机器学习技术的不断增长的复杂性在实践中越来越多地使用，因此需要解释这些模型的预测和决策，通常用作黑盒。可解释的AI方法要么是基于数值的特征，旨在量化每个功能在预测或符号中提供某些形式的符号解释（例如反事实）的贡献。本文提出了一种名为asteryx的通用不可知论方法，允许同时生成符号解释和基于分数的解释。我们的方法是声明性的，它基于在等效符号表示中进行解释的模型的编码，后者用于生成特定两种类型的符号解释，这些解释是足够的原因和反事实。然后，我们将反映解释和特征W.R.T功能的相关性与某些属性相关联。我们的实验结果表明，拟议方法的可行性及其在提供符号和基于得分的解释方面的有效性。

在本文中，标题为基于模型的SAT方法，用于符合符号解释列举，我们提出了一种通用的不可知论方法，允许生成不同和互补的符号解释。更确切地说，我们通过分析特征与输出之间的关系来生成解释以在本地解释单个预测。我们的方法使用预测模型的命题编码和基于SAT的设置来生成两种类型的符号解释，这些解释是足够的原因和反事实。图像分类任务的实验结果表明，拟议方法的可行性及其在提供充分的原因和反事实解释方面的有效性。

在本文的标题为反事实解释的符号方法中，我们提出了一种新颖的符号方法，以提供分类器预测的反事实解释。与大多数解释方法相反，目标是了解数据的哪些部分以及在多大程度上有助于提出预测，反事实说明表明必须在数据中更改哪些功能才能更改此分类器预测。我们的方法是象征性的，因为它基于在等效的CNF公式中编码分类器的决策功能。在这种方法中，反事实解释被视为最小校正子集（MCS），这是知识基础赔偿中众所周知的概念。因此，这种方法利用了已经存在的MCS生成的已经存在和经过验证的解决方案的优势。我们对贝叶斯分类器的初步实验研究表明，这种方法在几个数据集上的潜力。

Coronary Computed Tomography Angiography (CCTA) provides information on the presence, extent, and severity of obstructive coronary artery disease. Large-scale clinical studies analyzing CCTA-derived metrics typically require ground-truth validation in the form of high-fidelity 3D intravascular imaging. However, manual rigid alignment of intravascular images to corresponding CCTA images is both time consuming and user-dependent. Moreover, intravascular modalities suffer from several non-rigid motion-induced distortions arising from distortions in the imaging catheter path. To address these issues, we here present a semi-automatic segmentation-based framework for both rigid and non-rigid matching of intravascular images to CCTA images. We formulate the problem in terms of finding the optimal \emph{virtual catheter path} that samples the CCTA data to recapitulate the coronary artery morphology found in the intravascular image. We validate our co-registration framework on a cohort of $n=40$ patients using bifurcation landmarks as ground truth for longitudinal and rotational registration. Our results indicate that our non-rigid registration significantly outperforms other co-registration approaches for luminal bifurcation alignment in both longitudinal (mean mismatch: 3.3 frames) and rotational directions (mean mismatch: 28.6 degrees). By providing a differentiable framework for automatic multi-modal intravascular data fusion, our developed co-registration modules significantly reduces the manual effort required to conduct large-scale multi-modal clinical studies while also providing a solid foundation for the development of machine learning-based co-registration approaches.

Artificial intelligence(AI) systems based on deep neural networks (DNNs) and machine learning (ML) algorithms are increasingly used to solve critical problems in bioinformatics, biomedical informatics, and precision medicine. However, complex DNN or ML models that are unavoidably opaque and perceived as black-box methods, may not be able to explain why and how they make certain decisions. Such black-box models are difficult to comprehend not only for targeted users and decision-makers but also for AI developers. Besides, in sensitive areas like healthcare, explainability and accountability are not only desirable properties of AI but also legal requirements -- especially when AI may have significant impacts on human lives. Explainable artificial intelligence (XAI) is an emerging field that aims to mitigate the opaqueness of black-box models and make it possible to interpret how AI systems make their decisions with transparency. An interpretable ML model can explain how it makes predictions and which factors affect the model's outcomes. The majority of state-of-the-art interpretable ML methods have been developed in a domain-agnostic way and originate from computer vision, automated reasoning, or even statistics. Many of these methods cannot be directly applied to bioinformatics problems, without prior customization, extension, and domain adoption. In this paper, we discuss the importance of explainability with a focus on bioinformatics. We analyse and comprehensively overview of model-specific and model-agnostic interpretable ML methods and tools. Via several case studies covering bioimaging, cancer genomics, and biomedical text mining, we show how bioinformatics research could benefit from XAI methods and how they could help improve decision fairness.

