Creating a dataset for training supervised machine learning algorithms can be a demanding task. This is especially true for medical image segmentation since one or more specialists are usually required for image annotation, and creating ground truth labels for just a single image can take up to several hours. In addition, it is paramount that the annotated samples represent well the different conditions that might affect the imaged tissues as well as possible changes in the image acquisition process. This can only be achieved by considering samples that are typical in the dataset as well as atypical, or even outlier, samples. We introduce VessMAP, a heterogeneous blood vessel segmentation dataset acquired by carefully sampling relevant images from a larger non-annotated dataset. A methodology was developed to select both prototypical and atypical samples from the base dataset, thus defining an assorted set of images that can be used for measuring the performance of segmentation algorithms on samples that are highly distinct from each other. To demonstrate the potential of the new dataset, we show that the validation performance of a neural network changes significantly depending on the splits used for training the network.
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Case-control sampling is a commonly used retrospective sampling design to alleviate imbalanced structure of binary data. When fitting the logistic regression model with case-control data, although the slope parameter of the model can be consistently estimated, the intercept parameter is not identifiable, and the marginal case proportion is not estimatable, either. We consider the situations in which besides the case-control data from the main study, called internal study, there also exists summary-level information from related external studies. An empirical likelihood based approach is proposed to make inference for the logistic model by incorporating the internal case-control data and external information. We show that the intercept parameter is identifiable with the help of external information, and then all the regression parameters as well as the marginal case proportion can be estimated consistently. The proposed method also accounts for the possible variability in external studies. The resultant estimators are shown to be asymptotically normally distributed. The asymptotic variance-covariance matrix can be consistently estimated by the case-control data. The optimal way to utilized external information is discussed. Simulation studies are conducted to verify the theoretical findings. A real data set is analyzed for illustration.
Differential abundance analysis is a key component of microbiome studies. While dozens of methods for it exist, currently, there is no consensus on the preferred methods. Correctness of results in differential abundance analysis is an ambiguous concept that cannot be evaluated without employing simulated data, but we argue that consistency of results across datasets should be considered as an essential quality of a well-performing method. We compared the performance of 14 differential abundance analysis methods employing datasets from 54 taxonomic profiling studies based on 16S rRNA gene or shotgun sequencing. For each method, we examined how the results replicated between random partitions of each dataset and between datasets from independent studies. While certain methods showed good consistency, some widely used methods were observed to produce a substantial number of conflicting findings. Overall, the highest consistency without unnecessary reduction in sensitivity was attained by analyzing relative abundances with a non-parametric method (Wilcoxon test or ordinal regression model) or linear regression (MaAsLin2). Comparable performance was also attained by analyzing presence/absence of taxa with logistic regression.
Identifiability of statistical models is a key notion in unsupervised representation learning. Recent work of nonlinear independent component analysis (ICA) employs auxiliary data and has established identifiable conditions. This paper proposes a statistical model of two latent vectors with single auxiliary data generalizing nonlinear ICA, and establishes various identifiability conditions. Unlike previous work, the two latent vectors in the proposed model can have arbitrary dimensions, and this property enables us to reveal an insightful dimensionality relation among two latent vectors and auxiliary data in identifiability conditions. Furthermore, surprisingly, we prove that the indeterminacies of the proposed model has the same as \emph{linear} ICA under certain conditions: The elements in the latent vector can be recovered up to their permutation and scales. Next, we apply the identifiability theory to a statistical model for graph data. As a result, one of the identifiability conditions includes an appealing implication: Identifiability of the statistical model could depend on the maximum value of link weights in graph data. Then, we propose a practical method for identifiable graph embedding. Finally, we numerically demonstrate that the proposed method well-recovers the latent vectors and model identifiability clearly depends on the maximum value of link weights, which supports the implication of our theoretical results
Conventional computing paradigm struggles to fulfill the rapidly growing demands from emerging applications, especially those for machine intelligence, because much of the power and energy is consumed by constant data transfers between logic and memory modules. A new paradigm, called "computational random-access memory (CRAM)" has emerged to address this fundamental limitation. CRAM performs logic operations directly using the memory cells themselves, without having the data ever leave the memory. The energy and performance benefits of CRAM for both conventional and emerging applications have been well established by prior numerical studies. However, there lacks an experimental demonstration and study of CRAM to evaluate its computation accuracy, which is a realistic and application-critical metrics for its technological feasibility and competitiveness. In this work, a CRAM array based on magnetic tunnel junctions (MTJs) is experimentally demonstrated. First, basic memory operations as well as 2-, 3-, and 5-input logic operations are studied. Then, a 1-bit full adder with two different designs is demonstrated. Based on the experimental results, a suite of modeling has been developed to characterize the accuracy of CRAM computation. Scalar addition, multiplication, and matrix multiplication, which are essential building blocks for many conventional and machine intelligence applications, are evaluated and show promising accuracy performance. With the confirmation of MTJ-based CRAM's accuracy, there is a strong case that this technology will have a significant impact on power- and energy-demanding applications of machine intelligence.
