Digital Pathology is a cornerstone in the diagnosis and treatment of diseases. A key task in this field is the identification and segmentation of cells in hematoxylin and eosin-stained images. Existing methods for cell segmentation often require extensive annotated datasets for training and are limited to a predefined cell classification scheme. To overcome these limitations, we propose $\text{CellViT}^{{\scriptscriptstyle ++}}$, a framework for generalized cell segmentation in digital pathology. $\text{CellViT}^{{\scriptscriptstyle ++}}$ utilizes Vision Transformers with foundation models as encoders to compute deep cell features and segmentation masks simultaneously. To adapt to unseen cell types, we rely on a computationally efficient approach. It requires minimal data for training and leads to a drastically reduced carbon footprint. We demonstrate excellent performance on seven different datasets, covering a broad spectrum of cell types, organs, and clinical settings. The framework achieves remarkable zero-shot segmentation and data-efficient cell-type classification. Furthermore, we show that $\text{CellViT}^{{\scriptscriptstyle ++}}$ can leverage immunofluorescence stainings to generate training datasets without the need for pathologist annotations. The automated dataset generation approach surpasses the performance of networks trained on manually labeled data, demonstrating its effectiveness in creating high-quality training datasets without expert annotations. To advance digital pathology, $\text{CellViT}^{{\scriptscriptstyle ++}}$ is available as an open-source framework featuring a user-friendly, web-based interface for visualization and annotation. The code is available under https://github.com/TIO-IKIM/CellViT-plus-plus.

Context. Developing secure and reliable software remains a key challenge in software engineering (SE). The ever-evolving technological landscape offers both opportunities and threats, creating a dynamic space where chaos and order compete. Secure software engineering (SSE) must continuously address vulnerabilities that endanger software systems and carry broader socio-economic risks, such as compromising critical national infrastructure and causing significant financial losses. Researchers and practitioners have explored methodologies like Static Application Security Testing Tools (SASTTs) and artificial intelligence (AI) approaches, including machine learning (ML) and large language models (LLMs), to detect and mitigate these vulnerabilities. Each method has unique strengths and limitations. Aim. This thesis seeks to bring order to the chaos in SSE by addressing domain-specific differences that impact AI accuracy. Methodology. The research employs a mix of empirical strategies, such as evaluating effort-aware metrics, analyzing SASTTs, conducting method-level analysis, and leveraging evidence-based techniques like systematic dataset reviews. These approaches help characterize vulnerability prediction datasets. Results. Key findings include limitations in static analysis tools for identifying vulnerabilities, gaps in SASTT coverage of vulnerability types, weak relationships among vulnerability severity scores, improved defect prediction accuracy using just-in-time modeling, and threats posed by untouched methods. Conclusions. This thesis highlights the complexity of SSE and the importance of contextual knowledge in improving AI-driven vulnerability and defect prediction. The comprehensive analysis advances effective prediction models, benefiting both researchers and practitioners.

This paper explores the application of Explainable AI (XAI) techniques to improve the transparency and understanding of predictive models in control of automated supply air temperature (ASAT) of Air Handling Unit (AHU). The study focuses on forecasting of ASAT using a linear regression with Huber loss. However, having only a control curve without semantic and/or physical explanation is often not enough. The present study employs one of the XAI methods: Shapley values, which allows to reveal the reasoning and highlight the contribution of each feature to the final ASAT forecast. In comparison to other XAI methods, Shapley values have solid mathematical background, resulting in interpretation transparency. The study demonstrates the contrastive explanations--slices, for each control value of ASAT, which makes it possible to give the client objective justifications for curve changes.

Molecular conformation generation plays key roles in computational drug design. Recently developed deep learning methods, particularly diffusion models have reached competitive performance over traditional cheminformatical approaches. However, these methods are often time-consuming or require extra support from traditional methods. We propose EquiBoost, a boosting model that stacks several equivariant graph transformers as weak learners, to iteratively refine 3D conformations of molecules. Without relying on diffusion techniques, EquiBoost balances accuracy and efficiency more effectively than diffusion-based methods. Notably, compared to the previous state-of-the-art diffusion method, EquiBoost improves generation quality and preserves diversity, achieving considerably better precision of Average Minimum RMSD (AMR) on the GEOM datasets. This work rejuvenates boosting and sheds light on its potential to be a robust alternative to diffusion models in certain scenarios.

The availability of metadata for scientific documents is pivotal in propelling scientific knowledge forward and for adhering to the FAIR principles (i.e. Findability, Accessibility, Interoperability, and Reusability) of research findings. However, the lack of sufficient metadata in published documents, particularly those from smaller and mid-sized publishers, hinders their accessibility. This issue is widespread in some disciplines, such as the German Social Sciences, where publications often employ diverse templates. To address this challenge, our study evaluates various feature learning and prediction methods, including natural language processing (NLP), computer vision (CV), and multimodal approaches, for extracting metadata from documents with high template variance. We aim to improve the accessibility of scientific documents and facilitate their wider use. To support our comparison of these methods, we provide comprehensive experimental results, analyzing their accuracy and efficiency in extracting metadata. Additionally, we provide valuable insights into the strengths and weaknesses of various feature learning and prediction methods, which can guide future research in this field.

