Modern scientific discovery faces growing challenges in integrating vast and heterogeneous knowledge critical to breakthroughs in biomedicine and drug development. Traditional hypothesis-driven research, though effective, is constrained by human cognitive limits, the complexity of biological systems, and the high cost of trial-and-error experimentation. Deep learning models, especially graph neural networks (GNNs), have accelerated prediction generation, but the sheer volume of outputs makes manual selection for validation unscalable. Large language models (LLMs) offer promise in filtering and hypothesis generation, yet suffer from hallucinations and lack grounding in structured knowledge, limiting their reliability. To address these issues, we propose HypoChainer, a collaborative visualization framework that integrates human expertise, LLM-driven reasoning, and knowledge graphs (KGs) to enhance hypothesis generation and validation. HypoChainer operates in three stages: First, exploration and contextualization -- experts use retrieval-augmented LLMs (RAGs) and dimensionality reduction to navigate large-scale GNN predictions, assisted by interactive explanations. Second, hypothesis chain formation -- experts iteratively examine KG relationships around predictions and semantically linked entities, refining hypotheses with LLM and KG suggestions. Third, validation prioritization -- refined hypotheses are filtered based on KG-supported evidence to identify high-priority candidates for experimentation, with visual analytics further strengthening weak links in reasoning. We demonstrate HypoChainer's effectiveness through case studies in two domains and expert interviews, highlighting its potential to support interpretable, scalable, and knowledge-grounded scientific discovery.

Modern network intrusion detection systems (NIDS) frequently utilize the predictive power of complex deep learning models. However, the "black-box" nature of such deep learning methods adds a layer of opaqueness that hinders the proper understanding of detection decisions, trust in the decisions and prevent timely countermeasures against such attacks. Explainable AI (XAI) methods provide a solution to this problem by providing insights into the causes of the predictions. The majority of the existing XAI methods provide explanations which are not convenient to convert into actionable countermeasures. In this work, we propose a novel diffusion-based counterfactual explanation framework that can provide actionable explanations for network intrusion attacks. We evaluated our proposed algorithm against several other publicly available counterfactual explanation algorithms on 3 modern network intrusion datasets. To the best of our knowledge, this work also presents the first comparative analysis of existing counterfactual explanation algorithms within the context of network intrusion detection systems. Our proposed method provide minimal, diverse counterfactual explanations out of the tested counterfactual explanation algorithms in a more efficient manner by reducing the time to generate explanations. We also demonstrate how counterfactual explanations can provide actionable explanations by summarizing them to create a set of global rules. These rules are actionable not only at instance level but also at the global level for intrusion attacks. These global counterfactual rules show the ability to effectively filter out incoming attack queries which is crucial for efficient intrusion detection and defense mechanisms.

Spatial transcriptomics (ST) has revolutionized biomedical research by enabling high resolution gene expression profiling within tissues. However, the high cost and scarcity of high resolution ST data remain significant challenges. We present Single-shot Sparser-to-Sparse (S2S-ST), a novel framework for accurate ST imputation that requires only a single and low-cost sparsely sampled ST dataset alongside widely available natural images for co-training. Our approach integrates three key innovations: (1) a sparser-to-sparse self-supervised learning strategy that leverages intrinsic spatial patterns in ST data, (2) cross-domain co-learning with natural images to enhance feature representation, and (3) a Cascaded Data Consistent Imputation Network (CDCIN) that iteratively refines predictions while preserving sampled gene data fidelity. Extensive experiments on diverse tissue types, including breast cancer, liver, and lymphoid tissue, demonstrate that our method outperforms state-of-the-art approaches in imputation accuracy. By enabling robust ST reconstruction from sparse inputs, our framework significantly reduces reliance on costly high resolution data, facilitating potential broader adoption in biomedical research and clinical applications. Keywords: Spatial Transcriptomics, Gene Expression Imputation, Single-shot Learning, Natural Image Co-training, Cost Reduction 1. Introduction Spatial transcriptomics (ST) is a cutting-edge technology that enables the investigation of spatially resolved gene expression within tissues (Asp et al., 2020). Traditional transcriptomic approaches, such as single-cell RNA sequencing (scRNA-seq), provide high-throughput, high resolution gene expression profiles but inherently lack spatial context (Aung et al., 2024; Boe et al., 2024; Sankar et al., 2024). However, spatial information is crucial for identifying disease biomarkers, understanding disease progression, and developing personalized treatment strategies.

