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In the past decades, most work in the area of data analysis and machine learning was focused on optimizing predictive models and getting better results than what was possible with existing models. To what extent the metrics with which such improvements were measured were accurately capturing the intended goal, whether the numerical differences in the resulting values were significant, or whether uncertainty played a role in this study and if it should have been taken into account, was of secondary importance. Whereas probability theory, be it frequentist or Bayesian, used to be the gold standard in science before the advent of the supercomputer, it was quickly replaced in favor of black box models and sheer computing power because of their ability to handle large data sets. This evolution sadly happened at the expense of interpretability and trustworthiness. However, while people are still trying to improve the predictive power of their models, the community is starting to realize that for many applications it is not so much the exact prediction that is of importance, but rather the variability or uncertainty. The work in this dissertation tries to further the quest for a world where everyone is aware of uncertainty, of how important it is and how to embrace it instead of fearing it. A specific, though general, framework that allows anyone to obtain accurate uncertainty estimates is singled out and analysed. Certain aspects and applications of the framework -- dubbed `conformal prediction' -- are studied in detail. Whereas many approaches to uncertainty quantification make strong assumptions about the data, conformal prediction is, at the time of writing, the only framework that deserves the title `distribution-free'. No parametric assumptions have to be made and the nonparametric results also hold without having to resort to the law of large numbers in the asymptotic regime.

We study the potential of noisy labels y to pretrain semantic segmentation models in a multi-modal learning framework for geospatial applications. Specifically, we propose a novel Cross-modal Sample Selection method (CromSS) that utilizes the class distributions P^{(d)}(x,c) over pixels x and classes c modelled by multiple sensors/modalities d of a given geospatial scene. Consistency of predictions across sensors $d$ is jointly informed by the entropy of P^{(d)}(x,c). Noisy label sampling we determine by the confidence of each sensor d in the noisy class label, P^{(d)}(x,c=y(x)). To verify the performance of our approach, we conduct experiments with Sentinel-1 (radar) and Sentinel-2 (optical) satellite imagery from the globally-sampled SSL4EO-S12 dataset. We pair those scenes with 9-class noisy labels sourced from the Google Dynamic World project for pretraining. Transfer learning evaluations (downstream task) on the DFC2020 dataset confirm the effectiveness of the proposed method for remote sensing image segmentation.

The influence of natural image transformations on receptive field responses is crucial for modelling visual operations in computer vision and biological vision. In this regard, covariance properties with respect to geometric image transformations in the earliest layers of the visual hierarchy are essential for expressing robust image operations, and for formulating invariant visual operations at higher levels. This paper defines and proves a set of joint covariance properties under compositions of spatial scaling transformations, spatial affine transformations, Galilean transformations and temporal scaling transformations, which make it possible to characterize how different types of image transformations interact with each other and the associated spatio-temporal receptive field responses. In this regard, we also extend the notion of scale-normalized derivatives to affine-normalized derivatives, to be able to obtain true affine-covariant properties of spatial derivatives, that are computed based on spatial smoothing with affine Gaussian kernels. The derived relations show how the parameters of the receptive fields need to be transformed, in order to match the output from spatio-temporal receptive fields under composed spatio-temporal image transformations. As a side effect, the presented proof for the joint covariance property over the integrated combination of the different geometric image transformations also provides specific proofs for the individual transformation properties, which have not previously been fully reported in the literature. The paper also presents an in-depth theoretical analysis of geometric interpretations of the derived covariance properties, as well as outlines a number of biological interpretations of these results.

