Oscar Palomino

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Oscar Palomino

Oscar Palomino

@opehache

Cologne • Researcher in biomolecular simulations, JGU Mainz: I click buttons and proteins move.

Colonia Katılım Eylül 2009
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Oscar Palomino
Oscar Palomino@opehache·
📣 Hiring a postdoc! 📣 We are looking for a postdoctoral researcher in molecular simulations in Johannes Gutenberg Universität, Mainz, Germany. Please share! For details, visit the link below. euraxess.ec.europa.eu/jobs/312665
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Oscar Palomino
Oscar Palomino@opehache·
@PetarV_93 Dear Petar, this sounds very nice, thanks for sharing! One question: is there info about the lectures that will be covered?
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Petar Veličković
Petar Veličković@PetarV_93·
~3 days left to apply to attend EEML'26 in Cetinje 🇲🇪 (link below). We've faced unprecedented levels of interest and therefore will **not** be extending the deadline after the 31st. The speaker lineup is stellar, atmosphere will be amazing; you don't want to miss this one :)
Petar Veličković tweet media
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Kevin K. Yang 楊凱筌
Kevin K. Yang 楊凱筌@KevinKaichuang·
Hot take: it's 2026 we don't need to be manually doing citations or asking llms to do them overleaf should just autogenerate the citations from dois
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Michael - Protein Thx and Biologics
Here is a view of some of the minibinders and scFvs I have produced using Boltzgen. I have compared the residue count to the iPTM and the color scale represents the pae. You can see that Boltzgen generates a lot of different types of structures. There does not seem to be a bias towards 'high quality' and it is purely a numbers game. This is why I am working on a set of experiments which I hope to use the information learned to push these results directionally in my favor.
Michael - Protein Thx and Biologics tweet media
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Oscar Palomino
Oscar Palomino@opehache·
@AriWagen Dear Ari, thanks for the post! 1) will there be another one for TS opt benchmarking? And 2) is there any code associated to this benchmarks? Thanks!
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Ari Wagen
Ari Wagen@AriWagen·
I ran the same 25 optimizations with every combo. of four optimizers (Sella, geomeTRIC [both "cart" and "tric"], ASE/FIRE, and ASE/L-BFGS) and four NNPs (OrbMol, OMol25's eSEN sm. cons., AIMNet2, and Egret-1) & GFN2-xTB. rowansci.com/blog/which-opt…
Ari Wagen@AriWagen

@namankatyal14 @OrbMaterials The discussion about FIRE vs. LBFGS on this comment thread is quite nice as well: github.com/Radical-AI/tor…. In the future, I think it would be very interesting to test the matrix of [Sella, geomeTRIC, FIRE, LBFGS] x [OMol25's eSEN, OrbMol, AIMNet2, Egret/MACE].

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Oscar Palomino
Oscar Palomino@opehache·
@eigensteve I would be happy to: I am teaching also a course on similar lines! Would be nice to see other fresh perspectives!
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Steven Brunton
Steven Brunton@eigensteve·
New Book & Video Series!!! (late 2025) Optimization Bootcamp: Applications in Machine Learning, Control, and Inverse Problems Comment for a sneak peak to help proofread and I'll DM (proof reading, typos, HW problems, all get acknowledgment in book!)
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Gregoria
Gregoria@gregoria_i_·
No supe decir que no y terminé en estudiando procesos en el Instituto de Física 🙃
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Oscar Palomino
Oscar Palomino@opehache·
@jonkhler Do you think that the protests help shift the general view? Thinking on things like Fridays for future which I am also not sure of the impact on that. It is unfortunate how the general view is shifted now more to the right, but I see no way out now, sadly.
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Jonas Köhler
Jonas Köhler@jonkhler·
Germans are simply embarrassing. 🤦‍♂️ After the conservatives nearly passed unconstitutional nonsense law using right wing talk and the votes of the nazis resulting in mass protests all over the country: the voter just doesn't care... You vote what you deserve. 😓
Deutschland Wählt@Wahlen_DE

BUNDESTAGSWAHL | Sonntagsfrage Forschungsgruppe Wahlen/ZDF Union: 30% (+1) AfD: 20% (-1) SPD: 15% GRÜNE: 15% (+1) LINKE: 6% (+1) FDP: 4% BSW: 4% Sonstige: 6% (-2) Änderungen zur letzten Umfrage vom 30. Januar 2025 Verlauf: whln.eu/UmfragenDeutsc… #btw25

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kache
kache@yacineMTB·
Remember when LLMs used to make mistakes?
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Oscar Palomino
Oscar Palomino@opehache·
@camhowe1729 @francoisfleuret Assume that you are sampling from an area: the area between the x axis and the function. Ofc, if the distance between them x axis and the graph is higher might mean you get more chances of sampling from that value. Does this make sense?
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Cam Howe
Cam Howe@camhowe1729·
@francoisfleuret yeah but I'm struggling to get how uniform randomness changes into the distribution's randomness.
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Oscar Palomino
Oscar Palomino@opehache·
@alfcnz I mean, I remember that there was a time that I explained the results of concatenating neurons as when a cow has to digest the food multiple times. Kinda works, but I also don’t want to say that in class xD
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Alfredo Canziani
Alfredo Canziani@alfcnz·
@opehache Yeah, it allows for an intellectual playground to try out explanations before delivering them in class. 😀😀😀
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Alfredo Canziani
Alfredo Canziani@alfcnz·
Fuck it, I’m going back to mentoring students again. Three years ago, when I started writing my book, I decided it would be my only disciple, so that many would benefit from reading it. Now that I need to create more edu content, I’m going to seek help from my new mentees.
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Neil Renic
Neil Renic@NC_Renic·
“maybe I’ll do some writing between christmas and new year” Between christmas and new year:
Neil Renic tweet media
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Dr Meming
Dr Meming@Dr_Meming·
Spending an hour reading papers vs spending 10 hours perfecting my figures
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BURKOV
BURKOV@burkov·
Google has made us incapable of memorizing complex things by reducing memorization to search queries. LLMs will make us incapable of solving complex problems by reducing problem-solving skills to writing prompts.
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Daniel Probst @skepteis@skepteis.social
Here's a first: I'm hiring a PhD student at @WUR. If you have (or know someone who has) a strong background and interest in computational (bio)chemistry or computer science (especially 3D computer vision), let's work together 😊 wur.nl/nl/vacature/ph…
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Diego del Alamo
Diego del Alamo@DdelAlamo·
Papers combining MD & ML (MD is the gun)
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Diego del Alamo
Diego del Alamo@DdelAlamo·
Question for folks running MD on IDPs. Starting from spaghetti AF models len 50-150 residues, they nucleate/scrunch up into compact structures quickly, in 10s of ns. Is this normal/expected and/or protein-specific?? Are they ever expected to un-scrunch w/o enhanced sampling?
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Daniel Probst @skepteis@skepteis.social
One of the absolutely last things that science needs is to boost the egos of (already successful) scientists by giving them prizes.
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