Abstract: Background: Understanding cardiovascular artery disease risk factors, the leading global cause of mortality, is crucial for influencing its etiology, prevalence, and treatment. This study aims to evaluate prognostic markers for coronary artery disease in Mashhad using Naive Bayes, REP Tree, J48, CART, and CHAID algorithms. Methods: Using data from the 2009 MASHAD STUDY, prognostic factors for coronary artery disease were determined with Naive Bayes, REP Tree, J48, CART, CHAID, and Random Forest algorithms using R 3.5.3 and WEKA 3.9.4. Model efficiency was compared by sensitivity, specificity, and accuracy. Cases were patients with coronary artery disease; each had three controls (totally 940). Results: Prognostic factors for coronary artery disease in Mashhad residents varied by algorithm. CHAID identified age, myocardial infarction history, and hypertension. CART included depression score and physical activity. REP added education level and anxiety score. NB included diabetes and family history. J48 highlighted father's heart disease and weight loss. CHAID had the highest accuracy (0.80). Conclusion: Key prognostic factors for coronary artery disease in CART and CHAID models include age, myocardial infarction history, hypertension, depression score, physical activity, and BMI. NB, REP Tree, and J48 identified numerous factors. CHAID had the highest accuracy, sensitivity, and specificity. CART offers simpler interpretation, aiding physician and paramedic model selection based on specific. Keywords: RF, Na\"ive Bayes, REP, J48 algorithms, Coronary Artery Disease (CAD).

This review underscores the critical need for effective strategies to identify and support individuals with suicidal ideation, exploiting technological innovations in ML and DL to further suicide prevention efforts. The study details the application of these technologies in analyzing vast amounts of unstructured social media data to detect linguistic patterns, keywords, phrases, tones, and contextual cues associated with suicidal thoughts. It explores various ML and DL models like SVMs, CNNs, LSTM, neural networks, and their effectiveness in interpreting complex data patterns and emotional nuances within text data. The review discusses the potential of these technologies to serve as a life-saving tool by identifying at-risk individuals through their digital traces. Furthermore, it evaluates the real-world effectiveness, limitations, and ethical considerations of employing these technologies for suicide prevention, stressing the importance of responsible development and usage. The study aims to fill critical knowledge gaps by analyzing recent studies, methodologies, tools, and techniques in this field. It highlights the importance of synthesizing current literature to inform practical tools and suicide prevention efforts, guiding innovation in reliable, ethical systems for early intervention. This research synthesis evaluates the intersection of technology and mental health, advocating for the ethical and responsible application of ML, DL, and NLP to offer life-saving potential worldwide while addressing challenges like generalizability, biases, privacy, and the need for further research to ensure these technologies do not exacerbate existing inequities and harms.

This tutorial provides an in-depth guide on inference-time guidance and alignment methods for optimizing downstream reward functions in diffusion models. While diffusion models are renowned for their generative modeling capabilities, practical applications in fields such as biology often require sample generation that maximizes specific metrics (e.g., stability, affinity in proteins, closeness to target structures). In these scenarios, diffusion models can be adapted not only to generate realistic samples but also to explicitly maximize desired measures at inference time without fine-tuning. This tutorial explores the foundational aspects of such inference-time algorithms. We review these methods from a unified perspective, demonstrating that current techniques -- such as Sequential Monte Carlo (SMC)-based guidance, value-based sampling, and classifier guidance -- aim to approximate soft optimal denoising processes (a.k.a. policies in RL) that combine pre-trained denoising processes with value functions serving as look-ahead functions that predict from intermediate states to terminal rewards. Within this framework, we present several novel algorithms not yet covered in the literature. Furthermore, we discuss (1) fine-tuning methods combined with inference-time techniques, (2) inference-time algorithms based on search algorithms such as Monte Carlo tree search, which have received limited attention in current research, and (3) connections between inference-time algorithms in language models and diffusion models. The code of this tutorial on protein design is available at https://github.com/masa-ue/AlignInversePro

A machine learning tasks from observations must encounter and process uncertainty and novelty, especially when it is expected to maintain performance when observing new information and to choose the best fitting hypothesis to the currently observed information. In this context, some key questions arise: what is information, how much information did the observations provide, how much information is required to identify the data-generating process, how many observations remain to get that information, and how does a predictor determine that it has observed novel information? This paper strengthens existing answers to these questions by formalizing the notion of "identifiable information" that arises from the language used to express the relationship between distinct states. Model identifiability and sample complexity are defined via computation of an indicator function over a set of hypotheses. Their properties and asymptotic statistics are described for data-generating processes ranging from deterministic processes to ergodic stationary stochastic processes. This connects the notion of identifying information in finite steps with asymptotic statistics and PAC-learning. The indicator function's computation naturally formalizes novel information and its identification from observations with respect to a hypothesis set. We also proved that computable PAC-Bayes learners' sample complexity distribution is determined by its moments in terms of the the prior probability distribution over a fixed finite hypothesis set.

