Building Transferable Potential Energy Surfaces with Machine Learning
Bibliographic record
Abstract
Discovering and characterizing novel compounds to serve society is the overarching goal of chemical sciences. Nowadays, experimental and computational methods provide complementary approaches for navigating the vast diversity of chemical space to identify suitable compounds for a given task. A key component of many computational methods is accurate and efficient mapping of the potential energy surface (PES), which relates the geometry to the energy of a chemical system.1 From a quantum mechanical perspective, the PES can be accurately computed; however, existing methods are infeasible for large systems (e.g., proteins) because their computational cost grows explosively with the size of the system. For this reason, machine learning (ML) approaches are used to circumvent direct computation of the PES of various chemical systems.2 To obtain ML potentials, a supervised algorithm is trained to establish a relationship between the structure of a chemical system, such as a molecule or crystal, and an output, like the system’s total energy and the forces acting on each atom. Even though existing ML potentials can reach excellent accuracy when applied to structures within the training domain (i.e., interpolation), they typically have poor performance for structures outside their applicability domain (i.e., extrapolation). To overcome this, we train NewtonNet,3 a message-passing network for deep learning of interatomic potentials, with more chemically-inspired data to the ML algorithm than has been traditionally used. Our goal is to allow this ML potential to learn transferable chemical properties and test its performance when applied to systems beyond the scope of the training set. References Journal of Computational Chemistry, 2003, 24, 1514-1527. Chemical Reviews, 2021, 121, 9816-9872. Digital Discovery, 2022, 1, 333-343.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.005 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.005 | 0.001 |
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.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
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".