Jiangwen Sun

Mohammad Shiri, Jiangwen Sun

Deep neural networks trained for predicting cellular events from DNA sequence have become emerging tools to help elucidate the biological mechanism underlying the associations identified in genome-wide association studies. To enhance the training, multi-task learning (MTL) has been commonly exploited in previous works where trained networks were needed for multiple profiles differing in either event modality or cell type. All existing works adopted a simple MTL framework where all tasks share a single feature extraction network. Such a strategy even though effective to certain extent leads to substantial negative transfer, meaning the existence of large portion of tasks for which models obtained through MTL perform worse than those by single task learning. There have been methods developed to address such negative transfer in other domains, such as computer vision. However, these methods are generally difficult to scale up to handle large amount of tasks. In this paper, we propose a highly scalable task grouping framework to address negative transfer by only jointly training tasks that are potentially beneficial to each other. The proposed method exploits the network weights associated with task specific classification heads that can be cheaply obtained by one-time joint training of all tasks. Our results using a dataset consisting of 367 epigenetic profiles demonstrate the effectiveness of the proposed approach and its superiority over baseline methods.

Chao Shang, Aaron Palmer, Jiangwen Sun et al.

In an era when big data are becoming the norm, there is less concern with the quantity but more with the quality and completeness of the data. In many disciplines, data are collected from heterogeneous sources, resulting in multi-view or multi-modal datasets. The missing data problem has been challenging to address in multi-view data analysis. Especially, when certain samples miss an entire view of data, it creates the missing view problem. Classic multiple imputations or matrix completion methods are hardly effective here when no information can be based on in the specific view to impute data for such samples. The commonly-used simple method of removing samples with a missing view can dramatically reduce sample size, thus diminishing the statistical power of a subsequent analysis. In this paper, we propose a novel approach for view imputation via generative adversarial networks (GANs), which we name by VIGAN. This approach first treats each view as a separate domain and identifies domain-to-domain mappings via a GAN using randomly-sampled data from each view, and then employs a multi-modal denoising autoencoder (DAE) to reconstruct the missing view from the GAN outputs based on paired data across the views. Then, by optimizing the GAN and DAE jointly, our model enables the knowledge integration for domain mappings and view correspondences to effectively recover the missing view. Empirical results on benchmark datasets validate the VIGAN approach by comparing against the state of the art. The evaluation of VIGAN in a genetic study of substance use disorders further proves the effectiveness and usability of this approach in life science.

Xin Wang, Jinbo Bi, Shipeng Yu et al.

We investigate a general framework of multiplicative multitask feature learning which decomposes each task's model parameters into a multiplication of two components. One of the components is used across all tasks and the other component is task-specific. Several previous methods have been proposed as special cases of our framework. We study the theoretical properties of this framework when different regularization conditions are applied to the two decomposed components. We prove that this framework is mathematically equivalent to the widely used multitask feature learning methods that are based on a joint regularization of all model parameters, but with a more general form of regularizers. Further, an analytical formula is derived for the across-task component as related to the task-specific component for all these regularizers, leading to a better understanding of the shrinkage effect. Study of this framework motivates new multitask learning algorithms. We propose two new learning formulations by varying the parameters in the proposed framework. Empirical studies have revealed the relative advantages of the two new formulations by comparing with the state of the art, which provides instructive insights into the feature learning problem with multiple tasks.