Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Anchor Loss: Modulating Loss Scale Based on Prediction Difficulty

We propose a novel loss function that dynamically re-scales the cross entropy based on prediction difficulty regarding a sample. Deep neural network architectures in image classification tasks struggle to disambiguate visually similar objects. Likewise, in human pose estimation symmetric body parts often confuse the network with assigning indiscriminative scores to them. This is due to the output prediction, in which only the highest confidence label is selected without taking into consideration a measure of uncertainty. In this work, we define the prediction difficulty as a relative property coming from the confidence score gap between positive and negative labels. More precisely, the proposed loss function penalizes the network to avoid the score of a false prediction being significant. To demonstrate the efficacy of our loss function, we evaluate it on two different domains: image classification and human pose estimation. We find improvements in both applications by achieving higher accuracy compared to the baseline methods