ChemSpacE: Interpretable and Interactive Chemical Space Exploration
Bibliographic record
Abstract
Discovering meaningful molecules in the vast combinatorial chemical space has been a long-standing challenge in many fields from materials science to drug discovery. Recent advances in machine learning, especially generative models, have made remarkable progress and demonstrate considerable promise for automated molecule design. Nevertheless, most molecule generative models remain black-box systems, whose utility is limited by a lack of interpretability and human participation in the generation process. In this work we propose Chemical Space Explorer (ChemSpacE), a simple yet effective method for exploring the chemical space with pre-trained deep generative models. It enables users to interact with existing generative models and inform the molecule generation process. We demonstrate the efficacy of ChemSpacE on the molecule optimization task and the molecule manipulation task in single property and multi-property settings. On the molecule optimization task, the performance of ChemSpacE is on par with previous black-box optimization methods yet is considerably faster and more sample efficient. Furthermore, the interface from ChemSpacE facilitates human-in-the-loop chemical space exploration and interactive molecule design.
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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 | 0.003 |
| 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 | 0.003 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.022 | 0.004 |
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".