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In this thesis, I investigated and enhanced the visual counting task, which automatically estimates the number of objects in still images or video frames. Recently, due to the growing interest in it, several CNN-based solutions have been suggested by the scientific community. These artificial neural networks provide a way to automatically learn effective representations from raw visual data and can be successfully employed to address typical challenges characterizing this task, such as different illuminations and object scales. But apart from these difficulties, I targeted some other crucial limitations in the adoption of CNNs, proposing solutions that I experimentally evaluated in the context of the counting task which turns out to be particularly affected by these shortcomings. In particular, I tackled the problem related to the lack of data needed for training current CNN-based solutions. Given that the budget for labeling is limited, data scarcity still represents an open problem, particularly evident in tasks such as the counting one, where the objects to be labeled are thousands per image. Specifically, I introduced synthetic datasets gathered from virtual environments, where the training labels are automatically collected. I proposed Domain Adaptation strategies aiming at mitigating the domain gap existing between the training and test data distributions. I presented a counting strategy where I took advantage of the redundant information characterizing datasets labeled by multiple annotators. Moreover, I tackled the engineering challenges coming out of the adoption of CNN techniques in environments with limited power resources. I introduced solutions for counting vehicles directly onboard embedded vision systems. Finally, I designed an embedded modular Computer Vision-based system that can carry out several tasks to help monitor individual and collective human safety rules.

Combining information from multi-view images is crucial to improve the performance and robustness of automated methods for disease diagnosis. However, due to the non-alignment characteristics of multi-view images, building correlation and data fusion across views largely remain an open problem. In this study, we present TransFusion, a Transformer-based architecture to merge divergent multi-view imaging information using convolutional layers and powerful attention mechanisms. In particular, the Divergent Fusion Attention (DiFA) module is proposed for rich cross-view context modeling and semantic dependency mining, addressing the critical issue of capturing long-range correlations between unaligned data from different image views. We further propose the Multi-Scale Attention (MSA) to collect global correspondence of multi-scale feature representations. We evaluate TransFusion on the Multi-Disease, Multi-View \& Multi-Center Right Ventricular Segmentation in Cardiac MRI (M\&Ms-2) challenge cohort. TransFusion demonstrates leading performance against the state-of-the-art methods and opens up new perspectives for multi-view imaging integration towards robust medical image segmentation.

The goal of the Mars Sample Return campaign is to collect soil samples from the surface of Mars and return them to Earth for further study. The samples will be acquired and stored in metal tubes by the Perseverance rover and deposited on the Martian surface. As part of this campaign, it is expected the Sample Fetch Rover will be in charge of localizing and gathering up to 35 sample tubes over 150 Martian sols. Autonomous capabilities are critical for the success of the overall campaign and for the Sample Fetch Rover in particular. This work proposes a novel approach for the autonomous detection and pose estimation of the sample tubes. For the detection stage, a Deep Neural Network and transfer learning from a synthetic dataset are proposed. The dataset is created from photorealistic 3D simulations of Martian scenarios. Additionally, Computer Vision techniques are used to estimate the detected sample tubes poses. Finally, laboratory tests of the Sample Localization procedure are performed using the ExoMars Testing Rover on a Mars-like testbed. These tests validate the proposed approach in different hardware architectures, providing promising results related to the sample detection and pose estimation.

Owing to effective and flexible data acquisition, unmanned aerial vehicle (UAV) has recently become a hotspot across the fields of computer vision (CV) and remote sensing (RS). Inspired by recent success of deep learning (DL), many advanced object detection and tracking approaches have been widely applied to various UAV-related tasks, such as environmental monitoring, precision agriculture, traffic management. This paper provides a comprehensive survey on the research progress and prospects of DL-based UAV object detection and tracking methods. More specifically, we first outline the challenges, statistics of existing methods, and provide solutions from the perspectives of DL-based models in three research topics: object detection from the image, object detection from the video, and object tracking from the video. Open datasets related to UAV-dominated object detection and tracking are exhausted, and four benchmark datasets are employed for performance evaluation using some state-of-the-art methods. Finally, prospects and considerations for the future work are discussed and summarized. It is expected that this survey can facilitate those researchers who come from remote sensing field with an overview of DL-based UAV object detection and tracking methods, along with some thoughts on their further developments.

