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The superposition of data sets with internal parametric self-similarity is a longstanding and widespread technique for the analysis of many types of experimental data across the physical sciences. Typically, this superposition is performed manually, or recently by one of a few automated algorithms. However, these methods are often heuristic in nature, are prone to user bias via manual data shifting or parameterization, and lack a native framework for handling uncertainty in both the data and the resulting model of the superposed data. In this work, we develop a data-driven, non-parametric method for superposing experimental data with arbitrary coordinate transformations, which employs Gaussian process regression to learn statistical models that describe the data, and then uses maximum a posteriori estimation to optimally superpose the data sets. This statistical framework is robust to experimental noise, and automatically produces uncertainty estimates for the learned coordinate transformations. Moreover, it is distinguished from black-box machine learning in its interpretability -- specifically, it produces a model that may itself be interrogated to gain insight into the system under study. We demonstrate these salient features of our method through its application to four representative data sets characterizing the mechanics of soft materials. In every case, our method replicates results obtained using other approaches, but with reduced bias and the addition of uncertainty estimates. This method enables a standardized, statistical treatment of self-similar data across many fields, producing interpretable data-driven models that may inform applications such as materials classification, design, and discovery.

Machine learning is increasingly used to discover diagnostic and prognostic biomarkers from high-dimensional molecular data. However, a variety of factors related to experimental design may affect the ability to learn generalizable and clinically applicable diagnostics. Here, we argue that a causal perspective improves the identification of these challenges, and formalizes their relation to the robustness and generalization of machine learning-based diagnostics. To make for a concrete discussion, we focus on a specific, recently established high-dimensional biomarker - adaptive immune receptor repertoires (AIRRs). We discuss how the main biological and experimental factors of the AIRR domain may influence the learned biomarkers and provide easily adjustable simulations of such effects. In conclusion, we find that causal modeling improves machine learning-based biomarker robustness by identifying stable relations between variables and by guiding the adjustment of the relations and variables that vary between populations.

We provide a decision theoretic analysis of bandit experiments. The setting corresponds to a dynamic programming problem, but solving this directly is typically infeasible. Working within the framework of diffusion asymptotics, we define suitable notions of asymptotic Bayes and minimax risk for bandit experiments. For normally distributed rewards, the minimal Bayes risk can be characterized as the solution to a nonlinear second-order partial differential equation (PDE). Using a limit of experiments approach, we show that this PDE characterization also holds asymptotically under both parametric and non-parametric distribution of the rewards. The approach further describes the state variables it is asymptotically sufficient to restrict attention to, and therefore suggests a practical strategy for dimension reduction. The upshot is that we can approximate the dynamic programming problem defining the bandit experiment with a PDE which can be efficiently solved using sparse matrix routines. We derive the optimal Bayes and minimax policies from the numerical solutions to these equations. The proposed policies substantially dominate existing methods such as Thompson sampling. The framework also allows for substantial generalizations to the bandit problem such as time discounting and pure exploration motives.

The accurate diagnosis and molecular profiling of colorectal cancers are critical for planning the best treatment options for patients. Microsatellite instability (MSI) or mismatch repair (MMR) status plays a vital role inappropriate treatment selection, has prognostic implications and is used to investigate the possibility of patients having underlying genetic disorders (Lynch syndrome). NICE recommends that all CRC patients should be offered MMR/microsatellite instability (MSI) testing. Immunohistochemistry is commonly used to assess MMR status with subsequent molecular testing performed as required. This incurs significant extra costs and requires additional resources. The introduction of automated methods that can predict MSI or MMR status from a target image could substantially reduce the cost associated with MMR testing. Unlike previous studies on MSI prediction involving training a CNN using coarse labels (Microsatellite Instable vs Microsatellite Stable), we have utilised fine-grain MMR labels for training purposes. In this paper, we present our work on predicting MSI status in a two-stage process using a single target slide either stained with CK8/18 or H\&E. First, we trained a multi-headed convolutional neural network model where each head was responsible for predicting one of the MMR protein expressions. To this end, we performed the registration of MMR stained slides to the target slide as a pre-processing step. In the second stage, statistical features computed from the MMR prediction maps were used for the final MSI prediction. Our results demonstrated that MSI classification can be improved by incorporating fine-grained MMR labels in comparison to the previous approaches in which only coarse labels were utilised.

