Evidence map›Paper›PMID 37642660›Full record

ArticleJournal of chemical information and modeling2024

MELLODDY: Cross-pharma Federated Learning at Unprecedented Scale Unlocks Benefits in QSAR without Compromising Proprietary Information.

Wouter Heyndrickx, Lewis Mervin, Tobias Morawietz, Noé Sturm, Lukas Friedrich, Adam Zalewski, Anastasia Pentina, Lina Humbeck, Martijn Oldenhof, Ritsuya Niwayama and 39 more

Abstract read
In one paragraph

Article in Journal of chemical information and modeling, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
64citing papers in PubMed, 2 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

64 citing papers in PubMed, 2 syntheses or guidelines pooled it.

  1. Pooled it
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  15. Ocular Lymphatics in Health and Disease.Diagnostics (Basel, Switzerland) · 2026
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  18. Evaluating generalization in protein-ligand cofolding methods.Nature structural & molecular biology · 2026
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4 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

49 authors.

Wouter HeyndrickxJanssen Pharmaceutica NV, Turnhoutseweg 30, Beerse 2340, Belgium.ORCID 0000-0002-0809-9442
Lewis MervinAstraZeneca R&D, Biomedical Campus, 1 Francis Crick Ave, Cambridge CB2 0SL, U.K.ORCID 0000-0002-7271-0824
Tobias MorawietzBayer Pharma AG, Global Drug Discovery, Chemical Research, Computational Chemistry, Aprather Weg 18 a, Wuppertal 42096, Germany.
Noé SturmNovartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland.
Lukas FriedrichMerck KGaA, Global Research & Development, Frankfurter Strasse 250, Darmstadt 64293, Germany.
Adam ZalewskiAmgen Research (Munich) GmbH, Staffelseestraße 2, Munich 81477, Germany.
Anastasia PentinaBayer AG, Machine Learning Research, Research & Development, Pharmaceuticals, Berlin 10117, Germany.
Lina HumbeckBI Medicinal Chemistry Department, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, Biberach an der Riss 88397, Germany.
Martijn OldenhofKU Leuven, ESAT-STADIUS, Kasteelpark Arenberg 10, Heverlee 3001, Belgium.ORCID 0000-0003-4916-3014
Ritsuya NiwayamaInstitut de recherches Servier, 125 chemin de ronde Croissy-sur-Seine, Île-de-France 78290, France.
Peter SchmidtkeDiscngine, Avenue Ledru Rollin 79, Paris 75012, France.
Nikolas FechnerNovartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland.ORCID 0000-0003-3852-3950
Jaak SimmKU Leuven, ESAT-STADIUS, Kasteelpark Arenberg 10, Heverlee 3001, Belgium.
Adam AranyKU Leuven, ESAT-STADIUS, Kasteelpark Arenberg 10, Heverlee 3001, Belgium.
Nicolas DrizardIktos, 65 rue de Prony, Paris 75017, France.
Rama JabalIktos, 65 rue de Prony, Paris 75017, France.
Arina AfanasyevaModality Informatics Group, Digital Research Solutions, Advanced Informatics & Analytics, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba-shi, Ibaraki 305-8585, Japan.
Regis LoebKU Leuven, ESAT-STADIUS, Kasteelpark Arenberg 10, Heverlee 3001, Belgium.
Shlok VermaGlaxoSmithKline, Computational Sciences, Gunnels Wood Road Stevenage, Herts SG1 2NY, U.K.
Simon HarnqvistGlaxoSmithKline, Computational Sciences, Gunnels Wood Road Stevenage, Herts SG1 2NY, U.K.
Matthew HolmesGlaxoSmithKline, Computational Sciences, Gunnels Wood Road Stevenage, Herts SG1 2NY, U.K.
Balazs PejoBudapest University of Technology and Economics, Department of Networked Systems and Services, Műegyetem rkp. 3, Budapest 1111, Hungary.
Maria TelenczukOwkin, 12 Rue Martel, Paris 75010, France.
Nicholas HolwayNovartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland.ORCID 0000-0002-2126-5118
Arne DieckmannBayer AG, API Production, Product Supply, Pharmaceuticals, Ernst-Schering-Straße 14, Bergkamen 59192, Germany.
Nicola RiekeNVIDIA GmbH, Floessergasse 2, Munich 81369, Germany.
Friederike ZumsandeAmgen Research (Munich) GmbH, Staffelseestraße 2, Munich 81477, Germany.
Djork-Arné ClevertBayer AG, Machine Learning Research, Research & Development, Pharmaceuticals, Berlin 10117, Germany.
