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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.

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Explanation:生物信息學。 Publisher:Oxford University Press。 SIT:

Diffusion models are a class of deep generative models that have shown impressive results on various tasks with dense theoretical founding. Although diffusion models have achieved impressive quality and diversity of sample synthesis than other state-of-the-art models, they still suffer from costly sampling procedure and sub-optimal likelihood estimation. Recent studies have shown great enthusiasm on improving the performance of diffusion model. In this article, we present a first comprehensive review of existing variants of the diffusion models. Specifically, we provide a first taxonomy of diffusion models and categorize them variants to three types, namely sampling-acceleration enhancement, likelihood-maximization enhancement and data-generalization enhancement. We also introduce in detail other five generative models (i.e., variational autoencoders, generative adversarial networks, normalizing flow, autoregressive models, and energy-based models), and clarify the connections between diffusion models and these generative models. Then we make a thorough investigation into the applications of diffusion models, including computer vision, natural language processing, waveform signal processing, multi-modal modeling, molecular graph generation, time series modeling, and adversarial purification. Furthermore, we propose new perspectives pertaining to the development of this generative model.

Graph neural networks (GNNs) have emerged as a series of competent graph learning methods for diverse real-world scenarios, ranging from daily applications like recommendation systems and question answering to cutting-edge technologies such as drug discovery in life sciences and n-body simulation in astrophysics. However, task performance is not the only requirement for GNNs. Performance-oriented GNNs have exhibited potential adverse effects like vulnerability to adversarial attacks, unexplainable discrimination against disadvantaged groups, or excessive resource consumption in edge computing environments. To avoid these unintentional harms, it is necessary to build competent GNNs characterised by trustworthiness. To this end, we propose a comprehensive roadmap to build trustworthy GNNs from the view of the various computing technologies involved. In this survey, we introduce basic concepts and comprehensively summarise existing efforts for trustworthy GNNs from six aspects, including robustness, explainability, privacy, fairness, accountability, and environmental well-being. Additionally, we highlight the intricate cross-aspect relations between the above six aspects of trustworthy GNNs. Finally, we present a thorough overview of trending directions for facilitating the research and industrialisation of trustworthy GNNs.

Decision-making algorithms are being used in important decisions, such as who should be enrolled in health care programs and be hired. Even though these systems are currently deployed in high-stakes scenarios, many of them cannot explain their decisions. This limitation has prompted the Explainable Artificial Intelligence (XAI) initiative, which aims to make algorithms explainable to comply with legal requirements, promote trust, and maintain accountability. This paper questions whether and to what extent explainability can help solve the responsibility issues posed by autonomous AI systems. We suggest that XAI systems that provide post-hoc explanations could be seen as blameworthy agents, obscuring the responsibility of developers in the decision-making process. Furthermore, we argue that XAI could result in incorrect attributions of responsibility to vulnerable stakeholders, such as those who are subjected to algorithmic decisions (i.e., patients), due to a misguided perception that they have control over explainable algorithms. This conflict between explainability and accountability can be exacerbated if designers choose to use algorithms and patients as moral and legal scapegoats. We conclude with a set of recommendations for how to approach this tension in the socio-technical process of algorithmic decision-making and a defense of hard regulation to prevent designers from escaping responsibility.

The remarkable success of deep learning has prompted interest in its application to medical diagnosis. Even tough state-of-the-art deep learning models have achieved human-level accuracy on the classification of different types of medical data, these models are hardly adopted in clinical workflows, mainly due to their lack of interpretability. The black-box-ness of deep learning models has raised the need for devising strategies to explain the decision process of these models, leading to the creation of the topic of eXplainable Artificial Intelligence (XAI). In this context, we provide a thorough survey of XAI applied to medical diagnosis, including visual, textual, and example-based explanation methods. Moreover, this work reviews the existing medical imaging datasets and the existing metrics for evaluating the quality of the explanations . Complementary to most existing surveys, we include a performance comparison among a set of report generation-based methods. Finally, the major challenges in applying XAI to medical imaging are also discussed.

