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Manas Mahale

@manasmahale.bsky.social
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Cheminformatics | manasmahale.in

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Manas Mahale @manasmahale.bsky.social · 27/09/2026
This Week In Cheminformatics Issue #040 is out. This week we look into RetroChimera, HDACiAP, and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/forty
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #040
RetroChimera, HDACiAP, and a long list of papers
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Manas Mahale @manasmahale.bsky.social · 20/09/2026
This Week In Cheminformatics Issue #039 is out. This week we look into the scope concept from Novartis, SB2025 & FARMA2025 datasets, TDiMS and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/thirty-nine
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #039
The Scope Concept from Novartis, SB2025 & FARMA2025, TDiMS and a long list of papers
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Manas Mahale @manasmahale.bsky.social · 14/09/2026
This Week In Cheminformatics Issue #038 is out. This week we look into the CTMD, BONAFIDE and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/thirty-eight
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #038
CTMD, BONAFIDE and a long list of papers
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Manas Mahale @manasmahale.bsky.social · 07/09/2026
This Week In Cheminformatics Issue #037 is out. This week we look into the sr-SMILES, Markush structure image to SMILES, benchmarking GNNs on ChEMBL, and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/thirty-seven
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #037
sr-SMILES, Markush structure image to SMILES, benchmarking GNNs on ChEMBL, and a long list of papers
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Manas Mahale @manasmahale.bsky.social · 01/09/2026
This Week In Cheminformatics Issue #036 is out. This week we look into the Data leakage in knowledge graph, GOLLuM, which metrics best capture protein structural changes in MD and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/thirty-six
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #036
Data leakage in knowledge graph, GOLLuM, which metrics best capture protein structural changes in MD and a long list of papers
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Manas Mahale @manasmahale.bsky.social · 24/08/2026
This week in cheminformatics, we look into new OpenADMET CYP Blind Challenge, where simple models work, is structure prediction with ML for FEP good enough, Clustering Retrosynthetic Pathways with CGRs and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/thirty-five
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #035
OpenADMET CYP Blind Challenge, Simple models ftw, is structure prediction with ML for FEP good enough, Clustering Retrosynthetic Pathways with CGRs and a long list of papers
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Manas Mahale @manasmahale.bsky.social · 17/08/2026
This Week In Cheminformatics Issue #034 We look into whether LLMs plan synthesis like humans, Fragment-Level Shapley Values for model interpretation, Drug repurposing found Relugolix as BCL‑2 binder and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/thirty-four
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #034
Do LLMs plan synthesis like humans, Fragment-Level Shapley Values for interpretation, Q2 is apparently the metric for unbiased regression model selection and a long list of papers
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Manas Mahale @manasmahale.bsky.social · 11/08/2026
This Week In Cheminformatics Issue #033 is out. This week we look into Andreas's view of AI4DD, SynthEx, CheMeleon, and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/thirty-three
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Manas Mahale @manasmahale.bsky.social · 04/08/2026
This Week In Cheminformatics Issue #032 is out. This week we look into Domain adaptation for Transformers, MPO guided by Bioisostere replacement, yet another Boltz‑2 Evaluation, and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/thirty-two
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #032
Domain adaptation for Transformers, MPO guided by Bioisostere replacement, Boltz‑2 Evaluation, and a long list of papers
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Manas Mahale @manasmahale.bsky.social · 27/07/2026
This Week In Cheminformatics Issue #031 is out. This week we look into Equilibrist, DiffDock-Pocket on LIT-PCBA, Ligand Drift Rate Descriptor and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/thirty-one
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #031
Equilibrist, DiffDock-Pocket on LIT-PCBA, Ligand Drift Rate Descriptor and a long list of papers
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Reposted by Manas Mahale
Olexandr Isayev 🇺🇦 🇺🇸 @olexandr.bsky.social · 23/07/2026
In structure-based drug design, ligand conformational strain helps answer a key question: is this bound pose chemically plausible? But the usual gas-phase shortcut can misestimate strain, especially for charged and highly polar ligands. #compchem
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Manas Mahale @manasmahale.bsky.social · 22/07/2026
Extended-Connectivity Fingerprints in APL Post: butwhyisthat.substack.com/p/ecfp Code: github.com/manas02/ecfp
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Manas Mahale @manasmahale.bsky.social · 19/07/2026
This Week In Cheminformatics Issue #030 is out. This week we look into How useful are Cavity Prediction Algorithms, NMR-AI, (Failing at) Predicting Alternative Binding Modes via Docking and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/thirty
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #030
How useful are Cavity Prediction Algorithms, NMR-AI, (Failing at) Predicting Alternative Binding Modes via Docking and a long list of papers...and maybe the last one of these from PT.
