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Record W4321499530 · doi:10.2533/chimia.2023.22

Putting Chemical Knowledge to Work in Machine Learning for Reactivity

2023· article· en· W4321499530 on OpenAlexfundno aff
Kjell Jorner

Bibliographic record

VenueCHIMIA International Journal for Chemistry · 2023
Typearticle
Languageen
FieldComputer Science
TopicComputational Drug Discovery Methods
Canadian institutionsnot available
FundersVetenskapsrådetUniversity of Toronto
KeywordsCheminformaticsComputer scienceArtificial neural networkMachine learningArtificial intelligenceChemometricsDeep learningChemistryComputational chemistry

Abstract

fetched live from OpenAlex

Machine learning has been used to study chemical reactivity for a long time in fields such as physical organic chemistry, chemometrics and cheminformatics. Recent advances in computer science have resulted in deep neural networks that can learn directly from the molecular structure. Neural networks are a good choice when large amounts of data are available. However, many datasets in chemistry are small, and models utilizing chemical knowledge are required for good performance. Adding chemical knowledge can be achieved either by adding more information about the molecules or by adjusting the model architecture itself. The current method of choice for adding more information is descriptors based on computed quantum-chemical properties. Exciting new research directions show that it is possible to augment deep learning with such descriptors for better performance in the low-data regime. To modify the models, differentiable programming enables seamless merging of neural networks with mathematical models from chemistry and physics. The resulting methods are also more data-efficient and make better predictions for molecules that are different from the initial dataset on which they were trained. Application of these chemistry-informed machine learning methods promise to accelerate research in fields such as drug design, materials design, catalysis and reactivity.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame distilled prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.

metaresearch head score (Codex)0.001
metaresearch head score (Gemma)0.002
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Simulation or modeling · Consensus signal: none
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.603
Threshold uncertainty score0.639

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0010.002
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0000.000
Science and technology studies0.0000.000
Scholarly communication0.0000.000
Open science0.0010.000
Research integrity0.0000.000
Insufficient payload (model declined to judge)0.0000.000

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.039
GPT teacher head0.371
Teacher spread0.332 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one teacher head, not a consensus.

The models applied no category: nothing in the taxonomy fit this work.
Study designSimulation or modeling
Domainnot available
GenreEmpirical

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

Quick stats

Citations13
Published2023
Admission routes1
Has abstractyes

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