposted by Rishal Aggarwal
Our latest preprint is out on bioRxiv!
A collaboration between the groups of @martinsteinegger.bsky.social , David Jones and Christine Orengo, we clustered AlphaFold Database and ESMatlas, a whopping 821 million proteins!
We reveal biome-specific groups & over 11k novel domain combinations.
A collaboration between the groups of @martinsteinegger.bsky.social , David Jones and Christine Orengo, we clustered AlphaFold Database and ESMatlas, a whopping 821 million proteins!
We reveal biome-specific groups & over 11k novel domain combinations.
Metagenomic-scale analysis of the predicted protein structure universe
Protein structure prediction breakthroughs, notably AlphaFold2 and ESMfold, have led to an unprecedented influx of computationally derived structures. The AlphaFold Protein Structure Database now prov...
www.biorxiv.org
April 28, 2025 at 11:16 AM
Our latest preprint is out on bioRxiv!
A collaboration between the groups of @martinsteinegger.bsky.social , David Jones and Christine Orengo, we clustered AlphaFold Database and ESMatlas, a whopping 821 million proteins!
We reveal biome-specific groups & over 11k novel domain combinations.
A collaboration between the groups of @martinsteinegger.bsky.social , David Jones and Christine Orengo, we clustered AlphaFold Database and ESMatlas, a whopping 821 million proteins!
We reveal biome-specific groups & over 11k novel domain combinations.
Reposted by Rishal Aggarwal
Hello, we are AITHYRA!
I am very excited to share with you the corporate identity of AITHYRA, the Research Institute for Biomedical AI.
Check out the brand design video (sound on!) to learn more.
**REMINDER**
One week left to apply for Starting PI positions (Life Science and AI/ML). Come join us!
I am very excited to share with you the corporate identity of AITHYRA, the Research Institute for Biomedical AI.
Check out the brand design video (sound on!) to learn more.
**REMINDER**
One week left to apply for Starting PI positions (Life Science and AI/ML). Come join us!
We proudly present to you the #AITHYRA corporate identity, a mixture of logo, motion and sound design. Thanks to our Design Partner Studio Dumbar for a creative and joyful process, and the OeAW and BIS for giving us the confidence and trust to go new ways. More to come www.oeaw.ac.at/aithyra/news...
April 28, 2025 at 8:38 AM
Hello, we are AITHYRA!
I am very excited to share with you the corporate identity of AITHYRA, the Research Institute for Biomedical AI.
Check out the brand design video (sound on!) to learn more.
**REMINDER**
One week left to apply for Starting PI positions (Life Science and AI/ML). Come join us!
I am very excited to share with you the corporate identity of AITHYRA, the Research Institute for Biomedical AI.
Check out the brand design video (sound on!) to learn more.
**REMINDER**
One week left to apply for Starting PI positions (Life Science and AI/ML). Come join us!
Reposted by Rishal Aggarwal
"De novo prediction of protein structural dynamics"
I'll be presenting an overview of the field tomorrow at a workshop. Link to a PDF copy of the presentation: delalamo.xyz/assets/post_...
I'll be presenting an overview of the field tomorrow at a workshop. Link to a PDF copy of the presentation: delalamo.xyz/assets/post_...
delalamo.xyz
April 27, 2025 at 2:16 PM
"De novo prediction of protein structural dynamics"
I'll be presenting an overview of the field tomorrow at a workshop. Link to a PDF copy of the presentation: delalamo.xyz/assets/post_...
I'll be presenting an overview of the field tomorrow at a workshop. Link to a PDF copy of the presentation: delalamo.xyz/assets/post_...
Reposted by Rishal Aggarwal
Who is at #AACR25? I’m here representing my group’s work at the intersection of AI and drug resistance in cancer, and want to hear about what you’re doing!(1/4)
April 28, 2025 at 1:27 PM
Who is at #AACR25? I’m here representing my group’s work at the intersection of AI and drug resistance in cancer, and want to hear about what you’re doing!(1/4)
@iclr-conf.bsky.social blog posts are now live at iclr-blogposts.github.io/2025/blog! Unfortunately I won't be able to present our blog post at the conference in person 😔, but I am happy to chat about it online if you find it interesting! Poster attached 🙂.