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Manas Mahale @manasmahale.bsky.social · 18/07/2026
For those who use Garmin and are into mindfulness. github.com/Manas02/Here...
github.com
GitHub - Manas02/HereAndNow: Garmin App for gentle reminders to be present in the moment
Garmin App for gentle reminders to be present in the moment - Manas02/HereAndNow
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Reposted by Manas Mahale
Bettina Keller @bettinagkeller.bsky.social · 08/07/2026
📢 We're hiring a PhD student (4 years) in computational chemistry at Freie Universität Berlin. Research on molecular dynamics, molecular kinetics, rare events & machine learning. Apply by 3 Aug 2026: jobs.fu-berlin.de/job/Research... #CompChem
jobs.fu-berlin.de
Research assistant (praedoc) (f/m/d) DM-786
Research assistant (praedoc) (f/m/d) DM-786
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Manas Mahale @manasmahale.bsky.social · 05/07/2026
This Week In Cheminformatics Issue #028 is out. This week we look into Fingerprint benchmarking for metabolomics, Harmonizing pharmacogenomics DBs, Fast TS guesser in VeloxChem and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/twenty-eight
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #028
Fingerprint benchmarking for metabolomics, Harmonizing pharmacogenomics DBs, Fast TS guesser in VeloxChem and a long list of papers
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Manas Mahale @manasmahale.bsky.social · 29/06/2026
This Week In Cheminformatics: Issue #026 + #027 About Strasbourg Summer School In Cheminformatics 2026, Properties of Macrocycles, De Novo A2A Hit, PP-MAPS, PegaPlus and a long list of papers thisweekincheminformatics.substack.com/p/twenty-six thisweekincheminformatics.substack.com/p/twenty-seven
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #026
Strasbourg Summer School In Cheminformatics 2026, Properties of Macrocycles, De Novo A2A Hit and a long list of papers
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Manas Mahale @manasmahale.bsky.social · 16/06/2026
This Week In Cheminformatics Issue #025 is out. This week we look into BigSMILES canonicalization, Cleavage Rules Using SMIRKS Heuristics, EasyDock 1.3, and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/twenty-five
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #025
BigSMILES canonicalization, Cleavage Rules Using SMIRKS Heuristics, EasyDock 1.3, and a long list of papers
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Manas Mahale @manasmahale.bsky.social · 07/06/2026
This Week In Cheminformatics Issue #024 This week we look into Covalent Binders in PDB, Fast RMSD Calculations, Better Activity Cliff Prediction using Assay Information and a long list of (rather interesting chemistry) papers. Happy reading :) thisweekincheminformatics.substack.com/p/twenty-four
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #024
Covalent Binders in PDB, Fast RMSD Calculations, Better Activity Cliff Prediction using Assay and a long list of (rather interesting chemistry) papers
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Manas Mahale @manasmahale.bsky.social · 01/06/2026
This Week In Cheminformatics Issue #023 is out. This week we look into Tsetlin Machine, Are We Underestimating Overfitting ?, MCTS MOO on drug like space, and a long list of papers to end the month of May Happy reading :) thisweekincheminformatics.substack.com/p/twenty-three
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #023
Tsetlin Machine, Are We Underestimating Overfitting, MCTS MOO on drug like space, and a long list of papers to end the month of May
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Manas Mahale @manasmahale.bsky.social · 25/05/2026
This Week In Cheminformatics Issue #022 is out. This week we look into oral drug-likeness prediction, reaction discovery using AI-HTE and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/twenty-two
thisweekincheminformatics.substack.com
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Manas Mahale @manasmahale.bsky.social · 18/05/2026
This Week In Cheminformatics Issue #021 is out. This week we look into conformal prediction for molecular retrieval from MS2, how expensive should your conformer generation workflows be and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/twenty-one
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #021
conformal prediction for molecular retrieval from MS2, how expensive should your conformer generation workflows be and a long list of papers
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Manas Mahale @manasmahale.bsky.social · 03/05/2026
This Week In Cheminformatics Issue #019 is out. This week we look into Host–Guest kinetics & thermodynamics prediction using REMD, Photoswitchable COX-2 inhibitors, PROTAC generative model benchmark and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/nineteen
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Manas Mahale @manasmahale.bsky.social · 27/04/2026
This Week In Cheminformatics Issue #018 is out. This week we look into practical guide to molecular docking, stoichiometry informed symbolic regression, DiffDock-Glide and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/eighteen