Hausa Natural Language Processing (NLP) has gained increasing attention in recent years, yet remains understudied as a low-resource language despite having over 120 million first-language (L1) and 80 million second-language (L2) speakers worldwide. While significant advances have been made in high-resource languages, Hausa NLP faces persistent challenges, including limited open-source datasets and inadequate model representation. This paper presents an overview of the current state of Hausa NLP, systematically examining existing resources, research contributions, and gaps across fundamental NLP tasks: text classification, machine translation, named entity recognition, speech recognition, and question answering. We introduce HausaNLP (https://catalog.hausanlp.org), a curated catalog that aggregates datasets, tools, and research works to enhance accessibility and drive further development. Furthermore, we discuss challenges in integrating Hausa into large language models (LLMs), addressing issues of suboptimal tokenization and dialectal variation. Finally, we propose strategic research directions emphasizing dataset expansion, improved language modeling approaches, and strengthened community collaboration to advance Hausa NLP. Our work provides both a foundation for accelerating Hausa NLP progress and valuable insights for broader multilingual NLP research.

This thesis advances the computational understanding and manipulation of text styles through three interconnected pillars: (1) Text Style Transfer (TST), which alters stylistic properties (e.g., sentiment, formality) while preserving content; (2)Authorship Attribution (AA), identifying the author of a text via stylistic fingerprints; and (3) Authorship V erification (A V), determining whether two texts share the same authorship. We address critical challenges in these areas by leveraging parameter-efficient adaptation of large language models (LLMs), contrastive disentanglement of stylistic features, and instruction-based fine-tuning for explainable verification. First, for TST, we conduct a comprehensive survey and reproducibility study of 19 state-of-the-art algorithms, establishing benchmarks across diverse datasets. Building on these insights, we introduce LLM-Adapters, a unified framework for parameter-efficient fine-tuning (PEFT) that enables cost-effective adaptation of LLMs for style-centric tasks. This culminates in Adapter-TST, a novel architecture that models multiple stylistic attributes (e.g., sentiment, tense) using lightweight neural adapters. Adapter-TST achieves superior performance in multi-attribute transfer and compositional editing while reducing computational costs by 80% compared to full fine-tuning. For AA, we propose ContrastDistAA, a contrastive learning framework that disentangles content and style features to address performance degradation under topic shifts. Our method advances both individual-level attribution and regional linguistic analysis, achieving state-of-the-art accuracy by isolating culturally influenced stylistic patterns.

A "model" is a theory that describes the state of an environment and the effects of an agent's decisions on the environment. A model-based agent can use its model to predict the effects of its future actions and so plan ahead, but must know the state of the environment. A model-free agent cannot plan, but can act without a model and without completely observing the environment. An autonomous agent capable of acting independently in novel environments must combine both sets of capabilities. We show how to create such an agent with Meta-Interpretive Learning used to learn a model-based Solver used to train a model-free Controller that can solve the same planning problems as the Solver. We demonstrate the equivalence in problem-solving ability of the two agents on grid navigation problems in two kinds of environment: randomly generated mazes, and lake maps with wide open areas. We find that all navigation problems solved by the Solver are also solved by the Controller, indicating the two are equivalent.

