16 Feb 2024

Deep Learning Methods for Omics Data Imputation

Abstract: One common problem in omics data analysis is missing values, which can arise due to various reasons, such as poor tissue quality and insufficient sample volumes. Instead of discarding missing values and related data, imputation approaches offer an alternative means of handling missing data. However, the imputation of missing omics data is a non-trivial task. Difficulties mainly come from high dimensionality, non-linear or non-monotonic relationships within features, technical variations introduced by sampling methods, sample heterogeneity, and the non-random missingness mechanism. Several advanced imputation methods, including deep learning-based methods, have been proposed to address these challenges. Due to its capability of modeling complex patterns and relationships in large and high-dimensional datasets, many researchers have adopted deep learning models to impute missing omics data. This review provides a comprehensive overview of the currently available deep learning-based methods for omics imputation from the perspective of deep generative model architectures such as autoencoder, variational autoencoder, generative adversarial networks, and Transformer, with an emphasis on multi-omics data imputation. In addition, this review also discusses the opportunities that deep learning brings and the challenges that it might face in this field.

4 Nov 2022

Environmentally Informed Buried Object Recognition

The ability to detect and classify buried objects using thermal infrared imaging is affected by the environmental conditions at the time of imaging, which leads to an inconsistent probability of detection. For example, periods of dense overcast or recent precipitation events result in the suppression of the soil temperature difference between the buried object and soil, thus preventing detection. This work introduces an environmentally informed framework to reduce the false alarm rate in the classification of regions of interest (ROIs) in thermal IR images containing buried objects. Using a dataset that consists of thermal images containing buried objects paired with the corresponding environmental and meteorological conditions, we employ a machine learning approach to determine which environmental conditions are the most impactful on the visibility of the buried objects. We find the key environmental conditions include incoming short-wave solar radiation, soil volumetric water content, and average air temperature. For each image, ROIs are computed using a computer vision approach and these ROIs are coupled with the most important environmental conditions to form the input for the classification algorithm. The environmentally informed classification algorithm produces a decision on whether the ROI contains a buried object by simultaneously learning on the ROIs with a classification neural network and on the environmental data using a tabular neural network. On a given set of ROIs, we have shown that the environmentally informed classification approach improves the detection of buried objects within the ROIs.

28 Jul 2021

Deep Learning-Based Structure-Activity Relationship Modeling for Multi-Category Toxicity Classification: A Case Study of 10K Tox21 Chemicals with High-Throughput Cell-Based Androgen Receptor Bioassay Data

Abstract: Deep learning (DL) has attracted the attention of computational toxicologists as it offers a potentially greater power for in silico predictive toxicology than existing shallow learning algorithms. However, contradicting reports have been documented. To further explore the advantages of DL over shallow learning, we conducted this case study using two cell-based androgen receptor (AR) activity datasets with 10K chemicals generated from the Tox21 program. A nested double-loop cross-validation approach was adopted along with a stratified sampling strategy for partitioning chemicals of multiple AR activity classes (i.e., agonist, antagonist, inactive, and inconclusive) at the same distribution rates amongst the training, validation and test subsets. Deep neural networks (DNN) and random forest (RF), representing deep and shallow learning algorithms, respectively, were chosen to carry out structure-activity relationship-based chemical toxicity prediction. Results suggest that DNN significantly outperformed RF (p < 0.001, ANOVA) by 22–27% for four metrics (precision, recall, F-measure, and AUPRC) and by 11% for another (AUROC). Further in-depth analyses of chemical scaffolding shed insights on structural alerts for AR agonists/antagonists and inactive/inconclusive compounds, which may aid in future drug discovery and improvement of toxicity prediction modeling.