Aneesh Pappu

Zhenqin Wu, Bharath Ramsundar, Evan N. Feinberg et al.

Molecular machine learning has been maturing rapidly over the last few years. Improved methods and the presence of larger datasets have enabled machine learning algorithms to make increasingly accurate predictions about molecular properties. However, algorithmic progress has been limited due to the lack of a standard benchmark to compare the efficacy of proposed methods; most new algorithms are benchmarked on different datasets making it challenging to gauge the quality of proposed methods. This work introduces MoleculeNet, a large scale benchmark for molecular machine learning. MoleculeNet curates multiple public datasets, establishes metrics for evaluation, and offers high quality open-source implementations of multiple previously proposed molecular featurization and learning algorithms (released as part of the DeepChem open source library). MoleculeNet benchmarks demonstrate that learnable representations are powerful tools for molecular machine learning and broadly offer the best performance. However, this result comes with caveats. Learnable representations still struggle to deal with complex tasks under data scarcity and highly imbalanced classification. For quantum mechanical and biophysical datasets, the use of physics-aware featurizations can be more important than choice of particular learning algorithm.

Han Altae-Tran, Bharath Ramsundar, Aneesh S. Pappu et al.

Recent advances in machine learning have made significant contributions to drug discovery. Deep neural networks in particular have been demonstrated to provide significant boosts in predictive power when inferring the properties and activities of small-molecule compounds. However, the applicability of these techniques has been limited by the requirement for large amounts of training data. In this work, we demonstrate how one-shot learning can be used to significantly lower the amounts of data required to make meaningful predictions in drug discovery applications. We introduce a new architecture, the residual LSTM embedding, that, when combined with graph convolutional neural networks, significantly improves the ability to learn meaningful distance metrics over small-molecules. We open source all models introduced in this work as part of DeepChem, an open-source framework for deep-learning in drug discovery.

Aneesh Pappu, Brooks Paige

Graph neural networks have become very popular for machine learning on molecules due to the expressive power of their learnt representations. However, molecular machine learning is a classically low-data regime and it isn't clear that graph neural networks can avoid overfitting in low-resource settings. In contrast, fingerprint methods are the traditional standard for low-data environments due to their reduced number of parameters and manually engineered features. In this work, we investigate whether graph neural networks are competitive in small data settings compared to the parametrically 'cheaper' alternative of fingerprint methods. When we find that they are not, we explore pretraining and the meta-learning method MAML (and variants FO-MAML and ANIL) for improving graph neural network performance by transfer learning from related tasks. We find that MAML and FO-MAML do enable the graph neural network to outperform models based on fingerprints, providing a path to using graph neural networks even in settings with severely restricted data availability. In contrast to previous work, we find ANIL performs worse that other meta-learning approaches in this molecule setting. Our results suggest two reasons: molecular machine learning tasks may require significant task-specific adaptation, and distribution shifts in test tasks relative to train tasks may contribute to worse ANIL performance.

Abigail See, Aneesh Pappu, Rohun Saxena et al.

Large neural language models trained on massive amounts of text have emerged as a formidable strategy for Natural Language Understanding tasks. However, the strength of these models as Natural Language Generators is less clear. Though anecdotal evidence suggests that these models generate better quality text, there has been no detailed study characterizing their generation abilities. In this work, we compare the performance of an extensively pretrained model, OpenAI GPT2-117 (Radford et al., 2019), to a state-of-the-art neural story generation model (Fan et al., 2018). By evaluating the generated text across a wide variety of automatic metrics, we characterize the ways in which pretrained models do, and do not, make better storytellers. We find that although GPT2-117 conditions more strongly on context, is more sensitive to ordering of events, and uses more unusual words, it is just as likely to produce repetitive and under-diverse text when using likelihood-maximizing decoding algorithms.