Physics-Informed Neural Networks (PINNs) are gaining popularity as a method for solving differential equations. While being more feasible in some contexts than the classical numerical techniques, PINNs still lack credibility. A remedy for that can be found in Uncertainty Quantification (UQ) which is just beginning to emerge in the context of PINNs. Assessing how well the trained PINN complies with imposed differential equation is the key to tackling uncertainty, yet there is lack of comprehensive methodology for this task. We propose a framework for UQ in Bayesian PINNs (B-PINNs) that incorporates the discrepancy between the B-PINN solution and the unknown true solution. We exploit recent results on error bounds for PINNs on linear dynamical systems and demonstrate the predictive uncertainty on a class of linear ODEs.

We show that for a plane imaged by an endoscope the specular isophotes are concentric circles on the scene plane, which appear as nested ellipses in the image. We show that these ellipses can be detected and used to estimate the plane's normal direction, forming a normal reconstruction method, which we validate on simulated data. In practice, the anatomical surfaces visible in endoscopic images are locally planar. We use our method to show that the surface normal can thus be reconstructed for each of the numerous specularities typically visible on moist tissues. We show results on laparoscopic and colonoscopic images.

A significant level of stigma and inequality exists in mental healthcare, especially in under-served populations, which spreads through collected data. When not properly accounted for, machine learning (ML) models learned from data can reinforce the structural biases already present in society. Here, we present a systematic study of bias in ML models designed to predict depression in four different case studies covering different countries and populations. We find that standard ML approaches show regularly biased behaviors. However, we show that standard mitigation techniques, and our own post-hoc method, can be effective in reducing the level of unfair bias. We provide practical recommendations to develop ML models for depression risk prediction with increased fairness and trust in the real world. No single best ML model for depression prediction provides equality of outcomes. This emphasizes the importance of analyzing fairness during model selection and transparent reporting about the impact of debiasing interventions.

Word order, an essential property of natural languages, is injected in Transformer-based neural language models using position encoding. However, recent experiments have shown that explicit position encoding is not always useful, since some models without such feature managed to achieve state-of-the art performance on some tasks. To understand better this phenomenon, we examine the effect of removing position encodings on the pre-training objective itself (i.e., masked language modelling), to test whether models can reconstruct position information from co-occurrences alone. We do so by controlling the amount of masked tokens in the input sentence, as a proxy to affect the importance of position information for the task. We find that the necessity of position information increases with the amount of masking, and that masked language models without position encodings are not able to reconstruct this information on the task. These findings point towards a direct relationship between the amount of masking and the ability of Transformers to capture order-sensitive aspects of language using position encoding.

Mixture of factor analyzer (MFA) model is an efficient model for the analysis of high dimensional data through which the factor-analyzer technique based on the covariance matrices reducing the number of free parameters. The model also provides an important methodology to determine latent groups in data. There are several pieces of research to extend the model based on the asymmetrical and/or with outlier datasets with some known computational limitations that have been examined in frequentist cases. In this paper, an MFA model with a rich and flexible class of skew normal (unrestricted) generalized hyperbolic (called SUNGH) distributions along with a Bayesian structure with several computational benefits have been introduced. The SUNGH family provides considerable flexibility to model skewness in different directions as well as allowing for heavy tailed data. There are several desirable properties in the structure of the SUNGH family, including, an analytically flexible density which leads to easing up the computation applied for the estimation of parameters. Considering factor analysis models, the SUNGH family also allows for skewness and heavy tails for both the error component and factor scores. In the present study, the advantages of using this family of distributions have been discussed and the suitable efficiency of the introduced MFA model using real data examples and simulation has been demonstrated.