Michael KrugMerck KGaA, Global Research & Development, Frankfurter Strasse 250, Darmstadt 64293, Germany.
Christopher LuscombeGlaxoSmithKline, Computational Sciences, Gunnels Wood Road Stevenage, Herts SG1 2NY, U.K.
Darren GreenGlaxoSmithKline, Computational Sciences, Gunnels Wood Road Stevenage, Herts SG1 2NY, U.K.
Peter ErtlNovartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland.ORCID 0000-0001-6496-4448
Peter AntalBudapest University of Technology and Economics, Department of Measurement and Information Systems, Műegyetem rkp. 3, Budapest 1111, Hungary.
David MarcusGlaxoSmithKline, Computational Sciences, Gunnels Wood Road Stevenage, Herts SG1 2NY, U.K.
Nicolas Do HuuIktos, 65 rue de Prony, Paris 75017, France.
Hideyoshi FujiModality Informatics Group, Digital Research Solutions, Advanced Informatics & Analytics, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba-shi, Ibaraki 305-8585, Japan.ORCID 0000-0001-5537-3689
Stephen PickettGlaxoSmithKline, Computational Sciences, Gunnels Wood Road Stevenage, Herts SG1 2NY, U.K.ORCID 0000-0002-0958-9830
Gergely AcsBudapest University of Technology and Economics, Department of Networked Systems and Services, Műegyetem rkp. 3, Budapest 1111, Hungary.
Eric BonifaceSubstra Foundation - Labelia Labs, 4 rue Voltaire, Nantes 44000, France.
Bernd BeckBI Medicinal Chemistry Department, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, Biberach an der Riss 88397, Germany.
Yax SunAmgen Research, 1 Amgen Center Drive, Thousand Oaks, California 92130, United States.
Arnaud GohierInstitut de recherches Servier, 125 chemin de ronde Croissy-sur-Seine, Île-de-France 78290, France.
Friedrich RippmannMerck KGaA, Global Research & Development, Frankfurter Strasse 250, Darmstadt 64293, Germany.ORCID 0000-0002-4604-9251
Ola EngkvistAstraZeneca, Molecular AI, Discovery Sciences, R&D, Pepparedsleden 1, Mölndal 431 50, Sweden.ORCID 0000-0003-4970-6461
Andreas H GöllerBayer Pharma AG, Global Drug Discovery, Chemical Research, Computational Chemistry, Aprather Weg 18 a, Wuppertal 42096, Germany.ORCID 0000-0003-4343-4063
Yves MoreauKU Leuven, ESAT-STADIUS, Kasteelpark Arenberg 10, Heverlee 3001, Belgium.
Mathieu N GaltierOwkin, 4 Rue Voltaire, Nantes 44000, France.
Ansgar SchuffenhauerNovartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland.ORCID 0000-0001-6385-0414
Hugo CeulemansJanssen Pharmaceutica NV, Turnhoutseweg 30, Beerse 2340, Belgium.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Federated multipartner machine learning has been touted as an appealing and efficient method to increase the effective training data volume and thereby the predictivity of models, particularly when the generation of training data is resource-intensive. In the landmark MELLODDY project, indeed, each of ten pharmaceutical companies realized aggregated improvements on its own classification or regression models through federated learning. To this end, they leveraged a novel implementation extending multitask learning across partners, on a platform audited for privacy and security. The experiments involved an unprecedented cross-pharma data set of 2.6+ billion confidential experimental activity data points, documenting 21+ million physical small molecules and 40+ thousand assays in on-target and secondary pharmacodynamics and pharmacokinetics. Appropriate complementary metrics were developed to evaluate the predictive performance in the federated setting. In addition to predictive performance increases in labeled space, the results point toward an extended applicability domain in federated learning. Increases in collective training data volume, including by means of auxiliary data resulting from single concentration high-throughput and imaging assays, continued to boost predictive performance, albeit with a saturating return. Markedly higher improvements were observed for the pharmacokinetics and safety panel assay-based task subsets.

Indexed as

Quantitative Structure-Activity RelationshipBiological AssayMachine Learning

Identifiers

PMID37642660
PMCPMC11005050

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.