The last decade's research in artificial intelligence had a significant impact on the advance of autonomous driving. Yet, safety remains a major concern when it comes to deploying such systems in high-risk environments. The objective of this thesis is to develop methodological tools which provide reliable uncertainty estimates for deep neural networks. First, we introduce a new criterion to reliably estimate model confidence: the true class probability (TCP). We show that TCP offers better properties for failure prediction than current uncertainty measures. Since the true class is by essence unknown at test time, we propose to learn TCP criterion from data with an auxiliary model, introducing a specific learning scheme adapted to this context. The relevance of the proposed approach is validated on image classification and semantic segmentation datasets. Then, we extend our learned confidence approach to the task of domain adaptation where it improves the selection of pseudo-labels in self-training methods. Finally, we tackle the challenge of jointly detecting misclassification and out-of-distributions samples by introducing a new uncertainty measure based on evidential models and defined on the simplex.

The ROC curve is the major tool for assessing not only the performance but also the fairness properties of a similarity scoring function in Face Recognition. In order to draw reliable conclusions based on empirical ROC analysis, evaluating accurately the uncertainty related to statistical versions of the ROC curves of interest is necessary. For this purpose, we explain in this paper that, because the True/False Acceptance Rates are of the form of U-statistics in the case of similarity scoring, the naive bootstrap approach is not valid here and that a dedicated recentering technique must be used instead. This is illustrated on real data of face images, when applied to several ROC-based metrics such as popular fairness metrics.

Subgraph isomorphism or subgraph matching is generally considered as an NP-complete problem, made more complex in practical applications where the edge weights take real values and are subject to measurement noise and possible anomalies. To the best of our knowledge, almost all subgraph matching methods utilize node labels to perform node-node matching. In the absence of such labels (in applications such as image matching and map matching among others), these subgraph matching methods do not work. We propose a method for identifying the node correspondence between a subgraph and a full graph in the inexact case without node labels in two steps - (a) extract the minimal unique topology preserving subset from the subgraph and find its feasible matching in the full graph, and (b) implement a consensus-based algorithm to expand the matched node set by pairing unique paths based on boundary commutativity. Going beyond the existing subgraph matching approaches, the proposed method is shown to have realistically sub-linear computational efficiency, robustness to random measurement noise, and good statistical properties. Our method is also readily applicable to the exact matching case without loss of generality. To demonstrate the effectiveness of the proposed method, a simulation and a case study is performed on the Erdos-Renyi random graphs and the image-based affine covariant features dataset respectively.

The computer chip shortage has prompted Dr Geert van Kollenburg and his colleagues at Eindhoven University of Technology, the Netherlands, to find data-driven methods to optimise chip manufacturing processes. As part of the MadeIn4 project, they have developed a predictive discarding framework in which quality predictions from artificial intelligence (AI) algorithms are used to decide on whether to discard an unfinished product. This approach can improve both the profitability and sustainability of manufacturing processes. In line with Industry 5.0 goals, predictive discarding offers a way for humans and AI to work together to achieve sustainable manufacturing. Our digital society relies on computer chips, but these chips are currently in short supply.

Statistical analysis of tensor-valued data has largely used the tensor-variate normal (TVN) distribution that may be inadequate when data comes from distributions with heavier or lighter tails. We study a general family of elliptically contoured (EC) tensor-variate distributions and derive its characterizations, moments, marginal and conditional distributions, and the EC Wishart distribution. We describe procedures for maximum likelihood estimation from data that are (1) uncorrelated draws from an EC distribution, (2) from a scale mixture of the TVN distribution, and (3) from an underlying but unknown EC distribution, where we extend Tyler's robust estimator. A detailed simulation study highlights the benefits of choosing an EC distribution over the TVN for heavier-tailed data. We develop tensor-variate classification rules using discriminant analysis and EC errors and show that they better predict cats and dogs from images in the Animal Faces-HQ dataset than the TVN-based rules. A novel tensor-on-tensor regression and tensor-variate analysis of variance (TANOVA) framework under EC errors is also demonstrated to better characterize gender, age and ethnic origin than the usual TVN-based TANOVA in the celebrated Labeled Faces of the Wild dataset.