Conflicting objectives present a considerable challenge in interleaving multi-task learning, necessitating the need for meticulous design and balance to ensure effective learning of a representative latent data space across all tasks without mutual negative impact. Our proposed model, Deep Disentangled Interleaving Variational Encoding (Deep-DIVE) learns disentangled features from the original input to form clusters in the embedding space and unifies these features via the cross-attention mechanism in the fusion stage. We theoretically prove that combining the objectives for reconstruction and forecasting fully captures the lower bound and mathematically derive a loss function for disentanglement using Naïve Bayes. Experiments on two public datasets show that DeepDIVE disentangles the original input and yields forecast accuracies better than the original VAE and comparable to existing state-of-the-art baselines. In multi-objective deep learning, gradients from different objectives can conflict, when the different loss terms induce competing gradient directions during training of the network. Balancing these gradients to ensure stable and effective learning is a significant challenge prompting the development of methods to mitigate this issue, such as Liu et al. (2021); Yu et al. (2020); Sener & Koltun (2018) which solve an additional optmization problem before each gradient update step, to manipulate conflicting gradients before the update.

Distribution alignment has many applications in deep learning, including domain adaptation and unsupervised image-to-image translation. Most prior work on unsupervised distribution alignment relies either on minimizing simple non-parametric statistical distances such as maximum mean discrepancy or on adversarial alignment. However, the former fails to capture the structure of complex real-world distributions, while the latter is difficult to train and does not provide any universal convergence guarantees or automatic quantitative validation procedures. In this paper, we propose a new distribution alignment method based on a log-likelihood ratio statistic and normalizing flows. We show that, under certain assumptions, this combination yields a deep neural likelihood-based minimization objective that attains a known lower bound upon convergence.

Deep generative networks trained via maximum likelihood on a natural image dataset like CIFAR10 often assign high likelihoods to images from datasets with different objects (e.g., SVHN). We refine previous investigations of this failure at anomaly detection for invertible generative networks and provide a clear explanation of it as a combination of model bias and domain prior: Convolutional networks learn similar low-level feature distributions when trained on any natural image dataset and these low-level features dominate the likelihood. Hence, when the discriminative features between inliers and outliers are on a high-level, e.g., object shapes, anomaly detection becomes particularly challenging. To remove the negative impact of model bias and domain prior on detecting high-level differences, we propose two methods, first, using the log likelihood ratios of two identical models, one trained on the in-distribution data (e.g., CIFAR10) and the other one on a more general distribution of images (e.g., 80 Million Tiny Images). We also derive a novel outlier loss for the in-distribution network on samples from the more general distribution to further improve the performance.

An active learner is given a class of models, a large set of unlabeled examples, and the ability to interactively query labels of a subset of these examples; the goal of the learner is to learn a model in the class that fits the data well. Previous theoretical work has rigorously characterized label complexity of active learning, but most of this work has focused on the PAC or the agnostic PAC model. In this paper, we shift our attention to a more general setting -- maximum likelihood estimation. Provided certain conditions hold on the model class, we provide a two-stage active learning algorithm for this problem. The conditions we require are fairly general, and cover the widely popular class of Generalized Linear Models, which in turn, include models for binary and multi-class classification, regression, and conditional random fields.

Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades with many important applications across the life sciences. Established methods for classifying genomes can be broadly grouped into sequence alignment-based and alignment-free models. Conventional alignment-based models rely on genome similarity measures calculated based on local sequence alignments or consistent ordering among sequences. However, such methods are computationally expensive when dealing with large ensembles of even moderately sized genomes. In contrast, alignment-free (AF) approaches measure genome similarity based on summary statistics in an unsupervised setting and are efficient enough to analyze large datasets. However, both alignment-based and AF methods typically assume fixed scoring rubrics that lack the flexibility to assign varying importance to different parts of the sequences based on prior knowledge. In this study, we integrate AI and network science approaches to develop a comparative genomic analysis framework that addresses these limitations. Our approach, termed the Genome Misclassification Network Analysis (GMNA), simultaneously leverages misclassified instances, a learned scoring rubric, and label information to classify genomes based on associated metadata and better understand potential drivers of misclassification. We evaluate the utility of the GMNA using Naive Bayes and convolutional neural network models, supplemented by additional experiments with transformer-based models, to construct SARS-CoV-2 sampling location classifiers using over 500,000 viral genome sequences and study the resulting network of misclassifications. We demonstrate the global health potential of the GMNA by leveraging the SARS-CoV-2 genome misclassification networks to investigate the role human mobility played in structuring geographic clustering of SARS-CoV-2.

Introduction: Substance use disorders (SUDs) have emerged as a pressing public health crisis in the United States, with adolescent substance use often leading to SUDs in adulthood. Effective strategies are needed to prevent this progression. To help in filling this need, we develop a novel and the first-ever absolute risk prediction model for cannabis use disorder (CUD) for adolescent or young adult cannabis users. Methods: We train a Bayesian machine learning model that provides a personalized CUD absolute risk for adolescent or young adult cannabis users using data from the National Longitudinal Study of Adolescent to Adult Health. Model performance is assessed using 5-fold cross-validation (CV) with area under the curve (AUC) and ratio of the expected to observed number of cases (E/O). External validation of the final model is conducted using two independent datasets. Results: The proposed model has five risk factors: biological sex, delinquency, and scores on personality traits of conscientiousness, neuroticism, and openness. For predicting CUD risk within five years of first cannabis use, AUC and E/O, computed via 5-fold CV, were 0.68 and 0.95, respectively. For the same type of prediction in external validation, AUC values were 0.64 and 0.75, with E/O values of 0.98 and 1, indicating good discrimination and calibration performances of the model. Discussion and Conclusion: The proposed model is the first absolute risk prediction model for an SUD. It can aid clinicians in identifying adolescent/youth substance users at a high risk of developing CUD in future for clinically appropriate interventions.