TY - GEN
T1 - Functionally Regionalized Knowledge Transfer for Low-resource Drug Discovery
AU - Yao, Huaxiu
AU - Wei, Ying
AU - Huang, Long Kai
AU - Xue, Ding
AU - Huang, Junzhou
AU - Li, Zhenhui
N1 - Funding Information:
H.Y. and Z.L. are supported in part by NSF awards IIS-#1652525 and IIS-#1618448. The views and conclusions contained in this paper are those of the authors and should not be interpreted as representing any funding agencies. This work was also supported in part by the start-up grant from City University of Hong Kong (9610512). Besides, Y.W. would like to acknowledge the support from the Tencent AI Lab Rhino-Bird Gift Fund.
Publisher Copyright:
© 2021 Neural information processing systems foundation. All rights reserved.
PY - 2021
Y1 - 2021
N2 - More recently, there has been a surge of interest in employing machine learning approaches to expedite the drug discovery process where virtual screening for hit discovery and ADMET prediction for lead optimization play essential roles. One of the main obstacles to the wide success of machine learning approaches in these two tasks is that the number of compounds labeled with activities or ADMET properties is too small to build an effective predictive model. This paper seeks to remedy the problem by transferring the knowledge from previous assays, namely in-vivo experiments, by different laboratories and against various target proteins. To accommodate these wildly different assays and capture the similarity between assays, we propose a functional rationalized meta-learning algorithm FRML for such knowledge transfer. FRML constructs the predictive model with layers of neural sub-networks or so-called functional regions. Building on this, FRML shares an initialization for the weights of the predictive model across all assays, while customizes it to each assay with a region localization network choosing the pertinent regions. The compositionality of the model improves the capacity of generalization to various and even out-of-distribution tasks. Empirical results on both virtual screening and ADMET prediction validate the superiority of FRML over state-of-the-art baselines powered with interpretability in assay relationship.
AB - More recently, there has been a surge of interest in employing machine learning approaches to expedite the drug discovery process where virtual screening for hit discovery and ADMET prediction for lead optimization play essential roles. One of the main obstacles to the wide success of machine learning approaches in these two tasks is that the number of compounds labeled with activities or ADMET properties is too small to build an effective predictive model. This paper seeks to remedy the problem by transferring the knowledge from previous assays, namely in-vivo experiments, by different laboratories and against various target proteins. To accommodate these wildly different assays and capture the similarity between assays, we propose a functional rationalized meta-learning algorithm FRML for such knowledge transfer. FRML constructs the predictive model with layers of neural sub-networks or so-called functional regions. Building on this, FRML shares an initialization for the weights of the predictive model across all assays, while customizes it to each assay with a region localization network choosing the pertinent regions. The compositionality of the model improves the capacity of generalization to various and even out-of-distribution tasks. Empirical results on both virtual screening and ADMET prediction validate the superiority of FRML over state-of-the-art baselines powered with interpretability in assay relationship.
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M3 - Conference contribution
AN - SCOPUS:85131817659
T3 - Advances in Neural Information Processing Systems
SP - 8256
EP - 8268
BT - Advances in Neural Information Processing Systems 34 - 35th Conference on Neural Information Processing Systems, NeurIPS 2021
A2 - Ranzato, Marc'Aurelio
A2 - Beygelzimer, Alina
A2 - Dauphin, Yann
A2 - Liang, Percy S.
A2 - Wortman Vaughan, Jenn
PB - Neural information processing systems foundation
T2 - 35th Conference on Neural Information Processing Systems, NeurIPS 2021
Y2 - 6 December 2021 through 14 December 2021
ER -