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Test-time augmentation (TTA) is a well-known technique employed during the testing phase of computer vision tasks. It involves aggregating multiple augmented versions of input data. Combining predictions using a simple average formulation is a common and straightforward approach after performing TTA. This paper introduces a novel framework for optimizing TTA, called BayTTA (Bayesian-based TTA), which is based on Bayesian Model Averaging (BMA). First, we generate a prediction list associated with different variations of the input data created through TTA. Then, we use BMA to combine predictions weighted by the respective posterior probabilities. Such an approach allows one to take into account model uncertainty, and thus to enhance the predictive performance of the related machine learning or deep learning model. We evaluate the performance of BayTTA on various public data, including three medical image datasets comprising skin cancer, breast cancer, and chest X-ray images and two well-known gene editing datasets, CRISPOR and GUIDE-seq. Our experimental results indicate that BayTTA can be effectively integrated into state-of-the-art deep learning models used in medical image analysis as well as into some popular pre-trained CNN models such as VGG-16, MobileNetV2, DenseNet201, ResNet152V2, and InceptionRes-NetV2, leading to the enhancement in their accuracy and robustness performance. The source code of the proposed BayTTA method is freely available at: \underline {https://github.com/Z-Sherkat/BayTTA}.

Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species phylogenetic tree that represents the main patterns of vertical descent. However, the evolution of each gene is unique. It can be represented by its own gene tree which can differ substantially from a general species tree representation. Consensus trees and supertrees have been widely used in evolutionary studies to combine phylogenetic information contained in individual gene trees. Nevertheless, if the available gene trees are quite different from each other, then the resulting consensus tree or supertree can either include many unresolved subtrees corresponding to internal nodes of high degree or can simply be a star tree. This may happen if the available gene trees have been affected by different reticulate evolutionary events, such as horizontal gene transfer, hybridization or genetic recombination. Thus, the problem of inferring multiple alternative consensus trees or supertrees, using clustering, becomes relevant since it allows one to regroup in different clusters gene trees having similar evolutionary patterns (e.g. gene trees representing genes that have undergone the same horizontal gene transfer or recombination events). We critically review recent advances and methods in the field of phylogenetic tree clustering, discuss the methods' mathematical properties, and describe the main advantages and limitations of multiple consensus tree and supertree approaches. In the application section, we show how the multiple supertree clustering approach can be used to cluster aaRS gene trees according to their evolutionary patterns.

Phages are one of the most present groups of organisms in the biosphere. Their identification continues and their taxonomies are divergent. However, due to their evolution mode and the complexity of their species ecosystem, their classification is not complete. Here, we present a new approach to the phages classification that combines the methods of horizontal gene transfer detection and ancestral sequence reconstruction., Comment: in French

Motivation: Accurate detection of sequence similarity and homologous recombination are essential parts of many evolutionary analyses. Results: We have developed SimPlot++, an open-source multiplatform application implemented in Python, which can be used to produce publication quality sequence similarity plots using 63 nucleotide and 20 amino acid distance models, to detect intergenic and intragenic recombination events using Phi, Max-X2, NSS or proportion tests, and to generate and analyze interactive sequence similarity networks. SimPlot++ supports multicore data processing and provides useful distance calculability diagnostics. Availability: SimPlot++ is freely available on GitHub at: https://github.com/Stephane-S/Simplot_PlusPlus, as both an executable file (for Windows) and Python scripts (for Windows/Linux/MacOS).

The COVID-19 (Coronavirus disease 2019) pandemic has become a major global threat to human health and well-being. Thus, the development of computer-aided detection (CAD) systems that are capable to accurately distinguish COVID-19 from other diseases using chest computed tomography (CT) and X-ray data is of immediate priority. Such automatic systems are usually based on traditional machine learning or deep learning methods. Differently from most of existing studies, which used either CT scan or X-ray images in COVID-19-case classification, we present a simple but efficient deep learning feature fusion model, called UncertaintyFuseNet, which is able to classify accurately large datasets of both of these types of images. We argue that the uncertainty of the model's predictions should be taken into account in the learning process, even though most of existing studies have overlooked it. We quantify the prediction uncertainty in our feature fusion model using effective Ensemble MC Dropout (EMCD) technique. A comprehensive simulation study has been conducted to compare the results of our new model to the existing approaches, evaluating the performance of competing models in terms of Precision, Recall, F-Measure, Accuracy and ROC curves. The obtained results prove the efficiency of our model which provided the prediction accuracy of 99.08\% and 96.35\% for the considered CT scan and X-ray datasets, respectively. Moreover, our UncertaintyFuseNet model was generally robust to noise and performed well with previously unseen data. The source code of our implementation is freely available at: https://github.com/moloud1987/UncertaintyFuseNet-for-COVID-19-Classification., Comment: 16 pages, 18 figures

Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination events. Thus, the evolutionary history of each gene should be represented by its own phylogenetic tree which may display different evolutionary patterns from the species tree that accounts for the main patterns of vertical descent. The output of traditional consensus tree or supertree inference methods is a unique consensus tree or supertree. We describe a new efficient method for inferring multiple alternative consensus trees and supertrees to best represent the most important evolutionary patterns of a given set of gene phylogenies. We show how an adapted version of the popular k-means clustering algorithm, based on some interesting properties of the Robinson and Foulds distance, can be used to partition a given set of trees into one (for homogeneous data) or multiple (for heterogeneous data) cluster(s) of trees. Moreover, we adapt the popular Cali\'nski-Harabasz, Silhouette, Ball and Hall, and Gap cluster validity indices to tree clustering with k-means. A special attention is given to the relevant but very challenging problem of inferring alternative supertrees. The use of the Euclidean property of the objective function of the method makes it faster than the existing tree clustering techniques, and thus perfectly suitable for analyzing large evolutionary datasets. We apply the new method to discover alternative supertrees characterizing the main patterns of evolution of SARS-CoV-2 and genetically related betacoronaviruses., Comment: Bioinformatics (in press)

