[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] With the widespread usage of many different types of sensors in recent years, large amounts of diverse and complex sensor data have been generated and analyzed to extract useful information. This dissertation focuses on two types of data: aerial images and physiological sensor data. Several new methods have been proposed based on deep learning techniques to advance the state-of-the-art in analyzing these data. For aerial images, a new method for designing effective loss functions for training deep neural networks for object detection, called adaptive salience biased loss (ASBL), has been proposed. In addition, several state-of-the-art deep neural network models for object detection, including RetinaNet, UNet, Yolo, etc., have been adapted and modified to achieve improved performance on a new set of real-world aerial images for bird detection. For physiological sensor data, a deep learning method for alcohol usage detection, called Deep ADA, has been proposed to improve the automatic detection of alcohol usage (ADA) system, which is statistical data analysis pipeline to detect drinking episodes based on wearable physiological sensor data collected from real subjects. Object detection in aerial images remains a challenging problem due to low image resolutions, complex backgrounds, and variations of sizes and orientations of objects in images. The new ASBL method has been designed for training deep neural network object detectors to achieve improved performance. ASBL can be implemented at the image level, which is called image-based ASBL, or at the anchor level, which is called anchor-based ASBL. The method computes saliency information of input images and anchors generated by deep neural network object detectors, and weights different training examples and anchors differently based on their corresponding saliency measurements. It gives complex images and difficult targets more weights during training. In our experiments using two of the largest public benchmark data sets of aerial images, DOTA and NWPU VHR-10, the existing RetinaNet was trained using ASBL to generate an one-stage detector, ASBL-RetinaNet. ASBL-RetinaNet significantly outperformed the original RetinaNet by 3.61 mAP and 12.5 mAP on the two data sets, respectively. In addition, ASBL-RetinaNet outperformed 10 other state-of-art object detection methods. To improve bird detection in aerial images, the Little Birds in Aerial Imagery (LBAI) dataset has been created from real-life aerial imagery data. LBAI contains various flocks and species of birds that are small in size, ranging from 10 by 10 pixel to 40 by 40 pixel. The dataset was labeled and further divided into two subsets, Easy and Hard, based on the complex of background. We have applied and improved some of the best deep learning models to LBAI images, including object detection techniques, such as YOLOv3, SSD, and RetinaNet, and semantic segmentation techniques, such as U-Net and Mask R-CNN. Experimental results show that RetinaNet performed the best overall, outperforming other models by 1.4 and 4.9 F1 scores on the Easy and Hard LBAI dataset, respectively. For physiological sensor data analysis, Deep ADA has been developed to extract features from physiological signals and predict alcohol usage of real subjects in their daily lives. The features extracted are using Convolutional Neural Networks without any human intervention. A large amount of unlabeled data has been used in an unsupervised learning matter to improve the quality of learned features. The method outperformed traditional feature extraction methods by up to 19% higher accuracy.