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Counterfactual Explanations are becoming a de-facto standard in post-hoc interpretable machine learning. For a given classifier and an instance classified in an undesired class, its counterfactual explanation corresponds to small perturbations of that instance that allows changing the classification outcome. This work aims to leverage Counterfactual Explanations to detect the important decision boundaries of a pre-trained black-box model. This information is used to build a supervised discretization of the features in the dataset with a tunable granularity. Using the discretized dataset, an optimal Decision Tree can be trained that resembles the black-box model, but that is interpretable and compact. Numerical results on real-world datasets show the effectiveness of the approach in terms of accuracy and sparsity.

Comparison and contrast are the basic means to unveil causation and learn which treatments work. To build good comparisons that isolate the average effect of treatment from confounding factors, randomization is key, yet often infeasible. In such non-experimental settings, we illustrate and discuss how well the common linear regression approach to causal inference approximates features of randomized experiments, such as covariate balance, study representativeness, sample-grounded estimation, and unweighted analyses. We also discuss alternative regression modeling, weighting, and matching approaches. We argue they should be given strong consideration in empirical work.

In many contexts, customized and weighted classification scores are designed in order to evaluate the goodness of the predictions carried out by neural networks. However, there exists a discrepancy between the maximization of such scores and the minimization of the loss function in the training phase. In this paper, we provide a complete theoretical setting that formalizes weighted classification metrics and then allows the construction of losses that drive the model to optimize these metrics of interest. After a detailed theoretical analysis, we show that our framework includes as particular instances well-established approaches such as classical cost-sensitive learning, weighted cross entropy loss functions and value-weighted skill scores.

Tumor heterogeneity is a challenge to designing effective and targeted therapies. Glioma-type identification depends on specific molecular and histological features, which are defined by the official WHO classification CNS. These guidelines are constantly updated to support the diagnosis process, which affects all the successive clinical decisions. In this context, the search for new potential diagnostic and prognostic targets, characteristic of each glioma type, is crucial to support the development of novel therapies. Based on a TCGA glioma RNA-sequencing dataset updated according to the 2016 and 2021 WHO guidelines, we proposed a two-step variable selection approach for biomarker discovery. Our framework encompasses the graphical lasso algorithm to estimate sparse networks of genes carrying diagnostic information. These networks are then used as input for regularised Cox survival regression model, allowing the identification of a smaller subset of genes with prognostic value. In each step, the results derived from the 2016 and 2021 classes were discussed and compared. For both WHO glioma classifications, our analysis identifies potential biomarkers, characteristic of each glioma type. Yet, better results were obtained for the WHO CNS classification in 2021, thereby supporting recent efforts to include molecular data on glioma classification.

Conventional Gaussian process regression exclusively assumes the existence of noise in the output data of model observations. In many scientific and engineering applications, however, the input locations of observational data may also be compromised with uncertainties owing to modeling assumptions, measurement errors, etc. In this work, we propose a Bayesian method that integrates the variability of input data into Gaussian process regression. Considering two types of observables -- noise-corrupted outputs with fixed inputs and those with prior-distribution-defined uncertain inputs, a posterior distribution is estimated via a Bayesian framework to infer the uncertain data locations. Thereafter, such quantified uncertainties of inputs are incorporated into Gaussian process predictions by means of marginalization. The effectiveness of this new regression technique is demonstrated through several numerical examples, in which a consistently good performance of generalization is observed, while a substantial reduction in the predictive uncertainties is achieved by the Bayesian inference of uncertain inputs.

When dealing with time series data, causal inference methods often employ structural vector autoregressive (SVAR) processes to model time-evolving random systems. In this work, we rephrase recursive SVAR processes with possible latent component processes as a linear Structural Causal Model (SCM) of stochastic processes on a simple causal graph, the \emph{process graph}, that models every process as a single node. Using this reformulation, we generalise Wright's well-known path-rule for linear Gaussian SCMs to the newly introduced process SCMs and we express the auto-covariance sequence of an SVAR process by means of a generalised trek-rule. Employing the Fourier-Transformation, we derive compact expressions for causal effects in the frequency domain that allow us to efficiently visualise the causal interactions in a multivariate SVAR process. Finally, we observe that the process graph can be used to formulate graphical criteria for identifying causal effects and to derive algebraic relations with which these frequency domain causal effects can be recovered from the observed spectral density.