The problem of binary hypothesis testing between two probability measures is considered. New sharp bounds are derived for the best achievable error probability of such tests based on independent and identically distributed observations. Specifically, the asymmetric version of the problem is examined, where different requirements are placed on the two error probabilities. Accurate nonasymptotic expansions with explicit constants are obtained for the error probability, using tools from large deviations and Gaussian approximation. Examples are shown indicating that, in the asymmetric regime, the approximations suggested by the new bounds are significantly more accurate than the approximations provided by either of the two main earlier approaches -- normal approximation and error exponents.
Reinforcement learning is commonly concerned with problems of maximizing accumulated rewards in Markov decision processes. Oftentimes, a certain goal state or a subset of the state space attain maximal reward. In such a case, the environment may be considered solved when the goal is reached. Whereas numerous techniques, learning or non-learning based, exist for solving environments, doing so optimally is the biggest challenge. Say, one may choose a reward rate which penalizes the action effort. Reinforcement learning is currently among the most actively developed frameworks for solving environments optimally by virtue of maximizing accumulated reward, in other words, returns. Yet, tuning agents is a notoriously hard task as reported in a series of works. Our aim here is to help the agent learn a near-optimal policy efficiently while ensuring a goal reaching property of some basis policy that merely solves the environment. We suggest an algorithm, which is fairly flexible, and can be used to augment practically any agent as long as it comprises of a critic. A formal proof of a goal reaching property is provided. Simulation experiments on six problems under five agents, including the benchmarked one, provided an empirical evidence that the learning can indeed be boosted while ensuring goal reaching property.
Distributionally robust optimization has emerged as an attractive way to train robust machine learning models, capturing data uncertainty and distribution shifts. Recent statistical analyses have proved that robust models built from Wasserstein ambiguity sets have nice generalization guarantees, breaking the curse of dimensionality. However, these results are obtained in specific cases, at the cost of approximations, or under assumptions difficult to verify in practice. In contrast, we establish, in this article, exact generalization guarantees that cover all practical cases, including any transport cost function and any loss function, potentially non-convex and nonsmooth. For instance, our result applies to deep learning, without requiring restrictive assumptions. We achieve this result through a novel proof technique that combines nonsmooth analysis rationale with classical concentration results. Our approach is general enough to extend to the recent versions of Wasserstein/Sinkhorn distributionally robust problems that involve (double) regularizations.
In many statistical modeling problems, such as classification and regression, it is common to encounter sparse and blocky coefficients. Sparse fused Lasso is specifically designed to recover these sparse and blocky structured features, especially in cases where the design matrix has ultrahigh dimensions, meaning that the number of features significantly surpasses the number of samples. Quantile loss is a well-known robust loss function that is widely used in statistical modeling. In this paper, we propose a new sparse fused lasso classification model, and develop a unified multi-block linearized alternating direction method of multipliers algorithm that effectively selects sparse and blocky features for regression and classification. Our algorithm has been proven to converge with a derived linear convergence rate. Additionally, our algorithm has a significant advantage over existing methods for solving ultrahigh dimensional sparse fused Lasso regression and classification models due to its lower time complexity. Note that the algorithm can be easily extended to solve various existing fused Lasso models. Finally, we present numerical results for several synthetic and real-world examples, which demonstrate the robustness, scalability, and accuracy of the proposed classification model and algorithm
We consider the problem of sampling a high dimensional multimodal target probability measure. We assume that a good proposal kernel to move only a subset of the degrees of freedoms (also known as collective variables) is known a priori. This proposal kernel can for example be built using normalizing flows. We show how to extend the move from the collective variable space to the full space and how to implement an accept-reject step in order to get a reversible chain with respect to a target probability measure. The accept-reject step does not require to know the marginal of the original measure in the collective variable (namely to know the free energy). The obtained algorithm admits several variants, some of them being very close to methods which have been proposed previously in the literature. We show how the obtained acceptance ratio can be expressed in terms of the work which appears in the Jarzynski-Crooks equality, at least for some variants. Numerical illustrations demonstrate the efficiency of the approach on various simple test cases, and allow us to compare the variants of the algorithm.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
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