New powerful tools for tackling life science problems have been created by recent advances in machine learning. The purpose of the paper is to discuss the potential advantages of gene recommendation performed by artificial intelligence (AI). Indeed, gene recommendation engines try to solve this problem: if the user is interested in a set of genes, which other genes are likely to be related to the starting set and should be investigated? This task was solved with a custom deep learning recommendation engine, DeepProphet2 (DP2), which is freely available to researchers worldwide via https://www.generecommender.com?utm_source=DeepProphet2_paper&utm_medium=pdf. Hereafter, insights behind the algorithm and its practical applications are illustrated. The gene recommendation problem can be addressed by mapping the genes to a metric space where a distance can be defined to represent the real semantic distance between them. To achieve this objective a transformer-based model has been trained on a well-curated freely available paper corpus, PubMed. The paper describes multiple optimization procedures that were employed to obtain the best bias-variance trade-off, focusing on embedding size and network depth. In this context, the model's ability to discover sets of genes implicated in diseases and pathways was assessed through cross-validation. A simple assumption guided the procedure: the network had no direct knowledge of pathways and diseases but learned genes' similarities and the interactions among them. Moreover, to further investigate the space where the neural network represents genes, the dimensionality of the embedding was reduced, and the results were projected onto a human-comprehensible space. In conclusion, a set of use cases illustrates the algorithm's potential applications in a real word setting.

Undiagnosed diabetes is present in 21.4% of adults with diabetes. Diabetes can remain asymptomatic and undetected due to limitations in screening rates. To address this issue, questionnaires, such as the American Diabetes Association (ADA) Risk test, have been recommended for use by physicians and the public. Based on evidence that blood glucose concentration can affect cardiac electrophysiology, we hypothesized that an artificial intelligence (AI)-enhanced electrocardiogram (ECG) could identify adults with new-onset diabetes. We trained a neural network to estimate HbA1c using a 12-lead ECG and readily available demographics. We retrospectively assembled a dataset comprised of patients with paired ECG and HbA1c data. The population of patients who receive both an ECG and HbA1c may a biased sample of the complete outpatient population, so we adjusted the importance placed on each patient to generate a more representative pseudo-population. We found ECG-based assessment outperforms the ADA Risk test, achieving a higher area under the curve (0.80 vs. 0.68) and positive predictive value (13% vs. 9%) -- 2.6 times the prevalence of diabetes in the cohort. The AI-enhanced ECG significantly outperforms electrophysiologist interpretation of the ECG, suggesting that the task is beyond current clinical capabilities. Given the prevalence of ECGs in clinics and via wearable devices, such a tool would make precise, automated diabetes assessment widely accessible.

High-dimensional data can often display heterogeneity due to heteroscedastic variance or inhomogeneous covariate effects. Penalized quantile and expectile regression methods offer useful tools to detect heteroscedasticity in high-dimensional data. The former is computationally challenging due to the non-smooth nature of the check loss, and the latter is sensitive to heavy-tailed error distributions. In this paper, we propose and study (penalized) robust expectile regression (retire), with a focus on iteratively reweighted $\ell_1$-penalization which reduces the estimation bias from $\ell_1$-penalization and leads to oracle properties. Theoretically, we establish the statistical properties of the retire estimator under two regimes: (i) low-dimensional regime in which $d \ll n$; (ii) high-dimensional regime in which $s\ll n\ll d$ with $s$ denoting the number of significant predictors. In the high-dimensional setting, we carefully characterize the solution path of the iteratively reweighted $\ell_1$-penalized retire estimation, adapted from the local linear approximation algorithm for folded-concave regularization. Under a mild minimum signal strength condition, we show that after as many as $\log(\log d)$ iterations the final iterate enjoys the oracle convergence rate. At each iteration, the weighted $\ell_1$-penalized convex program can be efficiently solved by a semismooth Newton coordinate descent algorithm. Numerical studies demonstrate the competitive performance of the proposed procedure compared with either non-robust or quantile regression based alternatives.

For-profit companies have long sought to tap into the fears of consumers, offering pricey medical scans they can access without a doctor's recommendation, as long as they can pay the price out of pocket. Now, some of these ventures are trumpeting scans assisted by artificial intelligence, essentially cutting-edge computer technology they say can reveal hidden health problems, from cancer to obscure bone disorders, and analyze the results more quickly than those typically ordered by doctors. Researchers say artificial intelligence, known as AI, holds the promise of more precise diagnosis and also the ability to shorten waiting times for results. But are these new body scans for the "worried well" surging ahead of the current science on artificial intelligence? As the debate heats up, a California-based company is planning to open in Massachusetts.

