Machine learning and deep learning have been celebrating many successes in the application to biological problems, especially in the domain of protein folding. Another equally complex and important question has received relatively little attention by the machine learning community, namely the one of prediction of complex traits from genetics. Tackling this problem requires in-depth knowledge of the related genetics literature and awareness of various subtleties associated with genetic data. In this guide, we provide an overview for the machine learning community on current state of the art models and associated subtleties which need to be taken into consideration when developing new models for phenotype prediction. We use height as an example of a continuous-valued phenotype and provide an introduction to benchmark datasets, confounders, feature selection, and common metrics.
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In survival analysis, complex machine learning algorithms have been increasingly used for predictive modeling. Given a collection of features available for inclusion in a predictive model, it may be of interest to quantify the relative importance of a subset of features for the prediction task at hand. In particular, in HIV vaccine trials, participant baseline characteristics are used to predict the probability of infection over the intended follow-up period, and investigators may wish to understand how much certain types of predictors, such as behavioral factors, contribute toward overall predictiveness. Time-to-event outcomes such as time to infection are often subject to right censoring, and existing methods for assessing variable importance are typically not intended to be used in this setting. We describe a broad class of algorithm-agnostic variable importance measures for prediction in the context of survival data. We propose a nonparametric efficient estimation procedure that incorporates flexible learning of nuisance parameters, yields asymptotically valid inference, and enjoys double-robustness. We assess the performance of our proposed procedure via numerical simulations and analyze data from the HVTN 702 study to inform enrollment strategies for future HIV vaccine trials.
In many applications, it is of interest to identify a parsimonious set of features, or panel, from multiple candidates that achieves a desired level of performance in predicting a response. This task is often complicated in practice by missing data arising from the sampling design or other random mechanisms. Most recent work on variable selection in missing data contexts relies in some part on a finite-dimensional statistical model, e.g., a generalized or penalized linear model. In cases where this model is misspecified, the selected variables may not all be truly scientifically relevant and can result in panels with suboptimal classification performance. To address this limitation, we propose a nonparametric variable selection algorithm combined with multiple imputation to develop flexible panels in the presence of missing-at-random data. We outline strategies based on the proposed algorithm that achieve control of commonly used error rates. Through simulations, we show that our proposal has good operating characteristics and results in panels with higher classification and variable selection performance compared to several existing penalized regression approaches in cases where a generalized linear model is misspecified. Finally, we use the proposed method to develop biomarker panels for separating pancreatic cysts with differing malignancy potential in a setting where complicated missingness in the biomarkers arose due to limited specimen volumes.
Machine learning with neural networks is now becoming a more and more powerful tool for various tasks, such as natural language processing, image recognition, winning the game, and even for the issues of physics. Although there are many studies on the application of machine learning to numerical calculation and the assistance of experimental detection, the methods of applying machine learning to find the analytical method are poorly studied. In this paper, we propose the frameworks of developing analytical methods in physics by using the symbolic regression with the Alpha Zero algorithm, that is Alpha Zero for physics (AZfP). As a demonstration, we show that AZfP can derive the high-frequency expansion in the Floquet systems. AZfP may have the possibility of developing a new theoretical framework in physics.
Quantized tensor trains (QTTs) have recently emerged as a framework for the numerical discretization of continuous functions, with the potential for widespread applications in numerical analysis. However, the theory of QTT approximation is not fully understood. In this work, we advance this theory from the point of view of multiscale polynomial interpolation. This perspective clarifies why QTT ranks decay with increasing depth, quantitatively controls QTT rank in terms of smoothness of the target function, and explains why certain functions with sharp features and poor quantitative smoothness can still be well approximated by QTTs. The perspective also motivates new practical and efficient algorithms for the construction of QTTs from function evaluations on multiresolution grids.
In domains where sample sizes are limited, efficient learning algorithms are critical. Learning using privileged information (LuPI) offers increased sample efficiency by allowing prediction models access to auxiliary information at training time which is unavailable when the models are used. In recent work, it was shown that for prediction in linear-Gaussian dynamical systems, a LuPI learner with access to intermediate time series data is never worse and often better in expectation than any unbiased classical learner. We provide new insights into this analysis and generalize it to nonlinear prediction tasks in latent dynamical systems, extending theoretical guarantees to the case where the map connecting latent variables and observations is known up to a linear transform. In addition, we propose algorithms based on random features and representation learning for the case when this map is unknown. A suite of empirical results confirm theoretical findings and show the potential of using privileged time-series information in nonlinear prediction.