A common problem in numerous research areas, particularly in clinical trials, is to test whether the effect of an explanatory variable on an outcome variable is equivalent across different groups. In practice, these tests are frequently used to compare the effect between patient groups, e.g. based on gender, age or treatments. Equivalence is usually assessed by testing whether the difference between the groups does not exceed a pre-specified equivalence threshold. Classical approaches are based on testing the equivalence of single quantities, e.g. the mean, the area under the curve (AUC) or other values of interest. However, when differences depending on a particular covariate are observed, these approaches can turn out to be not very accurate. Instead, whole regression curves over the entire covariate range, describing for instance the time window or a dose range, are considered and tests are based on a suitable distance measure of two such curves, as, for example, the maximum absolute distance between them. In this regard, a key assumption is that the true underlying regression models are known, which is rarely the case in practice. However, misspecification can lead to severe problems as inflated type I errors or, on the other hand, conservative test procedures. In this paper, we propose a solution to this problem by introducing a flexible extension of such an equivalence test using model averaging in order to overcome this assumption and making the test applicable under model uncertainty. Precisely, we introduce model averaging based on smooth AIC weights and we propose a testing procedure which makes use of the duality between confidence intervals and hypothesis testing. We demonstrate the validity of our approach by means of a simulation study and demonstrate the practical relevance of the approach considering a time-response case study with toxicological gene expression data.

Breast cancer, the second most prevalent cancer among women worldwide, necessitates the exploration of novel therapeutic approaches. To target the four subgroups of breast cancer "hormone receptor-positive and HER2-negative, hormone receptor-positive and HER2-positive, hormone receptor-negative and HER2-positive, and hormone receptor-negative and HER2-negative" it is crucial to inhibit specific targets such as EGFR, HER2, ER, NF-kB, and PR. In this study, we evaluated various methods for binary and multiclass classification. Among them, the GA-SVM-SVM:GA-SVM-SVM model was selected with an accuracy of 0.74, an F1-score of 0.73, and an AUC of 0.94 for virtual screening of ligands from the BindingDB database. This model successfully identified 4454, 803, 438, and 378 ligands with over 90% precision in both active/inactive and target prediction for the classes of EGFR+HER2, ER, NF-kB, and PR, respectively, from the BindingDB database. Based on to the selected ligands, we created a dendrogram that categorizes different ligands based on their targets. This dendrogram aims to facilitate the exploration of chemical space for various therapeutic targets. Ligands that surpassed a 90% threshold in the product of activity probability and correct target selection probability were chosen for further investigation using molecular docking. The binding energy range for these ligands against their respective targets was calculated to be between -15 and -5 kcal/mol. Finally, based on general and common rules in medicinal chemistry, we selected 2, 3, 3, and 8 new ligands with high priority for further studies in the EGFR+HER2, ER, NF-kB, and PR classes, respectively.

Exploring the semantic context in scene images is essential for indoor scene recognition. However, due to the diverse intra-class spatial layouts and the coexisting inter-class objects, modeling contextual relationships to adapt various image characteristics is a great challenge. Existing contextual modeling methods for scene recognition exhibit two limitations: 1) They typically model only one kind of spatial relationship among objects within scenes in an artificially predefined manner, with limited exploration of diverse spatial layouts. 2) They often overlook the differences in coexisting objects across different scenes, suppressing scene recognition performance. To overcome these limitations, we propose SpaCoNet, which simultaneously models Spatial relation and Co-occurrence of objects guided by semantic segmentation. Firstly, the Semantic Spatial Relation Module (SSRM) is constructed to model scene spatial features. With the help of semantic segmentation, this module decouples the spatial information from the scene image and thoroughly explores all spatial relationships among objects in an end-to-end manner. Secondly, both spatial features from the SSRM and deep features from the Image Feature Extraction Module are allocated to each object, so as to distinguish the coexisting object across different scenes. Finally, utilizing the discriminative features above, we design a Global-Local Dependency Module to explore the long-range co-occurrence among objects, and further generate a semantic-guided feature representation for indoor scene recognition. Experimental results on three widely used scene datasets demonstrate the effectiveness and generality of the proposed method.

