A multiobjective deep learning approach for predictive classification in Neuroblastoma

Valerio Maggio; Marco Chierici; Giuseppe Jurman; Cesare Furlanello

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arXiv · 1711.08198

A multiobjective deep learning approach for predictive classification in Neuroblastoma

Valerio Maggio·Marco Chierici·Giuseppe Jurman·Cesare Furlanello

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Abstract

Neuroblastoma is a strongly heterogeneous cancer with very diverse clinical courses that may vary from spontaneous regression to fatal progression; an accurate patient's risk estimation at diagnosis is essential to design appropriate tumor treatment strategies. Neuroblastoma is a paradigm disease where different diagnostic and prognostic endpoints should be predicted from common molecular and clinical information, with increasing complexity, as shown in the FDA MAQC-II study. Here we introduce the novel multiobjective deep learning architecture CDRP (Concatenated Diagnostic Relapse Prognostic) composed by 8 layers to obtain a combined diagnostic and prognostic prediction from high-throughput transcriptomics data. Two distinct loss functions are optimized for the Event Free Survival (EFS) and Overall Survival (OS) prognosis, respectively. We use the High-Risk (HR) diagnostic information as an additional input generated by an autoencoder embedding. The latter is used as network regulariser, based on a clinical algorithm commonly adopted for stratifying patients from cancer stage, age at insurgence of disease, and MYCN, the specific molecular marker. The architecture was applied to Illumina HiSeq2000 RNA-Seq for 498 neuroblastoma patients (176 at high risk) from the Sequencing Quality Control (SEQC) study, obtaining state-of-art on the diagnostic endpoint and improving prediction of prognosis over the HR cohort.

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Valerio Maggio, Marco Chierici, Giuseppe Jurman, Cesare Furlanello. 2018-02-22. A multiobjective deep learning approach for predictive classification in Neuroblastoma. https://arxiv.org/abs/1711.08198

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