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Manas Mahale @manasmahale.bsky.social · 20/04/2026
This Week In Cheminformatics Issue #017 is out. This week we look into π-conjugated chemical space exploration, shape constrained diffusion model and long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/seventeen
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Manas Mahale @manasmahale.bsky.social · 12/04/2026
This Week In Cheminformatics Issue #016 is out. This week we look into how do degrading compounds perform in HTS, models for predicting NRPS A domain substrate specificity and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/sixteen
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Manas Mahale @manasmahale.bsky.social · 06/04/2026
This Week In Cheminformatics Issue #015 is out. This week we look into a model for carbohydrate-protein interaction, AFM based protein conformation estimation and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/fifteen
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Manas Mahale @manasmahale.bsky.social · 30/03/2026
This Week In Cheminformatics Issue #014 is out. This week we look into a guide to Mixed-Solvent MD and Solvent-Site-Biased Docking, StereoMolGraph and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/fourteen
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Manas Mahale @manasmahale.bsky.social · 22/03/2026
This Week In Cheminformatics Issue #013 is out. This week we look into Saturn for sample-efficient molecular generation, minimum message length based fingerprint, AF3 for covalent virtual screening and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/thirteen
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Manas Mahale @manasmahale.bsky.social · 16/03/2026
This Week In Cheminformatics Issue #012 is out. This week we look into AF2BIND, Automated R Group Recognition, Cyclovoltammetry KG and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/twelve
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Reposted by Manas Mahale
Helen Kennedy @helenkennedy.com · 15/03/2026
Happy March 15. Here is my favorite Ides of March meme:
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Manas Mahale @manasmahale.bsky.social · 09/03/2026
This Week In Cheminformatics Issue #011 is out. This week we look into Model for Pure Shift Proton NMR, Uncertainty Quantification, What Happens in Successful Optimizations and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/eleven
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Manas Mahale @manasmahale.bsky.social · 01/03/2026
This Week In Cheminformatics Issue #010 is out. This week we look into Novel NP Inspired Chemotypes for Kinase, Virtual Screening with GPU using UniDock-Pro, Benchmarking Count Fingerprint Performance and a Long List of Papers. Happy reading :) thisweekincheminformatics.substack.com/p/ten
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Manas Mahale @manasmahale.bsky.social · 23/02/2026
This Week In Cheminformatics Issue #009 is out. This week we look into New Ligand Target Prediction Models, Rules on model validation and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/nine
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Manas Mahale @manasmahale.bsky.social · 15/02/2026
This Week In Cheminformatics Issue #008 is out. This week we look into Weighted fingerprints, curated annotation of ChEMBL, a compound prioritization method and a long list of papers from last week. Happy reading :) thisweekincheminformatics.substack.com/p/eight
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Manas Mahale @manasmahale.bsky.social · 09/02/2026
This Week In Cheminformatics Issue #007 is out. This week we look into an intuitive method for improving reaction coverage in USPTO, Massive Crystal structure data release from FAIR and a Long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/seven
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Manas Mahale @manasmahale.bsky.social · 02/02/2026
This Week In Cheminformatics Issue #006 is out. This week we look into Binding Site Vectors to Compare Active Sites, ArtiDock, Benchmarking Boltz-2, and a long list of papers from last week of Jan. Happy reading :) thisweekincheminformatics.substack.com/p/six
This week we look into Binding Site Vectors to Compare Active Sites, ArtiDock, Benchmarking Boltz-2, and a long list of papers from last week of Jan.
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Reposted by Manas Mahale
Hannes Stark @hannes-stark.bsky.social · 01/02/2026
Tomorrow in the reading group we discuss "SeedFold: Scaling Biomolecular Structure Prediction" arxiv.org/abs/2512.24354 Outperforming AF3 on multiple tasks a little bit. Join us on zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/starklyspeak...
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Manas Mahale @manasmahale.bsky.social · 26/01/2026
This Week In Cheminformatics Issue #005 is out. thisweekincheminformatics.substack.com/p/five
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #005
CACHE Challenge #3, Digital pipette, Bias in retrosynthesis datasets, Benchmarking self-driving labs and a long list of papers to start the final week of January.