April 23, 2025 at 10:17 PM
@iclr-conf.bsky.social blog posts are now live at iclr-blogposts.github.io/2025/blog! Unfortunately I won't be able to present our blog post at the conference in person 😔, but I am happy to chat about it online if you find it interesting! Poster attached 🙂.
New "blogpost" from our lab, that got accepted at ICLR 2025! We compare an old MCMC method known as Sequential Monte Carlo to generative models trained on energy functions (iDEM/iEFM) and show that MCMC does better. Check it out here: rishalaggarwal.github.io/ebmvsmcmc/
March 31, 2025 at 4:57 PM
New "blogpost" from our lab, that got accepted at ICLR 2025! We compare an old MCMC method known as Sequential Monte Carlo to generative models trained on energy functions (iDEM/iEFM) and show that MCMC does better. Check it out here: rishalaggarwal.github.io/ebmvsmcmc/
New paper at the turn of the new year :)
Check out our latest paper on using reinforcement learning for pharmacophore elucidation on protein binding sites. It comes with a google colab notebook for use.
bmcbiol.biomedcentral.com/articles/10....
Check out our latest paper on using reinforcement learning for pharmacophore elucidation on protein binding sites. It comes with a google colab notebook for use.
bmcbiol.biomedcentral.com/articles/10....
PharmRL: pharmacophore elucidation with deep geometric reinforcement learning - BMC Biology
Background Molecular interactions between proteins and their ligands are important for drug design. A pharmacophore consists of favorable molecular interactions in a protein binding site and can be ut...
bmcbiol.biomedcentral.com
January 3, 2025 at 7:54 PM
New paper at the turn of the new year :)
Check out our latest paper on using reinforcement learning for pharmacophore elucidation on protein binding sites. It comes with a google colab notebook for use.
bmcbiol.biomedcentral.com/articles/10....
Check out our latest paper on using reinforcement learning for pharmacophore elucidation on protein binding sites. It comes with a google colab notebook for use.
bmcbiol.biomedcentral.com/articles/10....
Reposted by Rishal Aggarwal
Last week several of our students presented their research at NeurIPS 2024 in Vancouver. We are so proud of the excellent work that they've accomplished and shared with the scientific community! 🧪
Check out each of their papers below:
Check out each of their papers below:
December 19, 2024 at 6:51 PM
Last week several of our students presented their research at NeurIPS 2024 in Vancouver. We are so proud of the excellent work that they've accomplished and shared with the scientific community! 🧪
Check out each of their papers below:
Check out each of their papers below:
Reposted by Rishal Aggarwal
AlphaFold3 still tends to overfit regions that AF2 multimer predicts to be disordered. Almost all disordered regions become helices in AF3.
December 15, 2024 at 2:03 AM
AlphaFold3 still tends to overfit regions that AF2 multimer predicts to be disordered. Almost all disordered regions become helices in AF3.
Reposted by Rishal Aggarwal
Going into @workshopmlsb.bsky.social , a few thoughts on the PLINDER dataset. This is a monumental and highly appreciated undertaking for extracting protein-ligand interactions from the PDB. First the good...
December 15, 2024 at 6:52 PM
Going into @workshopmlsb.bsky.social , a few thoughts on the PLINDER dataset. This is a monumental and highly appreciated undertaking for extracting protein-ligand interactions from the PDB. First the good...
