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.

不确定性量化（UQ）有助于基于收集的观察和不确定域知识来制定值得信赖的预测。随着各种应用中深度学习的增加，需要使深层模型更加可靠的高效UQ方法的需求。在可以从有效处理不确定性中受益的应用中，是基于深度学习的微分方程（DE）求解器。我们适应了几种最先进的UQ方法，以获得DE解决方案的预测性不确定性，并显示出四种不同类型的结果。

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.

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.

Textual entailment recognition is one of the basic natural language understanding(NLU) tasks. Understanding the meaning of sentences is a prerequisite before applying any natural language processing(NLP) techniques to automatically recognize the textual entailment. A text entails a hypothesis if and only if the true value of the hypothesis follows the text. Classical approaches generally utilize the feature value of each word from word embedding to represent the sentences. In this paper, we propose a novel approach to identifying the textual entailment relationship between text and hypothesis, thereby introducing a new semantic feature focusing on empirical threshold-based semantic text representation. We employ an element-wise Manhattan distance vector-based feature that can identify the semantic entailment relationship between the text-hypothesis pair. We carried out several experiments on a benchmark entailment classification(SICK-RTE) dataset. We train several machine learning(ML) algorithms applying both semantic and lexical features to classify the text-hypothesis pair as entailment, neutral, or contradiction. Our empirical sentence representation technique enriches the semantic information of the texts and hypotheses found to be more efficient than the classical ones. In the end, our approach significantly outperforms known methods in understanding the meaning of the sentences for the textual entailment classification task.

生成模型生成的合成数据可以增强医学成像中渴望数据深度学习模型的性能和能力。但是，（1）（合成）数据集的可用性有限，并且（2）生成模型训练很复杂，这阻碍了它们在研究和临床应用中的采用。为了减少此入口障碍，我们提出了Medigan，Medigan是一站式商店，用于验证的生成型号，该型号是开源框架 - 不合骨python图书馆。 Medigan允许研究人员和开发人员仅在几行代码中创建，增加和域名。在基于收集的最终用户需求的设计决策的指导下，我们基于生成模型的模块化组件（i）执行，（ii）可视化，（iii）搜索和排名以及（iv）贡献。图书馆的可伸缩性和设计是通过其越来越多的综合且易于使用的验证生成模型来证明的，该模型由21种模型组成，利用9种不同的生成对抗网络体系结构在4个域中在11个数据集中训练，即乳腺摄影，内窥镜检查，X射线和X射线和X射线镜头，X射线和X型。 MRI。此外，在这项工作中分析了Medigan的3个应用，其中包括（a）启用社区范围内的限制数据共享，（b）研究生成模型评估指标以及（c）改进临床下游任务。在（b）中，扩展了公共医学图像综合评估和报告标准，我们根据图像归一化和特定于放射学特征提取了Fr \'Echet Inception距离变异性。