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Thinking Globally, Acting Locally: On the Issue of Training Set Imbalance and the Case for Local Machine Learning Models in Chemistry

revised on 25.10.2019 and posted on 29.10.2019 by Mojtaba Haghighatlari, Ching-Yen Shih, Johannes Hachmann

The appropriate sampling of training data out of a potentially imbalanced data set is of critical importance for the development of robust and accurate machine learning models. A challenge that underpins this task is the partitioning of the data into groups of similar instances, and the analysis of the group populations. In molecular data sets, different groups of molecules may be hard to identify. However, if the distribution of a given data set is ignored then some of these groups may remain under-represented and the sampling biased, even if the size of data is large. In this study, we use the example of the Harvard Clean Energy Project (CEP) data set to assess the challenges posed by imbalanced data and the impact that accounting for different groups during the selection of training data has on the quality of the resulting machine learning models. We employ a partitioning criterion based on the underlying rules for the CEP molecular library generation to identify groups of structurally similar compounds. First, we evaluate the performance of regression models that are trained globally (i.e., by randomly sampling the entire data set for training data). This traditional approach serves as the benchmark reference. We compare its results with those of models that are trained locally, i.e., within each of the identified molecular domains. We demonstrate that local models outperform the best reported global models by considerable margins and are more efficient in their training data needs. We propose a strategy to redesign training sets for the development of improved global models. While the resulting uniform training sets can successfully yield robust global models, we identify the distribution mismatch between feature representations of different molecular domains as a critical limitation for any further improvement. We take advantage of the discovered distribution shift and propose an ensemble of classification and regression models to achieve a generalized and reliable model that outperforms the state-of-the-art model, trained on the CEP data set. Moreover, this study provides a benchmark for the development of future methodologies concerned with imbalanced chemical data.


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University at Buffalo


United States

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Declaration of Conflict of Interest

The authors declare to have no conflict of interest.