Reposted by Rishal Aggarwal
I'm presenting a new paper "Exploring Discrete Flow Matching for 3D De Novo Molecule Generation" at @workshopmlsb.bsky.social this week! More info in this thread but reach out if want to chat at NeurIPS about generative models or molecular design. arxiv.org/abs/2411.16644
December 11, 2024 at 9:21 PM
I'm presenting a new paper "Exploring Discrete Flow Matching for 3D De Novo Molecule Generation" at @workshopmlsb.bsky.social this week! More info in this thread but reach out if want to chat at NeurIPS about generative models or molecular design. arxiv.org/abs/2411.16644
Reposted by Rishal Aggarwal
More excellent work from the indomitable @ian-dunn.bsky.social Come check it out at @workshopmlsb.bsky.social
I'm presenting a new paper "Exploring Discrete Flow Matching for 3D De Novo Molecule Generation" at @workshopmlsb.bsky.social this week! More info in this thread but reach out if want to chat at NeurIPS about generative models or molecular design. arxiv.org/abs/2411.16644
December 11, 2024 at 10:20 PM
More excellent work from the indomitable @ian-dunn.bsky.social Come check it out at @workshopmlsb.bsky.social
Reposted by Rishal Aggarwal
Excited about BioEmu?
Opening this position for just a few days over #NeurIPS2024. Looking especially for Bioinformatics + Structural Biology skills, MD/Stat Mech skills and/or #deeplearning architecture design + engineering skills
aka.ms/ai4science-r...
Opening this position for just a few days over #NeurIPS2024. Looking especially for Bioinformatics + Structural Biology skills, MD/Stat Mech skills and/or #deeplearning architecture design + engineering skills
aka.ms/ai4science-r...
December 11, 2024 at 9:20 PM
Excited about BioEmu?
Opening this position for just a few days over #NeurIPS2024. Looking especially for Bioinformatics + Structural Biology skills, MD/Stat Mech skills and/or #deeplearning architecture design + engineering skills
aka.ms/ai4science-r...
Opening this position for just a few days over #NeurIPS2024. Looking especially for Bioinformatics + Structural Biology skills, MD/Stat Mech skills and/or #deeplearning architecture design + engineering skills
aka.ms/ai4science-r...
Reposted by Rishal Aggarwal
Our paper describing our winning submission (tied with @olexandr.bsky.social) is out with some extra computational analysis of the predicted binding modes. We didn't do anything fancy (but the hits weren't that great either...).
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
CACHE Challenge #1: Docking with GNINA Is All You Need
We describe our winning submission to the first Critical Assessment of Computational Hit-Finding Experiments (CACHE) challenge. In this challenge, 23 participants employed a diverse array of structure...
pubs.acs.org
December 10, 2024 at 12:26 PM
Our paper describing our winning submission (tied with @olexandr.bsky.social) is out with some extra computational analysis of the predicted binding modes. We didn't do anything fancy (but the hits weren't that great either...).
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
Reposted by Rishal Aggarwal
do not assess & compare their methods on fair footing & in a meaningful way
For good or for bad, in the end, BLINDED COMMUNITY CHALLENGES are the only fair way to assess methods
Meaning: the proof is in the pudding. The methods who want to be taken seriously should ...
For good or for bad, in the end, BLINDED COMMUNITY CHALLENGES are the only fair way to assess methods
Meaning: the proof is in the pudding. The methods who want to be taken seriously should ...
December 9, 2024 at 3:46 AM
do not assess & compare their methods on fair footing & in a meaningful way
For good or for bad, in the end, BLINDED COMMUNITY CHALLENGES are the only fair way to assess methods
Meaning: the proof is in the pudding. The methods who want to be taken seriously should ...
For good or for bad, in the end, BLINDED COMMUNITY CHALLENGES are the only fair way to assess methods
Meaning: the proof is in the pudding. The methods who want to be taken seriously should ...
Reposted by Rishal Aggarwal
We're looking forward to presenting this @workshopmlsb.bsky.social . This work was conceived and led by a group CPCB (@cmupittcompbio.bsky.social) students and learns a co-embedding of proteins and ligands to support ultra fast virtual screening. arxiv.org/pdf/2411.15418
November 26, 2024 at 1:28 PM
We're looking forward to presenting this @workshopmlsb.bsky.social . This work was conceived and led by a group CPCB (@cmupittcompbio.bsky.social) students and learns a co-embedding of proteins and ligands to support ultra fast virtual screening. arxiv.org/pdf/2411.15418