Recently, there has been an upsurge in the research on maritime vision, where a lot of works are influenced by the application of computer vision for Unmanned Surface Vehicles (USVs). Various sensor modalities such as camera, radar, and lidar have been used to perform tasks such as object detection, segmentation, object tracking, and motion planning. A large subset of this research is focused on the video analysis, since most of the current vessel fleets contain the camera's onboard for various surveillance tasks. Due to the vast abundance of the video data, video scene change detection is an initial and crucial stage for scene understanding of USVs. This paper outlines our approach to detect dynamic scene changes in USVs. To the best of our understanding, this work represents the first investigation of scene change detection in the maritime vision application. Our objective is to identify significant changes in the dynamic scenes of maritime video data, particularly those scenes that exhibit a high degree of resemblance. In our system for dynamic scene change detection, we propose completely unsupervised learning method. In contrast to earlier studies, we utilize a modified cutting-edge generative picture model called VQ-VAE-2 to train on multiple marine datasets, aiming to enhance the feature extraction. Next, we introduce our innovative similarity scoring technique for directly calculating the level of similarity in a sequence of consecutive frames by utilizing grid calculation on retrieved features. The experiments were conducted using a nautical video dataset called RoboWhaler to showcase the efficient performance of our technique.
Despite the widespread use and success of machine-learning techniques for detecting phase transitions from data, their working principle and fundamental limits remain elusive. Here, we explain the inner workings and identify potential failure modes of these techniques by rooting popular machine-learning indicators of phase transitions in information-theoretic concepts. Using tools from information geometry, we prove that several machine-learning indicators of phase transitions approximate the square root of the system's (quantum) Fisher information from below -- a quantity that is known to indicate phase transitions but is often difficult to compute from data. We numerically demonstrate the quality of these bounds for phase transitions in classical and quantum systems.
In modern computational materials science, deep learning has shown the capability to predict interatomic potentials, thereby supporting and accelerating conventional simulations. However, existing models typically sacrifice either accuracy or efficiency. Moreover, lightweight models are highly demanded for offering simulating systems on a considerably larger scale at reduced computational costs. A century ago, Felix Bloch demonstrated how leveraging the equivariance of the translation operation on a crystal lattice (with geometric symmetry) could significantly reduce the computational cost of determining wavefunctions and accurately calculate material properties. Here, we introduce a lightweight equivariant interaction graph neural network (LEIGNN) that can enable accurate and efficient interatomic potential and force predictions in crystals. Rather than relying on higher-order representations, LEIGNN employs a scalar-vector dual representation to encode equivariant features. By extracting both local and global structures from vector representations and learning geometric symmetry information, our model remains lightweight while ensuring prediction accuracy and robustness through the equivariance. Our results show that LEIGNN consistently outperforms the prediction performance of the representative baselines and achieves significant efficiency across diverse datasets, which include catalysts, molecules, and organic isomers. Finally, to further validate the predicted interatomic potentials from our model, we conduct classical molecular dynamics (MD) and ab initio MD simulation across various systems, including solid, liquid, and gas. It is found that LEIGNN can achieve the accuracy of ab initio MD and retain the computational efficiency of classical MD across all examined systems, demonstrating its accuracy, efficiency, and universality.
The remarkable practical success of deep learning has revealed some major surprises from a theoretical perspective. In particular, simple gradient methods easily find near-optimal solutions to non-convex optimization problems, and despite giving a near-perfect fit to training data without any explicit effort to control model complexity, these methods exhibit excellent predictive accuracy. We conjecture that specific principles underlie these phenomena: that overparametrization allows gradient methods to find interpolating solutions, that these methods implicitly impose regularization, and that overparametrization leads to benign overfitting. We survey recent theoretical progress that provides examples illustrating these principles in simpler settings. We first review classical uniform convergence results and why they fall short of explaining aspects of the behavior of deep learning methods. We give examples of implicit regularization in simple settings, where gradient methods lead to minimal norm functions that perfectly fit the training data. Then we review prediction methods that exhibit benign overfitting, focusing on regression problems with quadratic loss. For these methods, we can decompose the prediction rule into a simple component that is useful for prediction and a spiky component that is useful for overfitting but, in a favorable setting, does not harm prediction accuracy. We focus specifically on the linear regime for neural networks, where the network can be approximated by a linear model. In this regime, we demonstrate the success of gradient flow, and we consider benign overfitting with two-layer networks, giving an exact asymptotic analysis that precisely demonstrates the impact of overparametrization. We conclude by highlighting the key challenges that arise in extending these insights to realistic deep learning settings.
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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