Understanding epistasis (genetic interaction) may shed some light on the genomic basis of common diseases, including disorders of maximum interest due to their high socioeconomic burden, like schizophrenia. Distance correlation is an association measure that characterises general statistical independence between random variables, not only the linear one. Here, we propose distance correlation as a novel tool for the detection of epistasis from case-control data of single-nucleotide polymorphisms (SNPs). On the methodological side, we highlight the derivation of the explicit asymptotic distribution of the test statistic. We show that this is the only way to obtain enough computational speed for the method to be used in practice, in a scenario where the resampling techniques found in the literature are impractical. Our simulations show satisfactory calibration of significance, as well as comparable or better power than existing methodology. We conclude with the application of our technique to a schizophrenia genetics dataset, obtaining biologically sound insights.
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Additive regression models with interactions are widely studied in the literature, using methods such as splines or Gaussian process regression. However, these methods can pose challenges for estimation and model selection, due to the presence of many smoothing parameters and the lack of suitable criteria. We propose to address these challenges by extending the I-prior methodology (Bergsma, 2020) to multiple covariates, which may be multidimensional. The I-prior methodology has some advantages over other methods, such as Gaussian process regression and Tikhonov regularization, both theoretically and practically. In particular, the I-prior is a proper prior, is based on minimal assumptions, yields an admissible posterior mean, and estimation of the scale (or smoothing) parameters can be done using an EM algorithm with simple E and M steps. Moreover, we introduce a parsimonious specification of models with interactions, which has two benefits: (i) it reduces the number of scale parameters and thus facilitates the estimation of models with interactions, and (ii) it enables straightforward model selection (among models with different interactions) based on the marginal likelihood.
Named Entity Recognition (NER) is a fundamental task in NLP that is used to locate the key information in text and is primarily applied in conversational and search systems. In commercial applications, NER or comparable slot-filling methods have been widely deployed for popular languages. NER is used in applications such as human resources, customer service, search engines, content classification, and academia. In this paper, we draw focus on identifying name entities for low-resource Indian languages that are closely related, like Hindi and Marathi. We use various adaptations of BERT such as baseBERT, AlBERT, and RoBERTa to train a supervised NER model. We also compare multilingual models with monolingual models and establish a baseline. In this work, we show the assisting capabilities of the Hindi and Marathi languages for the NER task. We show that models trained using multiple languages perform better than a single language. However, we also observe that blind mixing of all datasets doesn't necessarily provide improvements and data selection methods may be required.
The quality of the inferences we make from pathogen sequence data is determined by the number and composition of pathogen sequences that make up the sample used to drive that inference. However, there remains limited guidance on how to best structure and power studies when the end goal is phylogenetic inference. One question that we can attempt to answer with molecular data is whether some people are more likely to transmit a pathogen than others. Here we present an estimator to quantify differential transmission, as measured by the ratio of reproductive numbers between people with different characteristics, using transmission pairs linked by molecular data, along with a sample size calculation for this estimator. We also provide extensions to our method to correct for imperfect identification of transmission linked pairs, overdispersion in the transmission process, and group imbalance. We validate this method via simulation and provide tools to implement it in an R package, phylosamp.
Detecting change-points in data is challenging because of the range of possible types of change and types of behaviour of data when there is no change. Statistically efficient methods for detecting a change will depend on both of these features, and it can be difficult for a practitioner to develop an appropriate detection method for their application of interest. We show how to automatically generate new offline detection methods based on training a neural network. Our approach is motivated by many existing tests for the presence of a change-point being representable by a simple neural network, and thus a neural network trained with sufficient data should have performance at least as good as these methods. We present theory that quantifies the error rate for such an approach, and how it depends on the amount of training data. Empirical results show that, even with limited training data, its performance is competitive with the standard CUSUM-based classifier for detecting a change in mean when the noise is independent and Gaussian, and can substantially outperform it in the presence of auto-correlated or heavy-tailed noise. Our method also shows strong results in detecting and localising changes in activity based on accelerometer data.
Uncertainty quantification (UQ) is important for reliability assessment and enhancement of machine learning models. In deep learning, uncertainties arise not only from data, but also from the training procedure that often injects substantial noises and biases. These hinder the attainment of statistical guarantees and, moreover, impose computational challenges on UQ due to the need for repeated network retraining. Building upon the recent neural tangent kernel theory, we create statistically guaranteed schemes to principally \emph{quantify}, and \emph{remove}, the procedural uncertainty of over-parameterized neural networks with very low computation effort. In particular, our approach, based on what we call a procedural-noise-correcting (PNC) predictor, removes the procedural uncertainty by using only \emph{one} auxiliary network that is trained on a suitably labeled data set, instead of many retrained networks employed in deep ensembles. Moreover, by combining our PNC predictor with suitable light-computation resampling methods, we build several approaches to construct asymptotically exact-coverage confidence intervals using as low as four trained networks without additional overheads.
