This dissertation addresses achieving causal interpretability in Deep Learning for Software Engineering (DL4SE). While Neural Code Models (NCMs) show strong performance in automating software tasks, their lack of transparency in causal relationships between inputs and outputs limits full understanding of their capabilities. To build trust in NCMs, researchers and practitioners must explain code predictions. Associational interpretability, which identifies correlations, is often insufficient for tasks requiring intervention and change analysis. To address this, the dissertation introduces DoCode, a novel post hoc interpretability method for NCMs. DoCode uses causal inference to provide programming language-oriented explanations of model predictions. It follows a four-step pipeline: modeling causal problems using Structural Causal Models (SCMs), identifying the causal estimand, estimating effects with metrics like Average Treatment Effect (ATE), and refuting effect estimates. Its framework is extensible, with an example that reduces spurious correlations by grounding explanations in programming language properties. A case study on deep code generation across interpretability scenarios and various deep learning architectures demonstrates DoCode's benefits. Results show NCMs' sensitivity to code syntax changes and their ability to learn certain programming concepts while minimizing confounding bias. The dissertation also examines associational interpretability as a foundation, analyzing software information's causal nature using tools like COMET and TraceXplainer for traceability. It highlights the need to identify code confounders and offers practical guidelines for applying causal interpretability to NCMs, contributing to more trustworthy AI in software engineering.

Natural language processing (NLP) has witnessed a profound impact of large language models (LLMs) that excel in a multitude of tasks. However, the limitation of LLMs in multilingual settings, particularly in underrepresented languages, remains a significant hurdle. This thesis aims to bridge the gap in NLP research and development by focusing on underrepresented languages. A comprehensive evaluation of LLMs is conducted to assess their capabilities in these languages, revealing the challenges of multilingual and multicultural generalization. Addressing the multilingual generalization gap, this thesis proposes data-and-compute-efficient methods to mitigate the disparity in LLM ability in underrepresented languages, allowing better generalization on underrepresented languages without the loss of task generalization ability. The proposed solutions cover cross-lingual continual instruction tuning, retrieval-based cross-lingual in-context learning, and in-context query alignment. Furthermore, a novel method to measure cultural values alignment between LLMs operating in different languages is proposed, ensuring cultural sensitivity and inclusivity. These contributions aim to enhance the multilingual and multicultural alignment of LLMs in underrepresented languages, ultimately advancing the NLP field toward greater equality and inclusiveness.

Technical advances in collaborative robots (cobots) are making them increasingly attractive to companies. However, many human operators are not trained to program complex machines. Instead, humans are used to communicating with each other on a task-based level rather than through specific instructions, as is common with machines. The gap between low-level instruction-based and high-level task-based communication leads to low values for usability scores of teach pendant programming. As a solution, we propose a task-based interaction concept that allows human operators to delegate a complex task to a machine without programming by specifying a task via triplets. The concept is based on task decomposition and a reasoning system using a cognitive architecture. The approach is evaluated in an industrial use case where mineral cast basins have to be sanded by a cobot in a crafts enterprise.

Self-adaptive systems offer several attack surfaces due to the communication via different channels and the different sensors required to observe the environment. Often, attacks cause safety to be compromised as well, making it necessary to consider these two aspects together. Furthermore, the approaches currently used for safety and security analysis do not sufficiently take into account the intermediate steps of an adaptation. Current work in this area ignores the fact that a self-adaptive system also reveals possible vulnerabilities (even if only temporarily) during the adaptation. To address this issue, we propose a modeling approach that takes into account the different relevant aspects of a system, its adaptation process, as well as safety hazards and security attacks. We present several models that describe different aspects of a self-adaptive system and we outline our idea of how these models can then be combined into an Attack-Fault Tree. This allows modeling aspects of the system on different levels of abstraction and co-evolve the models using transformations according to the adaptation of the system. Finally, analyses can then be performed as usual on the resulting Attack-Fault Tree.

Intense debate in the Neurology community before 2010 culminated in hypothetical models of Alzheimer's disease progression: a pathophysiological cascade of biomarkers, each dynamic for only a segment of the full disease timeline. Inspired by this, data-driven disease progression modelling emerged from the computer science community with the aim to reconstruct neurodegenerative disease timelines using data from large cohorts of patients, healthy controls, and prodromal/at-risk individuals. This chapter describes selected highlights from the field, with a focus on utility for understanding and forecasting of disease progression.

Today, many industrial processes are undergoing digital transformation, which often requires the integration of well-understood domain models and state-of-the-art machine learning technology in business processes. However, requirements elicitation and design decision making about when, where and how to embed various domain models and end-to-end machine learning techniques properly into a given business workflow requires further exploration. This paper aims to provide an overview of the requirements engineering process for machine learning applications in terms of cross domain collaborations. We first review the literature on requirements engineering for machine learning, and then go through the collaborative requirements analysis process step-by-step. An example case of industrial data-driven intelligence applications is also discussed in relation to the aforementioned steps.

Various structures in human physiology follow a treelike morphology, which often expresses complexity at very fine scales. Examples of such structures are intrathoracic airways, retinal blood vessels, and hepatic blood vessels. Large collections of 2D and 3D images have been made available by medical imaging modalities such as magnetic resonance imaging (MRI), computed tomography (CT), Optical coherence tomography (OCT) and ultrasound in which the spatial arrangement can be observed. Segmentation of these structures in medical imaging is of great importance since the analysis of the structure provides insights into disease diagnosis, treatment planning, and prognosis. Manually labelling extensive data by radiologists is often time-consuming and error-prone. As a result, automated or semi-automated computational models have become a popular research field of medical imaging in the past two decades, and many have been developed to date. In this survey, we aim to provide a comprehensive review of currently publicly available datasets, segmentation algorithms, and evaluation metrics. In addition, current challenges and future research directions are discussed.

Closed-loop verification of cyber-physical systems with neural network controllers offers strong safety guarantees under certain assumptions. It is, however, difficult to determine whether these guarantees apply at run time because verification assumptions may be violated. To predict safety violations in a verified system, we propose a three-step framework for monitoring the confidence in verification assumptions. First, we represent the sufficient condition for verified safety with a propositional logical formula over assumptions. Second, we build calibrated confidence monitors that evaluate the probability that each assumption holds. Third, we obtain the confidence in the verification guarantees by composing the assumption monitors using a composition function suitable for the logical formula. Our framework provides theoretical bounds on the calibration and conservatism of compositional monitors. In two case studies, we demonstrate that the composed monitors improve over their constituents and successfully predict safety violations.

One way to achieve eXplainable artificial intelligence (XAI) is through the use of post-hoc analysis methods. In particular, methods that generate heatmaps have been used to explain black-box models, such as deep neural network. In some cases, heatmaps are appealing due to the intuitive and visual ways to understand them. However, quantitative analysis that demonstrates the actual potential of heatmaps have been lacking, and comparison between different methods are not standardized as well. In this paper, we introduce a synthetic data that can be generated adhoc along with the ground-truth heatmaps for better quantitative assessment. Each sample data is an image of a cell with easily distinguishable features, facilitating a more transparent assessment of different XAI methods. Comparison and recommendations are made, shortcomings are clarified along with suggestions for future research directions to handle the finer details of select post-hoc analysis methods.