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Manas Mahale @manasmahale.bsky.social · 12/01/2026
This Week In Cheminformatics Issue #003 is out. thisweekincheminformatics.substack.com/p/three
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #003
Better Ensemble For Federated Learning, A New Chirality, Transformer Model's Memorization Limiting Performance, Closed-Loop Molecular Discovery and Results of Blind Challenge on Pan-Coronavirus Data
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Manas Mahale @manasmahale.bsky.social · 04/01/2026
This Week In Cheminformatics, we look into massive validation study from Open Free Energy, Andrew Dalke’s clever method for preserving count magnitudes in binary fingerprints and results of Stanford Kaggle competition for RNA structure prediction. thisweekincheminformatics.substack.com/p/two
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #002
First week's readings, Big W for OpenFE, Andrew Dalke and RNA Structure Prediction
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Manas Mahale @manasmahale.bsky.social · 31/12/2025
literally no one asked, but I started a newsletter. it’s called "This Week In Cheminformatics" (very original, I know). First issue is out now. have a read and a very happy new year ! thisweekincheminformatics.substack.com/p/one #cheminformatics
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Manas Mahale @manasmahale.bsky.social · 21/12/2025
I sat for my Physical Organic Chemistry exam 48 hours ago. Naturally, immediately after the exam, my brain finally decided to better understand the material. So, to cope with the irony, I spent my weekend building this. butwhyisthat.substack.com/p/moj
butwhyisthat.substack.com
More on More O'Ferrall-Jencks Diagram
Surfing the Potential Energy Surface
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Reposted by Manas Mahale
Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 18/12/2025
Enjoyed reading “AI for chemistry in 2025 is like AI for images in 2010” leashbio.substack.com/p/ai-for-che...
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Reposted by Manas Mahale
Stephanie Hicks @stephaniehicks.bsky.social · 11/04/2025
Rafa has come out swinging this morning 😂
Rafa showing a UMAP
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Manas Mahale @manasmahale.bsky.social · 02/03/2025
I made a Terminal based Anki clone (Spaced Repetition System TUI) for no reason ! github.com/Manas02/Tanki
github.com
GitHub - Manas02/Tanki: Terminal Based SRS
Terminal Based SRS. Contribute to Manas02/Tanki development by creating an account on GitHub.
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Reposted by Manas Mahale
Olexandr Isayev 🇺🇦 🇺🇸 @olexandr.bsky.social · 14/12/2024
This is what happens when you let computer scientists design molecules 🤯 Oral presentation @neuripsconf.bsky.social #NeurIPS2024 #chemsky
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Reposted by Manas Mahale
Andreas Bender @andreasbender.bsky.social · 09/12/2024
I am speaking at CPHI Middle East in Riyadh this week, on "Artificial Intelligence Across Modalities - Small Molecules, Antibodies/Proteins, and Cell and Gene Therapy" Please don't hesitate to get in touch if you are interested in AI & drug discovery! Cheers, Andreas www.cphi.com/middle-east/...
cphi.com
CPHI Middle East 2024 | Region's largest pharma exhibition
Connect with 400+ pharma companies and 150+ global experts at the largest pharma conference in the region. Explore the latest innovations in API, drug manufacturing, and more in Riyadh, Saudi Arabia.
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Reposted by Manas Mahale
Srijit Seal 🇺🇸🇬🇧🇩🇪🇯🇵🇮🇳 @srijitseal.com · 23/11/2024
PKSmart v3.0 is now live! pk-predictor.serve.scilifelab.se PKSmart is an open-source app we built to predict human and animal pharmacokinetic parameters. Publication is coming soon and is also available for local implementation via pip install pksmart.
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Reposted by Manas Mahale
Srijit Seal 🇺🇸🇬🇧🇩🇪🇯🇵🇮🇳 @srijitseal.com · 21/11/2024
We translated a validation strategy in Materials to Small molecules. A key problem in cross-validation is splitting of data. Here we propose a step-forward CV. People are used to scaffold splits, time splits etc. but these all have limitations.
openreview.net
Out-of-Distribution Validation for Bioactivity Prediction in Drug...
Recent advances in machine learning for materials science have significantly improved the prediction of novel materials. Building on these methods, we have adapted them for drug discovery...
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