Convex factorization machine for toxicogenomics prediction

Makoto Yamada, Wenzhao Lian, Amit Goyal, Jianhui Chen, Kishan Wimalawarne, Suleiman A. Khan, Samuel Kaski, Hiroshi Mamitsuka, Yi Chang

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

23 Citations (Scopus)


We introduce the convex factorization machine (CFM), which is a convex variant of the widely used Factorization Machines (FMs). Specifically, we employ a linear+quadratic model and regularize the linear term with the l2-regularizer and the quadratic term with the trace norm regularizer. Then, we formulate the CFM optimization as a semidefinite programming problem and propose an efficient optimization procedure with Hazan's algorithm. A key advantage of CFM over existing FMs is that it can find a globally optimal solution, while FMs may get a poor locally optimal solution since the objective function of FMs is non-convex. In addition, the proposed algorithm is simple yet effective and can be implemented easily. Finally, CFM is a general factorization method and can also be used for other factorization problems, including multi-view matrix factorization and tensor completion problems, in various domains including toxicogenomics and bioinformatics. Through synthetic and traditionally used movielens datasets, we first show that the proposed CFM achieves results competitive to FMs. We then show in a toxicogenomics prediction task that CFM predicts the toxic outcomes of a collection of drugs better than a state-of-the-art tensor factorization method.

Original languageEnglish
Title of host publicationKDD 2017 - Proceedings of the 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining
Number of pages10
ISBN (Electronic)9781450348874
Publication statusPublished - 13 Aug 2017
MoE publication typeA4 Article in a conference publication
EventACM SIGKDD International Conference on Knowledge Discovery and Data Mining - Halifax, Canada
Duration: 13 Aug 201717 Aug 2017
Conference number: 23


ConferenceACM SIGKDD International Conference on Knowledge Discovery and Data Mining
Abbreviated titleKDD


  • Convex
  • Factorization machines
  • Toxicogenomics prediction


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