A High-dimensional and sparse (HiDS) matrix is frequently encountered in a big data-related application like an e-commerce system or a social network services system. To perform highly accurate representation learning on it is of great significance owing to the great desire of extracting latent knowledge and patterns from it. Latent factor analysis (LFA), which represents an HiDS matrix by learning the low-rank embeddings based on its observed entries only, is one of the most effective and efficient approaches to this issue. However, most existing LFA-based models perform such embeddings on a HiDS matrix directly without exploiting its hidden graph structures, thereby resulting in accuracy loss. To address this issue, this paper proposes a graph-incorporated latent factor analysis (GLFA) model. It adopts two-fold ideas: 1) a graph is constructed for identifying the hidden high-order interaction (HOI) among nodes described by an HiDS matrix, and 2) a recurrent LFA structure is carefully designed with the incorporation of HOI, thereby improving the representa-tion learning ability of a resultant model. Experimental results on three real-world datasets demonstrate that GLFA outperforms six state-of-the-art models in predicting the missing data of an HiDS matrix, which evidently supports its strong representation learning ability to HiDS data.

Recently, numerous studies have demonstrated the presence of bias in machine learning powered decision-making systems. Although most definitions of algorithmic bias have solid mathematical foundations, the corresponding bias detection techniques often lack statistical rigor, especially for non-iid data. We fill this gap in the literature by presenting a rigorous non-parametric testing procedure for bias according to Predictive Rate Parity, a commonly considered notion of algorithmic bias. We adapt traditional asymptotic results for non-parametric estimators to test for bias in the presence of dependence commonly seen in user-level data generated by technology industry applications and illustrate how these approaches can be leveraged for mitigation. We further propose modifications of this methodology to address bias measured through marginal outcome disparities in classification settings and extend notions of predictive rate parity to multi-objective models. Experimental results on real data show the efficacy of the proposed detection and mitigation methods.

Bayesian model selection provides a powerful framework for objectively comparing models directly from observed data, without reference to ground truth data. However, Bayesian model selection requires the computation of the marginal likelihood (model evidence), which is computationally challenging, prohibiting its use in many high-dimensional Bayesian inverse problems. With Bayesian imaging applications in mind, in this work we present the proximal nested sampling methodology to objectively compare alternative Bayesian imaging models for applications that use images to inform decisions under uncertainty. The methodology is based on nested sampling, a Monte Carlo approach specialised for model comparison, and exploits proximal Markov chain Monte Carlo techniques to scale efficiently to large problems and to tackle models that are log-concave and not necessarily smooth (e.g., involving l_1 or total-variation priors). The proposed approach can be applied computationally to problems of dimension O(10^6) and beyond, making it suitable for high-dimensional inverse imaging problems. It is validated on large Gaussian models, for which the likelihood is available analytically, and subsequently illustrated on a range of imaging problems where it is used to analyse different choices of dictionary and measurement model.

It is shown, with two sets of indicators that separately load on two distinct factors, independent of one another conditional on the past, that if it is the case that at least one of the factors causally affects the other, then, in many settings, the process will converge to a factor model in which a single factor will suffice to capture the covariance structure among the indicators. Factor analysis with one wave of data can then not distinguish between factor models with a single factor versus those with two factors that are causally related. Therefore, unless causal relations between factors can be ruled out a priori, alleged empirical evidence from one-wave factor analysis for a single factor still leaves open the possibilities of a single factor or of two factors that causally affect one another. The implications for interpreting the factor structure of psychological scales, such as self-report scales for anxiety and depression, or for happiness and purpose, are discussed. The results are further illustrated through simulations to gain insight into the practical implications of the results in more realistic settings prior to the convergence of the processes. Some further generalizations to an arbitrary number of underlying factors are noted.

This paper proposes an active learning algorithm for solving regression and classification problems based on inverse-distance weighting functions for selecting the feature vectors to query. The algorithm has the following features: (i) supports both pool-based and population-based sampling; (ii) is independent of the type of predictor used; (iii) can handle known and unknown constraints on the queryable feature vectors; and (iv) can run either sequentially, or in batch mode, depending on how often the predictor is retrained. The method's potential is shown in numerical tests on illustrative synthetic problems and real-world regression and classification datasets from the UCI repository. A Python implementation of the algorithm that we call IDEAL (Inverse-Distance based Exploration for Active Learning), is available at \url{//cse.lab.imtlucca.it/~bemporad/ideal}.

Many tasks in natural language processing can be viewed as multi-label classification problems. However, most of the existing models are trained with the standard cross-entropy loss function and use a fixed prediction policy (e.g., a threshold of 0.5) for all the labels, which completely ignores the complexity and dependencies among different labels. In this paper, we propose a meta-learning method to capture these complex label dependencies. More specifically, our method utilizes a meta-learner to jointly learn the training policies and prediction policies for different labels. The training policies are then used to train the classifier with the cross-entropy loss function, and the prediction policies are further implemented for prediction. Experimental results on fine-grained entity typing and text classification demonstrate that our proposed method can obtain more accurate multi-label classification results.