Deep neural networks (DNNs) have achieved unprecedented success in the field of artificial intelligence (AI), including computer vision, natural language processing and speech recognition. However, their superior performance comes at the considerable cost of computational complexity, which greatly hinders their applications in many resource-constrained devices, such as mobile phones and Internet of Things (IoT) devices. Therefore, methods and techniques that are able to lift the efficiency bottleneck while preserving the high accuracy of DNNs are in great demand in order to enable numerous edge AI applications. This paper provides an overview of efficient deep learning methods, systems and applications. We start from introducing popular model compression methods, including pruning, factorization, quantization as well as compact model design. To reduce the large design cost of these manual solutions, we discuss the AutoML framework for each of them, such as neural architecture search (NAS) and automated pruning and quantization. We then cover efficient on-device training to enable user customization based on the local data on mobile devices. Apart from general acceleration techniques, we also showcase several task-specific accelerations for point cloud, video and natural language processing by exploiting their spatial sparsity and temporal/token redundancy. Finally, to support all these algorithmic advancements, we introduce the efficient deep learning system design from both software and hardware perspectives.

Graph neural networks generalize conventional neural networks to graph-structured data and have received widespread attention due to their impressive representation ability. In spite of the remarkable achievements, the performance of Euclidean models in graph-related learning is still bounded and limited by the representation ability of Euclidean geometry, especially for datasets with highly non-Euclidean latent anatomy. Recently, hyperbolic space has gained increasing popularity in processing graph data with tree-like structure and power-law distribution, owing to its exponential growth property. In this survey, we comprehensively revisit the technical details of the current hyperbolic graph neural networks, unifying them into a general framework and summarizing the variants of each component. More importantly, we present various HGNN-related applications. Last, we also identify several challenges, which potentially serve as guidelines for further flourishing the achievements of graph learning in hyperbolic spaces.

Autonomous driving has achieved a significant milestone in research and development over the last decade. There is increasing interest in the field as the deployment of self-operating vehicles on roads promises safer and more ecologically friendly transportation systems. With the rise of computationally powerful artificial intelligence (AI) techniques, autonomous vehicles can sense their environment with high precision, make safe real-time decisions, and operate more reliably without human interventions. However, intelligent decision-making in autonomous cars is not generally understandable by humans in the current state of the art, and such deficiency hinders this technology from being socially acceptable. Hence, aside from making safe real-time decisions, the AI systems of autonomous vehicles also need to explain how these decisions are constructed in order to be regulatory compliant across many jurisdictions. Our study sheds a comprehensive light on developing explainable artificial intelligence (XAI) approaches for autonomous vehicles. In particular, we make the following contributions. First, we provide a thorough overview of the present gaps with respect to explanations in the state-of-the-art autonomous vehicle industry. We then show the taxonomy of explanations and explanation receivers in this field. Thirdly, we propose a framework for an architecture of end-to-end autonomous driving systems and justify the role of XAI in both debugging and regulating such systems. Finally, as future research directions, we provide a field guide on XAI approaches for autonomous driving that can improve operational safety and transparency towards achieving public approval by regulators, manufacturers, and all engaged stakeholders.

Predictions obtained by, e.g., artificial neural networks have a high accuracy but humans often perceive the models as black boxes. Insights about the decision making are mostly opaque for humans. Particularly understanding the decision making in highly sensitive areas such as healthcare or fifinance, is of paramount importance. The decision-making behind the black boxes requires it to be more transparent, accountable, and understandable for humans. This survey paper provides essential definitions, an overview of the different principles and methodologies of explainable Supervised Machine Learning (SML). We conduct a state-of-the-art survey that reviews past and recent explainable SML approaches and classifies them according to the introduced definitions. Finally, we illustrate principles by means of an explanatory case study and discuss important future directions.

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.

Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics system, learning molecular fingerprints, predicting protein interface, and classifying diseases require that a model to learn from graph inputs. In other domains such as learning from non-structural data like texts and images, reasoning on extracted structures, like the dependency tree of sentences and the scene graph of images, is an important research topic which also needs graph reasoning models. Graph neural networks (GNNs) are connectionist models that capture the dependence of graphs via message passing between the nodes of graphs. Unlike standard neural networks, graph neural networks retain a state that can represent information from its neighborhood with an arbitrary depth. Although the primitive graph neural networks have been found difficult to train for a fixed point, recent advances in network architectures, optimization techniques, and parallel computation have enabled successful learning with them. In recent years, systems based on graph convolutional network (GCN) and gated graph neural network (GGNN) have demonstrated ground-breaking performance on many tasks mentioned above. In this survey, we provide a detailed review over existing graph neural network models, systematically categorize the applications, and propose four open problems for future research.

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