Chronic obstructive pulmonary disease (COPD) is one of the most common chronic illnesses in the world and the third leading cause of mortality worldwide. It is often underdiagnosed or not diagnosed until later in the disease course. Spirometry tests are the gold standard for diagnosing COPD but can be difficult to obtain, especially in resource-poor countries. Chest X-rays (CXRs), however, are readily available and may serve as a screening tool to identify patients with COPD who should undergo further testing. Currently, no research applies deep learning (DL) algorithms that use large multi-site and multi-modal data to detect COPD patients and evaluate fairness across demographic groups. We use three CXR datasets in our study, CheXpert to pre-train models, MIMIC-CXR to develop, and Emory-CXR to validate our models. The CXRs from patients in the early stage of COPD and not on mechanical ventilation are selected for model training and validation. We visualize the Grad-CAM heatmaps of the true positive cases on the base model for both MIMIC-CXR and Emory-CXR test datasets. We further propose two fusion schemes, (1) model-level fusion, including bagging and stacking methods using MIMIC-CXR, and (2) data-level fusion, including multi-site data using MIMIC-CXR and Emory-CXR, and multi-modal using MIMIC-CXRs and MIMIC-IV EHR, to improve the overall model performance. Fairness analysis is performed to evaluate if the fusion schemes have a discrepancy in the performance among different demographic groups. The results demonstrate that DL models can detect COPD using CXRs, which can facilitate early screening, especially in low-resource regions where CXRs are more accessible than spirometry. The multi-site data fusion scheme could improve the model generalizability on the Emory-CXR test data. Further studies on using CXR or other modalities to predict COPD ought to be in future work.

Automated planetary transit detection has become vital to prioritize candidates for expert analysis given the scale of modern telescopic surveys. While current methods for short-period exoplanet detection work effectively due to periodicity in the light curves, there lacks a robust approach for detecting single-transit events. However, volunteer-labelled transits recently collected by the Planet Hunters TESS (PHT) project now provide an unprecedented opportunity to investigate a data-driven approach to long-period exoplanet detection. In this work, we train a 1-D convolutional neural network to classify planetary transits using PHT volunteer scores as training data. We find using volunteer scores significantly improves performance over synthetic data, and enables the recovery of known planets at a precision and rate matching that of the volunteers. Importantly, the model also recovers transits found by volunteers but missed by current automated methods.

Characterizing the differential excision of mRNA is critical for understanding the functional complexity of a cell or tissue, from normal developmental processes to disease pathogenesis. Most transcript reconstruction methods infer full-length transcripts from high-throughput sequencing data. However, this is a challenging task due to incomplete annotations and the differential expression of transcripts across cell-types, tissues, and experimental conditions. Several recent methods circumvent these difficulties by considering local splicing events, but these methods lose transcript-level splicing information and may conflate transcripts. We develop the first probabilistic model that reconciles the transcript and local splicing perspectives. First, we formalize the sequence of mRNA excisions (SME) reconstruction problem, which aims to assemble variable-length sequences of mRNA excisions from RNA-sequencing data. We then present a novel hierarchical Bayesian admixture model for the Reconstruction of Excised mRNA (BREM). BREM interpolates between local splicing events and full-length transcripts and thus focuses only on SMEs that have high posterior probability. We develop posterior inference algorithms based on Gibbs sampling and local search of independent sets and characterize differential SME usage using generalized linear models based on converged BREM model parameters. We show that BREM achieves higher F1 score for reconstruction tasks and improved accuracy and sensitivity in differential splicing when compared with four state-of-the-art transcript and local splicing methods on simulated data. Lastly, we evaluate BREM on both bulk and scRNA sequencing data based on transcript reconstruction, novelty of transcripts produced, model sensitivity to hyperparameters, and a functional analysis of differentially expressed SMEs, demonstrating that BREM captures relevant biological signal.

Ransomware has appeared as one of the major global threats in recent days. The alarming increasing rate of ransomware attacks and new ransomware variants intrigue the researchers to constantly examine the distinguishing traits of ransomware and refine their detection strategies. Application Programming Interface (API) is a way for one program to collaborate with another; API calls are the medium by which they communicate. Ransomware uses this strategy to interact with the OS and makes a significantly higher number of calls in different sequences to ask for taking action. This research work utilizes the frequencies of different API calls to detect and classify ransomware families. First, a Web-Crawler is developed to automate collecting the Windows Portable Executable (PE) files of 15 different ransomware families. By extracting different frequencies of 68 API calls, we develop our dataset in the first phase of the two-phase feature engineering process. After selecting the most significant features in the second phase of the feature engineering process, we deploy six Supervised Machine Learning models: Na"ive Bayes, Logistic Regression, Random Forest, Stochastic Gradient Descent, K-Nearest Neighbor, and Support Vector Machine. Then, the performances of all the classifiers are compared to select the best model. The results reveal that Logistic Regression can efficiently classify ransomware into their corresponding families securing 99.15% overall accuracy. Finally, instead of relying on the 'Black box' characteristic of the Machine Learning models, we present the post-hoc analysis of our best-performing model using 'SHapley Additive exPlanations' or SHAP values to ascertain the transparency and trustworthiness of the model's prediction.

We all know a single image may convey a message more effectively than a lot of written words. But what consists of an image? When it comes to image segmentation, a common answer might be "things" and "stuff". The concept of things and stuff is used when describing image segmentation methods such as instance and semantic segmentation. Instance segmentation is the identification of countable objects, while semantic segmentation is the identification of regions of texture.