Sign in

Jose Arjona-Medina

@arjonamedina.bsky.social
1.3K followers 186 following 16 posts

AI/ML Principal Scientist at J&J External lecturer at Johannes Kepler University Linz, Austria Drug Discovery | Deep Learning | RL www.arjonamedina.com

PostsRepliesMedia
Jose Arjona-Medina @arjonamedina.bsky.social · 01/03/2025
(5/5) Perhaps I'm overlooking something-open to your insights 😀
000
Jose Arjona-Medina @arjonamedina.bsky.social · 01/03/2025
(4/5) However, what we see in DeepSeek's formulation is that 1) there is no sequence of actions, and 2) the reference policy remains the same. I don't see the credit assignment mechanism from future rewards to current actions in this formulation, which is the key factor in RL.
100
Jose Arjona-Medina @arjonamedina.bsky.social · 01/03/2025
(3/5) Because this objective is difficult to compute (there are two distributions from two different policies involved) a constrain on how far these two policies can be is included so we can just "ignore" this mismatch.
100
Jose Arjona-Medina @arjonamedina.bsky.social · 01/03/2025
(2/5) In TRPO and PPO, you maximize the expected sum of advantages over a sequence of actions as a way to optimize policy improvement steps.
100
Jose Arjona-Medina @arjonamedina.bsky.social · 01/03/2025
I still uncertain about the RL aspect in DeepSeek. To me it looks like a clever way of applaying a PPO-like clipping within a supervised framework, constrained by a fixed reference model. Althought some parts in its formulation are very similar to PPO, I wouldn't describe it as RL. (1/5)🧵
120
Jose Arjona-Medina @arjonamedina.bsky.social · 10/01/2025
Any recommendation for a drug discovery related confernece in Europe this year? Im all ears 😄
020
Jose Arjona-Medina @arjonamedina.bsky.social · 29/12/2024
*generalize
020
Jose Arjona-Medina @arjonamedina.bsky.social · 29/12/2024
Why your transformer-based net does not generalized from small molecules to peptides? Well, here one of the reasons: arxiv.org/abs/2410.01104 Once you know the root of the problem, you can find nice solutions 😉 In our case, a very simple regularization term did the job.
arxiv.org
softmax is not enough (for sharp out-of-distribution)
A key property of reasoning systems is the ability to make sharp decisions on their input data. For contemporary AI systems, a key carrier of sharp behaviour is the softmax function, with its capabili...
1164
Jose Arjona-Medina @arjonamedina.bsky.social · 26/12/2024
Great book. I also enjoyed it a lot.
010
Jose Arjona-Medina @arjonamedina.bsky.social · 02/12/2024
Thanks! We introduce inductive bias at different levels. For instance, we refined the centrality encoder to implicitly capture atom hybridization. We have other examples in the paper, and many others that we hope to publish soon 😉
100
Reposted by Jose Arjona-Medina
Willie Neiswanger @willieneis.bsky.social · 10/11/2024
I'm making a list of AI for Science researchers on bluesky — let me know if I missed you / if you'd like to join! go.bsky.app/AcP9Lix
16225389
Jose Arjona-Medina @arjonamedina.bsky.social · 16/11/2024
Same here! Thanks :)
110
Jose Arjona-Medina @arjonamedina.bsky.social · 16/11/2024
Thanks a lot!
000
Jose Arjona-Medina @arjonamedina.bsky.social · 16/11/2024
I'm working on improving molecular GNN models by adding inductive bias and integrating different data modalities. We recently presented part of our work in a workshop at ICML last July: arxiv.org/abs/2405.14837
arxiv.org
Analysis of Atom-level pretraining with Quantum Mechanics (QM) data for Graph Neural Networks Molecular property models
Despite the rapid and significant advancements in deep learning for Quantitative Structure-Activity Relationship (QSAR) models, the challenge of learning robust molecular representations that effectiv...
110
Jose Arjona-Medina @arjonamedina.bsky.social · 16/11/2024
Thanks a lot!
010
Reposted by Jose Arjona-Medina
Caitlin Mellor @caitlinmellor.bsky.social · 15/11/2024
A starter pack for anyone interested in AI & drug discovery :) go.bsky.app/AgYHc8j
295315
Jose Arjona-Medina @arjonamedina.bsky.social · 16/11/2024
Hi, just arrived here. Nice to see this starter pack. Im also doing some research in drug design and I would love to be inluded there as well. Thanks!
200
Reposted by Jose Arjona-Medina
Ben Blaiszik @benblaiszik.bsky.social · 15/11/2024
Follow leading researchers, practitioners, and thought leaders exploring the intersection of #AI, machine learning, data science, and scientific research. 🦋 ➕We are just getting started, please send me others who should be added go.bsky.app/JeFdryY #ML
4310441
Jose Arjona-Medina @arjonamedina.bsky.social · 16/11/2024
Great initiative! I'd love to be there as well
110