Purpose: Radiologists are tasked with visually scrutinizing large amounts of data produced by 3D volumetric imaging modalities. Small signals can go unnoticed during the 3d search because they are hard to detect in the visual periphery. Recent advances in machine learning and computer vision have led to effective computer-aided detection (CADe) support systems with the potential to mitigate perceptual errors. Approach: Sixteen non-expert observers searched through digital breast tomosynthesis (DBT) phantoms and single cross-sectional slices of the DBT phantoms. The 3D/2D searches occurred with and without a convolutional neural network (CNN)-based CADe support system. The model provided observers with bounding boxes superimposed on the image stimuli while they looked for a small microcalcification signal and a large mass signal. Eye gaze positions were recorded and correlated with changes in the area under the ROC curve (AUC). Results: The CNN-CADe improved the 3D search for the small microcalcification signal (delta AUC = 0.098, p = 0.0002) and the 2D search for the large mass signal (delta AUC = 0.076, p = 0.002). The CNN-CADe benefit in 3D for the small signal was markedly greater than in 2D (delta delta AUC = 0.066, p = 0.035). Analysis of individual differences suggests that those who explored the least with eye movements benefited the most from the CNN-CADe (r = -0.528, p = 0.036). However, for the large signal, the 2D benefit was not significantly greater than the 3D benefit (delta delta AUC = 0.033, p = 0.133). Conclusion: The CNN-CADe brings unique performance benefits to the 3D (vs. 2D) search of small signals by reducing errors caused by the under-exploration of the volumetric data.

Artificial neural networks thrive in solving the classification problem for a particular rigid task, acquiring knowledge through generalized learning behaviour from a distinct training phase. The resulting network resembles a static entity of knowledge, with endeavours to extend this knowledge without targeting the original task resulting in a catastrophic forgetting. Continual learning shifts this paradigm towards networks that can continually accumulate knowledge over different tasks without the need to retrain from scratch. We focus on task incremental classification, where tasks arrive sequentially and are delineated by clear boundaries. Our main contributions concern 1) a taxonomy and extensive overview of the state-of-the-art, 2) a novel framework to continually determine the stability-plasticity trade-off of the continual learner, 3) a comprehensive experimental comparison of 11 state-of-the-art continual learning methods and 4 baselines. We empirically scrutinize method strengths and weaknesses on three benchmarks, considering Tiny Imagenet and large-scale unbalanced iNaturalist and a sequence of recognition datasets. We study the influence of model capacity, weight decay and dropout regularization, and the order in which the tasks are presented, and qualitatively compare methods in terms of required memory, computation time, and storage.

Radiologist is "doctor's doctor", biomedical image segmentation plays a central role in quantitative analysis, clinical diagnosis, and medical intervention. In the light of the fully convolutional networks (FCN) and U-Net, deep convolutional networks (DNNs) have made significant contributions in biomedical image segmentation applications. In this paper, based on U-Net, we propose MDUnet, a multi-scale densely connected U-net for biomedical image segmentation. we propose three different multi-scale dense connections for U shaped architectures encoder, decoder and across them. The highlights of our architecture is directly fuses the neighboring different scale feature maps from both higher layers and lower layers to strengthen feature propagation in current layer. Which can largely improves the information flow encoder, decoder and across them. Multi-scale dense connections, which means containing shorter connections between layers close to the input and output, also makes much deeper U-net possible. We adopt the optimal model based on the experiment and propose a novel Multi-scale Dense U-Net (MDU-Net) architecture with quantization. Which reduce overfitting in MDU-Net for better accuracy. We evaluate our purpose model on the MICCAI 2015 Gland Segmentation dataset (GlaS). The three multi-scale dense connections improve U-net performance by up to 1.8% on test A and 3.5% on test B in the MICCAI Gland dataset. Meanwhile the MDU-net with quantization achieves the superiority over U-Net performance by up to 3% on test A and 4.1% on test B.

Deep learning constitutes a recent, modern technique for image processing and data analysis, with promising results and large potential. As deep learning has been successfully applied in various domains, it has recently entered also the domain of agriculture. In this paper, we perform a survey of 40 research efforts that employ deep learning techniques, applied to various agricultural and food production challenges. We examine the particular agricultural problems under study, the specific models and frameworks employed, the sources, nature and pre-processing of data used, and the overall performance achieved according to the metrics used at each work under study. Moreover, we study comparisons of deep learning with other existing popular techniques, in respect to differences in classification or regression performance. Our findings indicate that deep learning provides high accuracy, outperforming existing commonly used image processing techniques.