Machine learning models have made many decision support systems to be faster, more accurate, and more efficient. However, applications of machine learning in network security face a more disproportionate threat of active adversarial attacks compared to other domains. This is because machine learning applications in network security such as malware detection, intrusion detection, and spam filtering are by themselves adversarial in nature. In what could be considered an arm's race between attackers and defenders, adversaries constantly probe machine learning systems with inputs that are explicitly designed to bypass the system and induce a wrong prediction. In this survey, we first provide a taxonomy of machine learning techniques, tasks, and depth. We then introduce a classification of machine learning in network security applications. Next, we examine various adversarial attacks against machine learning in network security and introduce two classification approaches for adversarial attacks in network security. First, we classify adversarial attacks in network security based on a taxonomy of network security applications. Secondly, we categorize adversarial attacks in network security into a problem space vs feature space dimensional classification model. We then analyze the various defenses against adversarial attacks on machine learning-based network security applications. We conclude by introducing an adversarial risk grid map and evaluating several existing adversarial attacks against machine learning in network security using the risk grid map. We also identify where each attack classification resides within the adversarial risk grid map.

Out-of-distribution (OOD) detection is a crucial aspect of deploying machine learning models in open-world applications. Empirical evidence suggests that training with auxiliary outliers substantially improves OOD detection. However, such outliers typically exhibit a distribution gap compared to the test OOD data and do not cover all possible test OOD scenarios. Additionally, incorporating these outliers introduces additional training burdens. In this paper, we introduce a novel paradigm called test-time OOD detection, which utilizes unlabeled online data directly at test time to improve OOD detection performance. While this paradigm is efficient, it also presents challenges such as catastrophic forgetting. To address these challenges, we propose adaptive outlier optimization (AUTO), which consists of an in-out-aware filter, an ID memory bank, and a semantically-consistent objective. AUTO adaptively mines pseudo-ID and pseudo-OOD samples from test data, utilizing them to optimize networks in real time during inference. Extensive results on CIFAR-10, CIFAR-100, and ImageNet benchmarks demonstrate that AUTO significantly enhances OOD detection performance.

Labeled data are often scarce and expensive to obtain in many real-world applications, making training machine-learning models a challenging task [1]. In traditional supervised learning, the goal is to train a model to predict the correct class label for every sample in a training dataset [2]. The training data consist of labeled examples associated with a known class label. Typically, the class distribution of labeled data is assumed to be representative of the class distribution of unlabeled ones. Prior knowledge of the labels makes it easy to train a model to accurately predict the class labels for unseen samples. As Figure 1 shows, in the case of PU learning, the class label is known only for data belonging to a single class; thus, for negative samples, the label is unknown [3]. The lack of this knowledge makes it impossible to effectively train a typical binary classification model to distinguish between positive and negative classes.

Federated learning, which allows multiple client devices in a network to jointly train a machine learning model without direct exposure of clients' data, is an emerging distributed learning technique due to its nature of privacy preservation. However, it has been found that models trained with federated learning usually have worse performance than their counterparts trained in the standard centralized learning mode, especially when the training data is imbalanced. In the context of federated learning, data imbalance may occur either locally one one client device, or globally across many devices. The complexity of different types of data imbalance has posed challenges to the development of federated learning technique, especially considering the need of relieving data imbalance issue and preserving data privacy at the same time. Therefore, in the literature, many attempts have been made to handle class imbalance in federated learning. In this paper, we present a detailed review of recent advancements along this line. We first introduce various types of class imbalance in federated learning, after which we review existing methods for estimating the extent of class imbalance without the need of knowing the actual data to preserve data privacy. After that, we discuss existing methods for handling class imbalance in FL, where the advantages and disadvantages of the these approaches are discussed. We also summarize common evaluation metrics for class imbalanced tasks, and point out potential future directions.

Many datasets in scientific and engineering applications are comprised of objects which have specific geometric structure. A common example is data which inhabits a representation of the group SO$(3)$ of 3D rotations: scalars, vectors, tensors, \textit{etc}. One way for a neural network to exploit prior knowledge of this structure is to enforce SO$(3)$-equivariance throughout its layers, and several such architectures have been proposed. While general methods for handling arbitrary SO$(3)$ representations exist, they computationally intensive and complicated to implement. We show that by judicious symmetry breaking, we can efficiently increase the expressiveness of a network operating only on vector and order-2 tensor representations of SO$(2)$. We demonstrate the method on an important problem from High Energy Physics known as \textit{b-tagging}, where particle jets originating from b-meson decays must be discriminated from an overwhelming QCD background. In this task, we find that augmenting a standard architecture with our method results in a \ensuremath{2.3\times} improvement in rejection score.

An algorithm based on a deep probabilistic architecture referred to as a tree-structured sum-product network (t-SPN) is considered for cell classification. The t-SPN is constructed such that the unnormalized probability is represented as conditional probabilities of a subset of most similar cell classes. The constructed t-SPN architecture is learned by maximizing the margin, which is the difference in the conditional probability between the true and the most competitive false label. To enhance the generalization ability of the architecture, L2-regularization (REG) is considered along with the maximum margin (MM) criterion in the learning process. To highlight cell features, this paper investigates the effectiveness of two generic high-pass filters: ideal high-pass filtering and the Laplacian of Gaussian (LOG) filtering. On both HEp-2 and Feulgen benchmark datasets, the t-SPN architecture learned based on the max-margin criterion with regularization produced the highest accuracy rate compared to other state-of-the-art algorithms that include convolutional neural network (CNN) based algorithms. The ideal high-pass filter was more effective on the HEp-2 dataset, which is based on immunofluorescence staining, while the LOG was more effective on the Feulgen dataset, which is based on Feulgen staining.