Gene expression profiling was made more cost-effective by the NIH LINCS program that profiles only ∼1, 000 selected landmark genes and uses them to reconstruct the whole profile. The D–GEX method employs neural networks to infer the entire profile. However, the original D–GEX can be significantly improved. We propose a novel transformative adaptive activation function that improves the gene expression inference even further and which generalizes several existing adaptive activation functions. Our improved neural network achieves an average mean absolute error of 0.1340, which is a significant improvement over our reimplementation of the original D–GEX, which achieves an average mean absolute error of 0.1637. The proposed transformative adaptive function enables a significantly more accurate reconstruction of the full gene expression profiles with only a small increase in the complexity of the model and its training procedure compared to other methods.

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In many contemporary optimization problems, such as hyperparameter tuning for deep learning architectures, it is computationally challenging or even infeasible to evaluate an entire function or its derivatives. This necessitates the use of stochastic algorithms that sample problem data, which can jeopardize the guarantees classically obtained through globalization techniques via a trust region or a line search. Using subsampled function values is particularly challenging for the latter strategy, that relies upon multiple evaluations. On top of that all, there has been an increasing interest for nonconvex formulations of data-related problems. For such instances, one aims at developing methods that converge to second-order stationary points, which is particularly delicate to ensure when one only accesses subsampled approximations of the objective and its derivatives.This paper contributes to this rapidly expanding field by presenting a stochastic algorithm based on negative curvature and Newton-type directions, computed for a subsampling model of the objective. A line-search technique is used to enforce suitable decrease for this model, and for a sufficiently large sample, a similar amount of reduction holds for the true objective. By using probabilistic reasoning, we can then obtain worst-case complexity guarantees for our framework, leading us to discuss appropriate notions of stationarity in a subsampling context. Our analysis, which we illustrate through real data experiments, encompasses the full sampled regime as a special case: it thus provides an insightful generalization of secondorder line-search paradigms to subsampled settings.

Motivation: Gene expression profiling was made cheaper by the NIH LINCS program that profiles only ∼1, 000 selected landmark genes and uses them to reconstruct the whole profile. The D-GEX method employs neural networks to infer the whole profile. However, the original D-GEX can be further significantly improved. Results: We have analyzed the D-GEX method and determined that the inference can be improved using a logistic sigmoid activation function instead of the hyperbolic tangent. Moreover, we propose a novel transformative adaptive activation function that improves the gene expression inference even further and which generalizes several existing adaptive activation functions. Our improved neural network achieves average mean absolute error of 0.1340 which is a significant improvement over our reimplementation of the original D-GEX which achieves average mean absolute error 0.1637

No abstract