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This paper brings mathematical tools to bear on the study of package dependencies in software systems. We introduce structures known as Dependency Structures with Choice (DSC) that provide a mathematical account of such dependencies, inspired by the definition of general event structures in the study of concurrency. We equip DSCs with a particular notion of morphism and show that the category of DSCs is isomorphic to the category of antimatroids. We study the exactness properties of these equivalent categories, and show that they are finitely complete, have finite coproducts but not all coequalizers. Further, we show construct a functor from a category of DSCs equipped with a certain subclass of morphisms to the opposite of the category of finite distributive lattices, making use of a simple finite characterization of the Bruns-Lakser completion, and finally, we introduce a formal account of versions of packages and introduce a mathematical account of package version-bound policies.

The applications of Artificial Intelligence (AI) methods especially machine learning techniques have increased in recent years. Classification algorithms have been successfully applied to different problems such as requirement classification. Although these algorithms have good performance, most of them cannot explain how they make a decision. Explainable Artificial Intelligence (XAI) is a set of new techniques that explain the predictions of machine learning algorithms. In this work, the applicability of XAI for software requirement classification is studied. An explainable software requirement classifier is presented using the LIME algorithm. The explainability of the proposed method is studied by applying it to the PROMISE software requirement dataset. The results show that XAI can help the analyst or requirement specifier to better understand why a specific requirement is classified as functional or non-functional. The important keywords for such decisions are identified and analyzed in detail. The experimental study shows that the XAI can be used to help analysts and requirement specifiers to better understand the predictions of the classifiers for categorizing software requirements. Also, the effect of the XAI on feature reduction is analyzed. The results showed that the XAI model has a positive role in feature analysis.

Artificial intelligence (AI) systems utilizing deep neural networks (DNNs) and machine learning (ML) algorithms are widely used for solving important problems in bioinformatics, biomedical informatics, and precision medicine. However, complex DNNs or ML models, which are often perceived as opaque and black-box, can make it difficult to understand the reasoning behind their decisions. This lack of transparency can be a challenge for both end-users and decision-makers, as well as AI developers. Additionally, in sensitive areas like healthcare, explainability and accountability are not only desirable but also legally required for AI systems that can have a significant impact on human lives. Fairness is another growing concern, as algorithmic decisions should not show bias or discrimination towards certain groups or individuals based on sensitive attributes. Explainable artificial intelligence (XAI) aims to overcome the opaqueness of black-box models and provide transparency in how AI systems make decisions. Interpretable ML models can explain how they make predictions and the factors that influence their outcomes. However, most state-of-the-art interpretable ML methods are domain-agnostic and evolved from fields like computer vision, automated reasoning, or statistics, making direct application to bioinformatics problems challenging without customization and domain-specific adaptation. In this paper, we discuss the importance of explainability in the context of bioinformatics, provide an overview of model-specific and model-agnostic interpretable ML methods and tools, and outline their potential caveats and drawbacks. Besides, we discuss how to customize existing interpretable ML methods for bioinformatics problems. Nevertheless, we demonstrate how XAI methods can improve transparency through case studies in bioimaging, cancer genomics, and text mining.

Software is a great enabler for a number of projects that otherwise would be impossible to perform. Such projects include Space Exploration, Weather Modeling, Genome Projects, and many others. It is critical that software aiding these projects does what it is expected to do. In the terminology of software engineering, software that corresponds to requirements, that is does what it is expected to do is called correct. Checking the correctness of software has been the focus of a great deal of research in the area of software engineering. Practitioners in the field in which software is applied quite often do not assign much value to checking this correctness. Yet, as software systems become larger, potentially combined with distributed subsystems written by different authors, such verification becomes even more important. Concurrent, distributed systems are prone to dangerous errors due to different speeds of execution of their components such as deadlocks, race conditions, or violation of project-specific properties. This project describes an application of a static analysis method called model checking to verification of a distributed system for the Bioinformatics process. In it, we evaluate the efficiency of the model checking approach to the verification of combined processes with an increasing number of concurrently executed steps. We show that our experimental results correspond to analytically derived expectations. We also highlight the importance of static analysis to combined processes in the Bioinformatics field.

Artificial Intelligence (AI) is rapidly becoming integrated into military Command and Control (C2) systems as a strategic priority for many defence forces. The successful implementation of AI is promising to herald a significant leap in C2 agility through automation. However, realistic expectations need to be set on what AI can achieve in the foreseeable future. This paper will argue that AI could lead to a fragility trap, whereby the delegation of C2 functions to an AI could increase the fragility of C2, resulting in catastrophic strategic failures. This calls for a new framework for AI in C2 to avoid this trap. We will argue that antifragility along with agility should form the core design principles for AI-enabled C2 systems. This duality is termed Agile, Antifragile, AI-Enabled Command and Control (A3IC2). An A3IC2 system continuously improves its capacity to perform in the face of shocks and surprises through overcompensation from feedback during the C2 decision-making cycle. An A3IC2 system will not only be able to survive within a complex operational environment, it will also thrive, benefiting from the inevitable shocks and volatility of war.