Federated Learning (FL) is a decentralized machine-learning paradigm, in which a global server iteratively averages the model parameters of local users without accessing their data. User heterogeneity has imposed significant challenges to FL, which can incur drifted global models that are slow to converge. Knowledge Distillation has recently emerged to tackle this issue, by refining the server model using aggregated knowledge from heterogeneous users, other than directly averaging their model parameters. This approach, however, depends on a proxy dataset, making it impractical unless such a prerequisite is satisfied. Moreover, the ensemble knowledge is not fully utilized to guide local model learning, which may in turn affect the quality of the aggregated model. Inspired by the prior art, we propose a data-free knowledge distillation} approach to address heterogeneous FL, where the server learns a lightweight generator to ensemble user information in a data-free manner, which is then broadcasted to users, regulating local training using the learned knowledge as an inductive bias. Empirical studies powered by theoretical implications show that, our approach facilitates FL with better generalization performance using fewer communication rounds, compared with the state-of-the-art.
Current deep learning research is dominated by benchmark evaluation. A method is regarded as favorable if it empirically performs well on the dedicated test set. This mentality is seamlessly reflected in the resurfacing area of continual learning, where consecutively arriving sets of benchmark data are investigated. The core challenge is framed as protecting previously acquired representations from being catastrophically forgotten due to the iterative parameter updates. However, comparison of individual methods is nevertheless treated in isolation from real world application and typically judged by monitoring accumulated test set performance. The closed world assumption remains predominant. It is assumed that during deployment a model is guaranteed to encounter data that stems from the same distribution as used for training. This poses a massive challenge as neural networks are well known to provide overconfident false predictions on unknown instances and break down in the face of corrupted data. In this work we argue that notable lessons from open set recognition, the identification of statistically deviating data outside of the observed dataset, and the adjacent field of active learning, where data is incrementally queried such that the expected performance gain is maximized, are frequently overlooked in the deep learning era. Based on these forgotten lessons, we propose a consolidated view to bridge continual learning, active learning and open set recognition in deep neural networks. Our results show that this not only benefits each individual paradigm, but highlights the natural synergies in a common framework. We empirically demonstrate improvements when alleviating catastrophic forgetting, querying data in active learning, selecting task orders, while exhibiting robust open world application where previously proposed methods fail.
Multivariate time series forecasting is extensively studied throughout the years with ubiquitous applications in areas such as finance, traffic, environment, etc. Still, concerns have been raised on traditional methods for incapable of modeling complex patterns or dependencies lying in real word data. To address such concerns, various deep learning models, mainly Recurrent Neural Network (RNN) based methods, are proposed. Nevertheless, capturing extremely long-term patterns while effectively incorporating information from other variables remains a challenge for time-series forecasting. Furthermore, lack-of-explainability remains one serious drawback for deep neural network models. Inspired by Memory Network proposed for solving the question-answering task, we propose a deep learning based model named Memory Time-series network (MTNet) for time series forecasting. MTNet consists of a large memory component, three separate encoders, and an autoregressive component to train jointly. Additionally, the attention mechanism designed enable MTNet to be highly interpretable. We can easily tell which part of the historic data is referenced the most.
As a new classification platform, deep learning has recently received increasing attention from researchers and has been successfully applied to many domains. In some domains, like bioinformatics and robotics, it is very difficult to construct a large-scale well-annotated dataset due to the expense of data acquisition and costly annotation, which limits its development. Transfer learning relaxes the hypothesis that the training data must be independent and identically distributed (i.i.d.) with the test data, which motivates us to use transfer learning to solve the problem of insufficient training data. This survey focuses on reviewing the current researches of transfer learning by using deep neural network and its applications. We defined deep transfer learning, category and review the recent research works based on the techniques used in deep transfer learning.
Recommender System (RS) is a hot area where artificial intelligence (AI) techniques can be effectively applied to improve performance. Since the well-known Netflix Challenge, collaborative filtering (CF) has become the most popular and effective recommendation method. Despite their success in CF, various AI techniques still have to face the data sparsity and cold start problems. Previous works tried to solve these two problems by utilizing auxiliary information, such as social connections among users and meta-data of items. However, they process different types of information separately, leading to information loss. In this work, we propose to utilize Heterogeneous Information Network (HIN), which is a natural and general representation of different types of data, to enhance CF-based recommending methods. HIN-based recommender systems face two problems: how to represent high-level semantics for recommendation and how to fuse the heterogeneous information to recommend. To address these problems, we propose to applying meta-graph to HIN-based RS and solve the information fusion problem with a "matrix factorization (MF) + factorization machine (FM)" framework. For the "MF" part, we obtain user-item similarity matrices from each meta-graph and adopt low-rank matrix approximation to get latent features for both users and items. For the "FM" part, we propose to apply FM with Group lasso (FMG) on the obtained features to simultaneously predict missing ratings and select useful meta-graphs. Experimental results on two large real-world datasets, i.e., Amazon and Yelp, show that our proposed approach is better than that of the state-of-the-art FM and other HIN-based recommending methods.
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