The data preprocessing stage is crucial in clustering. Features may describe entities using different scales. To rectify this, one usually applies feature normalisation aiming at rescaling features so that none of them overpowers the others in the objective function of the selected clustering algorithm. In this paper, we argue that the rescaling procedure should not treat all features identically. Instead, it should favour the features that are more meaningful for clustering. With this in mind, we introduce a feature rescaling method that takes into account the within-cluster degree of relevance of each feature. Our comprehensive simulation study, carried out on real and synthetic data, with and without noise features, clearly demonstrates that clustering methods that use the proposed data normalization strategy clearly outperform those that use traditional data normalization.

Uncertainty quantification (UQ) plays a pivotal role in reduction of uncertainties during both optimization and decision making processes. It can be applied to solve a variety of real-world applications in science and engineering. Bayesian approximation and ensemble learning techniques are two most widely-used UQ methods in the literature. In this regard, researchers have proposed different UQ methods and examined their performance in a variety of applications such as computer vision (e.g., self-driving cars and object detection), image processing (e.g., image restoration), medical image analysis (e.g., medical image classification and segmentation), natural language processing (e.g., text classification, social media texts and recidivism risk-scoring), bioinformatics, etc. This study reviews recent advances in UQ methods used in deep learning. Moreover, we also investigate the application of these methods in reinforcement learning (RL). Then, we outline a few important applications of UQ methods. Finally, we briefly highlight the fundamental research challenges faced by UQ methods and discuss the future research directions in this field.

Bootstrap aggregation, known as bagging, is one of the most popular ensemble methods used in machine learning (ML). An ensemble method is a ML method that combines multiple hypotheses to form a single hypothesis used for prediction. A bagging algorithm combines multiple classifiers modeled on different sub-samples of the same data set to build one large classifier. Banks, and their retail banking activities, are nowadays using the power of ML algorithms, including decision trees and random forests, to optimize their processes. However, banks have to comply with regulators and governance and, hence, delivering effective ML solutions is a challenging task. It starts with the bank's validation and governance department, followed by the deployment of the solution in a production environment up to the external validation of the national financial regulator. Each proposed ML model has to be validated and clear rules for every algorithm-based decision must be justified. In this context, we propose XtracTree, an algorithm capable of efficiently converting an ML bagging classifier, such as a random forest, into simple "if-then" rules satisfying the requirements of model validation. We use a public loan data set from Kaggle to illustrate the usefulness of our approach. Our experiments demonstrate that using XtracTree, one can convert an ML model into a rule-based algorithm, leading to easier model validation by national financial regulators and the bank's validation department. The proposed approach allowed our banking institution to reduce up to 50% the time of delivery of our AI solutions to the end-user.

We propose a general framework for policy representation for reinforcement learning tasks. This framework involves finding a low-dimensional embedding of the policy on a reproducing kernel Hilbert space (RKHS). The usage of RKHS based methods allows us to derive strong theoretical guarantees on the expected return of the reconstructed policy. Such guarantees are typically lacking in black-box models, but are very desirable in tasks requiring stability. We conduct several experiments on classic RL domains. The results confirm that the policies can be robustly embedded in a low-dimensional space while the embedded policy incurs almost no decrease in return.

Tensor decomposition, a collection of factorization techniques for multidimensional arrays, are among the most general and powerful tools for scientific analysis. However, because of their increasing size, today's data sets require more complex tensor decomposition involving factorization with multiple matrices and diagonal tensors such as DEDICOM or PARATUCK2. Traditional tensor resolution algorithms such as Stochastic Gradient Descent (SGD), Non-linear Conjugate Gradient descent (NCG) or Alternating Least Square (ALS), cannot be easily applied to complex tensor decomposition or often lead to poor accuracy at convergence. We propose a new resolution algorithm, called VecHGrad, for accurate and efficient stochastic resolution over all existing tensor decomposition, specifically designed for complex decomposition. VecHGrad relies on gradient, Hessian-vector product and adaptive line search to ensure the convergence during optimization. Our experiments on five real-world data sets with the state-of-the-art deep learning gradient optimization models show that VecHGrad is capable of converging considerably faster because of its superior theoretical convergence rate per step. Therefore, VecHGrad targets as well deep learning optimizer algorithms. The experiments are performed for various tensor decomposition including CP, DEDICOM and PARATUCK2. Although it involves a slightly more complex update rule, VecHGrad's runtime is similar in practice to that of gradient methods such as SGD, Adam or RMSProp.

In this paper we make two novel contributions to hierarchical clustering. First, we introduce an anomalous pattern initialisation method for hierarchical clustering algorithms, called A-Ward, capable of substantially reducing the time they take to converge. This method generates an initial partition with a sufficiently large number of clusters. This allows the cluster merging process to start from this partition rather than from a trivial partition composed solely of singletons. Our second contribution is an extension of the Ward and Ward p algorithms to the situation where the feature weight exponent can differ from the exponent of the Minkowski distance. This new method, called A-Ward p\b{eta} , is able to generate a much wider variety of clustering solutions. We also demonstrate that its parameters can be estimated reasonably well by using a cluster validity index. We perform numerous experiments using data sets with two types of noise, insertion of noise features and blurring within-cluster values of some features. These experiments allow us to conclude: (i) our anomalous pattern initialisation method does indeed reduce the time a hierarchical clustering algorithm takes to complete, without negatively impacting its cluster recovery ability; (ii) A-Ward p\b{eta} provides better cluster recovery than both Ward and Ward p.