Human-in-the-loop aims to train an accurate prediction model with minimum cost by integrating human knowledge and experience. Humans can provide training data for machine learning applications and directly accomplish some tasks that are hard for computers in the pipeline with the help of machine-based approaches. In this paper, we survey existing works on human-in-the-loop from a data perspective and classify them into three categories with a progressive relationship: (1) the work of improving model performance from data processing, (2) the work of improving model performance through interventional model training, and (3) the design of the system independent human-in-the-loop. Using the above categorization, we summarize major approaches in the field, along with their technical strengths/ weaknesses, we have simple classification and discussion in natural language processing, computer vision, and others. Besides, we provide some open challenges and opportunities. This survey intends to provide a high-level summarization for human-in-the-loop and motivates interested readers to consider approaches for designing effective human-in-the-loop solutions.

Despite its great success, machine learning can have its limits when dealing with insufficient training data. A potential solution is the additional integration of prior knowledge into the training process which leads to the notion of informed machine learning. In this paper, we present a structured overview of various approaches in this field. We provide a definition and propose a concept for informed machine learning which illustrates its building blocks and distinguishes it from conventional machine learning. We introduce a taxonomy that serves as a classification framework for informed machine learning approaches. It considers the source of knowledge, its representation, and its integration into the machine learning pipeline. Based on this taxonomy, we survey related research and describe how different knowledge representations such as algebraic equations, logic rules, or simulation results can be used in learning systems. This evaluation of numerous papers on the basis of our taxonomy uncovers key methods in the field of informed machine learning.

Interest in the field of Explainable Artificial Intelligence has been growing for decades and has accelerated recently. As Artificial Intelligence models have become more complex, and often more opaque, with the incorporation of complex machine learning techniques, explainability has become more critical. Recently, researchers have been investigating and tackling explainability with a user-centric focus, looking for explanations to consider trustworthiness, comprehensibility, explicit provenance, and context-awareness. In this chapter, we leverage our survey of explanation literature in Artificial Intelligence and closely related fields and use these past efforts to generate a set of explanation types that we feel reflect the expanded needs of explanation for today's artificial intelligence applications. We define each type and provide an example question that would motivate the need for this style of explanation. We believe this set of explanation types will help future system designers in their generation and prioritization of requirements and further help generate explanations that are better aligned to users' and situational needs.

Causal inference is a critical research topic across many domains, such as statistics, computer science, education, public policy and economics, for decades. Nowadays, estimating causal effect from observational data has become an appealing research direction owing to the large amount of available data and low budget requirement, compared with randomized controlled trials. Embraced with the rapidly developed machine learning area, various causal effect estimation methods for observational data have sprung up. In this survey, we provide a comprehensive review of causal inference methods under the potential outcome framework, one of the well known causal inference framework. The methods are divided into two categories depending on whether they require all three assumptions of the potential outcome framework or not. For each category, both the traditional statistical methods and the recent machine learning enhanced methods are discussed and compared. The plausible applications of these methods are also presented, including the applications in advertising, recommendation, medicine and so on. Moreover, the commonly used benchmark datasets as well as the open-source codes are also summarized, which facilitate researchers and practitioners to explore, evaluate and apply the causal inference methods.

Machine-learning models have demonstrated great success in learning complex patterns that enable them to make predictions about unobserved data. In addition to using models for prediction, the ability to interpret what a model has learned is receiving an increasing amount of attention. However, this increased focus has led to considerable confusion about the notion of interpretability. In particular, it is unclear how the wide array of proposed interpretation methods are related, and what common concepts can be used to evaluate them. We aim to address these concerns by defining interpretability in the context of machine learning and introducing the Predictive, Descriptive, Relevant (PDR) framework for discussing interpretations. The PDR framework provides three overarching desiderata for evaluation: predictive accuracy, descriptive accuracy and relevancy, with relevancy judged relative to a human audience. Moreover, to help manage the deluge of interpretation methods, we introduce a categorization of existing techniques into model-based and post-hoc categories, with sub-groups including sparsity, modularity and simulatability. To demonstrate how practitioners can use the PDR framework to evaluate and understand interpretations, we provide numerous real-world examples. These examples highlight the often under-appreciated role played by human audiences in discussions of interpretability. Finally, based on our framework, we discuss limitations of existing methods and directions for future work. We hope that this work will provide a common vocabulary that will make it easier for both practitioners and researchers to discuss and choose from the full range of interpretation methods.