Multiple instance learning (MIL) is a powerful tool to solve the weakly supervised classification in whole slide image (WSI) based pathology diagnosis. However, the current MIL methods are usually based on independent and identical distribution hypothesis, thus neglect the correlation among different instances. To address this problem, we proposed a new framework, called correlated MIL, and provided a proof for convergence. Based on this framework, we devised a Transformer based MIL (TransMIL), which explored both morphological and spatial information. The proposed TransMIL can effectively deal with unbalanced/balanced and binary/multiple classification with great visualization and interpretability. We conducted various experiments for three different computational pathology problems and achieved better performance and faster convergence compared with state-of-the-art methods. The test AUC for the binary tumor classification can be up to 93.09% over CAMELYON16 dataset. And the AUC over the cancer subtypes classification can be up to 96.03% and 98.82% over TCGA-NSCLC dataset and TCGA-RCC dataset, respectively.

Artificial neural networks thrive in solving the classification problem for a particular rigid task, acquiring knowledge through generalized learning behaviour from a distinct training phase. The resulting network resembles a static entity of knowledge, with endeavours to extend this knowledge without targeting the original task resulting in a catastrophic forgetting. Continual learning shifts this paradigm towards networks that can continually accumulate knowledge over different tasks without the need to retrain from scratch. We focus on task incremental classification, where tasks arrive sequentially and are delineated by clear boundaries. Our main contributions concern 1) a taxonomy and extensive overview of the state-of-the-art, 2) a novel framework to continually determine the stability-plasticity trade-off of the continual learner, 3) a comprehensive experimental comparison of 11 state-of-the-art continual learning methods and 4 baselines. We empirically scrutinize method strengths and weaknesses on three benchmarks, considering Tiny Imagenet and large-scale unbalanced iNaturalist and a sequence of recognition datasets. We study the influence of model capacity, weight decay and dropout regularization, and the order in which the tasks are presented, and qualitatively compare methods in terms of required memory, computation time, and storage.

In recent years, there has been an exponential growth in the number of complex documents and texts that require a deeper understanding of machine learning methods to be able to accurately classify texts in many applications. Many machine learning approaches have achieved surpassing results in natural language processing. The success of these learning algorithms relies on their capacity to understand complex models and non-linear relationships within data. However, finding suitable structures, architectures, and techniques for text classification is a challenge for researchers. In this paper, a brief overview of text classification algorithms is discussed. This overview covers different text feature extractions, dimensionality reduction methods, existing algorithms and techniques, and evaluations methods. Finally, the limitations of each technique and their application in the real-world problem are discussed.

Few-shot image classification aims to classify unseen classes with limited labeled samples. Recent works benefit from the meta-learning process with episodic tasks and can fast adapt to class from training to testing. Due to the limited number of samples for each task, the initial embedding network for meta learning becomes an essential component and can largely affects the performance in practice. To this end, many pre-trained methods have been proposed, and most of them are trained in supervised way with limited transfer ability for unseen classes. In this paper, we proposed to train a more generalized embedding network with self-supervised learning (SSL) which can provide slow and robust representation for downstream tasks by learning from the data itself. We evaluate our work by extensive comparisons with previous baseline methods on two few-shot classification datasets ({\em i.e.,} MiniImageNet and CUB). Based on the evaluation results, the proposed method achieves significantly better performance, i.e., improve 1-shot and 5-shot tasks by nearly \textbf{3\%} and \textbf{4\%} on MiniImageNet, by nearly \textbf{9\%} and \textbf{3\%} on CUB. Moreover, the proposed method can gain the improvement of (\textbf{15\%}, \textbf{13\%}) on MiniImageNet and (\textbf{15\%}, \textbf{8\%}) on CUB by pretraining using more unlabeled data. Our code will be available at \hyperref[//github.com/phecy/SSL-FEW-SHOT.]{//github.com/phecy/ssl-few-shot.}