The remarkable practical success of deep learning has revealed some major surprises from a theoretical perspective. In particular, simple gradient methods easily find near-optimal solutions to non-convex optimization problems, and despite giving a near-perfect fit to training data without any explicit effort to control model complexity, these methods exhibit excellent predictive accuracy. We conjecture that specific principles underlie these phenomena: that overparametrization allows gradient methods to find interpolating solutions, that these methods implicitly impose regularization, and that overparametrization leads to benign overfitting. We survey recent theoretical progress that provides examples illustrating these principles in simpler settings. We first review classical uniform convergence results and why they fall short of explaining aspects of the behavior of deep learning methods. We give examples of implicit regularization in simple settings, where gradient methods lead to minimal norm functions that perfectly fit the training data. Then we review prediction methods that exhibit benign overfitting, focusing on regression problems with quadratic loss. For these methods, we can decompose the prediction rule into a simple component that is useful for prediction and a spiky component that is useful for overfitting but, in a favorable setting, does not harm prediction accuracy. We focus specifically on the linear regime for neural networks, where the network can be approximated by a linear model. In this regime, we demonstrate the success of gradient flow, and we consider benign overfitting with two-layer networks, giving an exact asymptotic analysis that precisely demonstrates the impact of overparametrization. We conclude by highlighting the key challenges that arise in extending these insights to realistic deep learning settings.

A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark.

In this paper, we adopt 3D Convolutional Neural Networks to segment volumetric medical images. Although deep neural networks have been proven to be very effective on many 2D vision tasks, it is still challenging to apply them to 3D tasks due to the limited amount of annotated 3D data and limited computational resources. We propose a novel 3D-based coarse-to-fine framework to effectively and efficiently tackle these challenges. The proposed 3D-based framework outperforms the 2D counterpart to a large margin since it can leverage the rich spatial infor- mation along all three axes. We conduct experiments on two datasets which include healthy and pathological pancreases respectively, and achieve the current state-of-the-art in terms of Dice-S{\o}rensen Coefficient (DSC). On the NIH pancreas segmentation dataset, we outperform the previous best by an average of over 2%, and the worst case is improved by 7% to reach almost 70%, which indicates the reliability of our framework in clinical applications.

Deep neural network architectures have traditionally been designed and explored with human expertise in a long-lasting trial-and-error process. This process requires huge amount of time, expertise, and resources. To address this tedious problem, we propose a novel algorithm to optimally find hyperparameters of a deep network architecture automatically. We specifically focus on designing neural architectures for medical image segmentation task. Our proposed method is based on a policy gradient reinforcement learning for which the reward function is assigned a segmentation evaluation utility (i.e., dice index). We show the efficacy of the proposed method with its low computational cost in comparison with the state-of-the-art medical image segmentation networks. We also present a new architecture design, a densely connected encoder-decoder CNN, as a strong baseline architecture to apply the proposed hyperparameter search algorithm. We apply the proposed algorithm to each layer of the baseline architectures. As an application, we train the proposed system on cine cardiac MR images from Automated Cardiac Diagnosis Challenge (ACDC) MICCAI 2017. Starting from a baseline segmentation architecture, the resulting network architecture obtains the state-of-the-art results in accuracy without performing any trial-and-error based architecture design approaches or close supervision of the hyperparameters changes.

In this paper, we focus on three problems in deep learning based medical image segmentation. Firstly, U-net, as a popular model for medical image segmentation, is difficult to train when convolutional layers increase even though a deeper network usually has a better generalization ability because of more learnable parameters. Secondly, the exponential ReLU (ELU), as an alternative of ReLU, is not much different from ReLU when the network of interest gets deep. Thirdly, the Dice loss, as one of the pervasive loss functions for medical image segmentation, is not effective when the prediction is close to ground truth and will cause oscillation during training. To address the aforementioned three problems, we propose and validate a deeper network that can fit medical image datasets that are usually small in the sample size. Meanwhile, we propose a new loss function to accelerate the learning process and a combination of different activation functions to improve the network performance. Our experimental results suggest that our network is comparable or superior to state-of-the-art methods.

Deep learning (DL) based semantic segmentation methods have been providing state-of-the-art performance in the last few years. More specifically, these techniques have been successfully applied to medical image classification, segmentation, and detection tasks. One deep learning technique, U-Net, has become one of the most popular for these applications. In this paper, we propose a Recurrent Convolutional Neural Network (RCNN) based on U-Net as well as a Recurrent Residual Convolutional Neural Network (RRCNN) based on U-Net models, which are named RU-Net and R2U-Net respectively. The proposed models utilize the power of U-Net, Residual Network, as well as RCNN. There are several advantages of these proposed architectures for segmentation tasks. First, a residual unit helps when training deep architecture. Second, feature accumulation with recurrent residual convolutional layers ensures better feature representation for segmentation tasks. Third, it allows us to design better U-Net architecture with same number of network parameters with better performance for medical image segmentation. The proposed models are tested on three benchmark datasets such as blood vessel segmentation in retina images, skin cancer segmentation, and lung lesion segmentation. The experimental results show superior performance on segmentation tasks compared to equivalent models including U-Net and residual U-Net (ResU-Net).