We introduce a retrieval approach leveraging Support Vector Regression (SVR) ensembles, bootstrap aggregation (bagging), and embedding spaces on the German Dataset for Legal Information Retrieval (GerDaLIR). By conceptualizing the retrieval task in terms of multiple binary needle-in-a-haystack subtasks, we show improved recall over the baselines (0.849 > 0.803 | 0.829) using our voting ensemble, suggesting promising initial results, without training or fine-tuning any deep learning models. Our approach holds potential for further enhancement, particularly through refining the encoding models and optimizing hyperparameters.

Adversarial attacks are allegedly unnoticeable. Prior studies have designed attack noticeability measures on graphs, primarily using statistical tests to compare the topology of original and (possibly) attacked graphs. However, we observe two critical limitations in the existing measures. First, because the measures rely on simple rules, attackers can readily enhance their attacks to bypass them, reducing their attack "noticeability" and, yet, maintaining their attack performance. Second, because the measures naively leverage global statistics, such as degree distributions, they may entirely overlook attacks until severe perturbations occur, letting the attacks be almost "totally unnoticeable." To address the limitations, we introduce HideNSeek, a learnable measure for graph attack noticeability. First, to mitigate the bypass problem, HideNSeek learns to distinguish the original and (potential) attack edges using a learnable edge scorer (LEO), which scores each edge on its likelihood of being an attack. Second, to mitigate the overlooking problem, HideNSeek conducts imbalance-aware aggregation of all the edge scores to obtain the final noticeability score. Using six real-world graphs, we empirically demonstrate that HideNSeek effectively alleviates the observed limitations, and LEO (i.e., our learnable edge scorer) outperforms eleven competitors in distinguishing attack edges under five different attack methods. For an additional application, we show that LEO boost the performance of robust GNNs by removing attack-like edges.

The UAV-VLA (Visual-Language-Action) system is a tool designed to facilitate communication with aerial robots. By integrating satellite imagery processing with the Visual Language Model (VLM) and the powerful capabilities of GPT, UAV-VLA enables users to generate general flight paths-and-action plans through simple text requests. This system leverages the rich contextual information provided by satellite images, allowing for enhanced decision-making and mission planning. The combination of visual analysis by VLM and natural language processing by GPT can provide the user with the path-and-action set, making aerial operations more efficient and accessible. The newly developed method showed the difference in the length of the created trajectory in 22% and the mean error in finding the objects of interest on a map in 34.22 m by Euclidean distance in the K-Nearest Neighbors (KNN) approach.

The discovery of causal relationships from observed data has attracted significant interest from disciplines such as economics, social sciences, epidemiology, and biology. In practical applications, considerable knowledge of the underlying systems is often unavailable, and real data are often associated with nonlinear causal structures, which make the direct use of most conventional causality analysis methods difficult. This study proposes a novel quantum Peter-Clark (qPC) algorithm for causal discovery that does not assume any underlying model structures. Based on the independence conditional tests in a class of reproducing kernel Hilbert spaces characterized by quantum circuits, the proposed qPC algorithm can explore causal relationships from the observed data drawn from arbitrary distributions. We conducted systematic experiments on fundamental graph parts of causal structures, demonstrating that the qPC algorithm exhibits a significantly better performance, particularly with smaller sample sizes compared to its classical counterpart. Furthermore, we proposed a novel optimization approach based on Kernel Target Alignment (KTA) for determining hyperparameters of quantum kernels. This method effectively reduced the risk of false positives in causal discovery, enabling more reliable inference. Our theoretical and experimental results demonstrate that the proposed quantum algorithm can empower classical algorithms for robust and accurate inference in causal discovery, supporting them in regimes where classical algorithms typically fail. Additionally, the effectiveness of this method was validated using the Boston Housing dataset as a real-world application. These findings demonstrate the new potential of quantum circuit-based causal discovery methods in addressing practical challenges, particularly in small-sample scenarios where traditional approaches have shown limitations.

3D Referring Expression Segmentation (3D-RES) aims to segment point cloud scenes based on a given expression. However, existing 3D-RES approaches face two major challenges: feature ambiguity and intent ambiguity. Feature ambiguity arises from information loss or distortion during point cloud acquisition due to limitations such as lighting and viewpoint. Intent ambiguity refers to the model's equal treatment of all queries during the decoding process, lacking top-down task-specific guidance. In this paper, we introduce an Image enhanced Prompt Decoding Network (IPDN), which leverages multi-view images and task-driven information to enhance the model's reasoning capabilities. To address feature ambiguity, we propose the Multi-view Semantic Embedding (MSE) module, which injects multi-view 2D image information into the 3D scene and compensates for potential spatial information loss. To tackle intent ambiguity, we designed a Prompt-Aware Decoder (PAD) that guides the decoding process by deriving task-driven signals from the interaction between the expression and visual features. Comprehensive experiments demonstrate that IPDN outperforms the state-ofthe-art by 1.9 and 4.2 points in mIoU metrics on the 3D-RES and 3D-GRES tasks, respectively.