The emergence of deep research systems presents significant capabilities in problem-solving, extending from basic queries to sophisticated research tasks. However, existing benchmarks primarily evaluate these systems as agents for web retrieval and report generation, overlooking their potential to discover novel insights on the frontiers of scientific research. To address this gap, we introduce ResearcherBench, the first benchmark focused on evaluating the capabilities of these advanced, agentic systems - which we refer to as Deep AI Research Systems (DARS) - on frontier AI scientific questions. We compiled a dataset of 65 research questions expertly selected from real-world scientific scenarios such as laboratory discussions and interviews, spanning 35 different AI subjects and categorized into three types: technical details, literature review, and open consulting. Our dual evaluation framework combines rubric assessment, which uses expert-designed criteria to evaluate insight quality, with factual assessment, which measures citation accuracy (faithfulness) and coverage (groundedness). We evaluated several leading commercial DARS and baseline systems. Results show that OpenAI Deep Research and Gemini Deep Research significantly outperform other systems, with particular strength in open-ended consulting questions. Such capabilities represent a meaningful step toward AI self-improvement, aligning with the vision of ASI for AI. We open-source ResearcherBench to provide a standardized platform for promoting the development of next-generation AI research assistants, hoping to foster a new perspective in AI research evaluation for a novel pattern of scientific collaboration: https://github.com/GAIR-NLP/ResearcherBench.

Combining an energy-efficient drone with a high-capacity truck for last-mile package delivery can benefit operators and customers by reducing delivery times and environmental impact. However, directly integrating drone flight dynamics into the combinatorially hard truck route planning problem is challenging. Simplified models that ignore drone flight physics can lead to suboptimal delivery plans. We propose an integrated formulation for the joint problem of truck route and drone trajectory planning and a new end-to-end solution approach that combines optimization and machine learning to generate high-quality solutions in practical online runtimes. Our solution method trains neural network predictors based on offline solutions to the drone trajectory optimization problem instances to approximate drone flight times, and uses these approximations to optimize the overall truck-and-drone delivery plan by augmenting an existing order-first-split-second heuristic. Our method explicitly incorporates key kinematics and energy equations in drone trajectory optimization, and thereby outperforms state-of-the-art benchmarks that ignore drone flight physics. Extensive experimentation using synthetic datasets and real-world case studies shows that the integration of drone trajectories into package delivery planning substantially improves system performance in terms of tour duration and drone energy consumption. Our modeling and computational framework can help delivery planners achieve annual savings worth millions of dollars while also benefiting the environment.

In large organisations, knowledge is mainly shared in meetings, which takes up significant amounts of work time. Additionally, frequent in-person meetings produce inconsistent documentation -- official minutes, personal notes, presentations may or may not exist. Shared information therefore becomes hard to retrieve outside of the meeting, necessitating lengthy updates and high-frequency meeting schedules. Generative Artificial Intelligence (genAI) models like Large Language Models (LLMs) exhibit an impressive performance on spoken and written language processing. This motivates a practical usage of genAI for knowledge management in engineering departments: using genAI for transcribing meetings and integrating heterogeneous additional information sources into an easily usable format for ad-hoc searches. We implement an end-to-end pipeline to automate the entire meeting documentation workflow in a proof-of-concept state: meetings are recorded and minutes are created by genAI. These are further made easily searchable through a chatbot interface. The core of our work is to test this genAI-based software tooling in a real-world engineering department and collect extensive survey data on both ethical and technical aspects. Direct feedback from this real-world setup points out both opportunities and risks: a) users agree that the effort for meetings could be significantly reduced with the help of genAI models, b) technical aspects are largely solved already, c) organizational aspects are crucial for a successful ethical usage of such a system.

In line with the development of deep learning, this survey examines the trans-formative role of T ransformers and foundation models in advancing visual anomaly detection (VAD). We explore how these architectures, with their global receptive fields and adaptability, address challenges such as long-range dependency modeling, contextual modeling and data scarcity . The survey categorizes VAD methods into reconstruction-based, feature-based and zero/few-shot approaches, highlighting the paradigm shift brought about by foundation models. By integrating attention mechanisms and leveraging large-scale pre-training, T ransformers and foundation models enable more robust, interpretable, and scalable anomaly detection solutions. This work provides a comprehensive review of state-of-the-art techniques, their strengths, limitations, and emerging trends in leveraging these architectures for VAD.