In this paper, we propose new listwise learning-to-rank models that mitigate the shortcomings of existing ones. Existing listwise learning-to-rank models are generally derived from the classical Plackett-Luce model, which has three major limitations. (1) Its permutation probabilities overlook ties, i.e., a situation when more than one document has the same rating with respect to a query. This can lead to imprecise permutation probabilities and inefficient training because of selecting documents one by one. (2) It does not favor documents having high relevance. (3) It has a loose assumption that sampling documents at different steps is independent. To overcome the first two limitations, we model ranking as selecting documents from a candidate set based on unique rating levels in decreasing order. The number of steps in training is determined by the number of unique rating levels. We propose a new loss function and associated four models for the entire sequence of weighted classification tasks by assigning high weights to the selected documents with high ratings for optimizing Normalized Discounted Cumulative Gain (NDCG). To overcome the final limitation, we further propose a novel and efficient way of refining prediction scores by combining an adapted Vanilla Recurrent Neural Network (RNN) model with pooling given selected documents at previous steps. We encode all of the documents already selected by an RNN model. In a single step, we rank all of the documents with the same ratings using the last cell of the RNN multiple times. We have implemented our models using three settings: neural networks, neural networks with gradient boosting, and regression trees with gradient boosting. We have conducted experiments on four public datasets. The experiments demonstrate that the models notably outperform state-of-the-art learning-to-rank models.
Our research focuses on studying and developing methods for reducing the dimensionality of large datasets, common in biomedical applications. A major problem when learning information about patients based on genetic sequencing data is that there are often more feature variables (genetic data) than observations (patients). This makes direct supervised learning difficult. One way of reducing the feature space is to use latent Dirichlet allocation in order to group genetic variants in an unsupervised manner. Latent Dirichlet allocation is a common model in natural language processing, which describes a document as a mixture of topics, each with a probability of generating certain words. This can be generalized as a Bayesian tensor decomposition to account for multiple feature variables. While we made some progress improving and modifying these methods, our significant contributions are with hierarchical topic modeling. We developed distinct methods of incorporating hierarchical topic modeling, based on nested Chinese restaurant processes and Pachinko Allocation Machine, into Bayesian tensor decompositions. We apply these models to predict whether or not patients have autism spectrum disorder based on genetic sequencing data. We examine a dataset from National Database for Autism Research consisting of paired siblings -- one with autism, and the other without -- and counts of their genetic variants. Additionally, we linked the genes with their Reactome biological pathways. We combine this information into a tensor of patients, counts of their genetic variants, and the membership of these genes in pathways. Once we decompose this tensor, we use logistic regression on the reduced features in order to predict if patients have autism. We also perform a similar analysis of a dataset of patients with one of four common types of cancer (breast, lung, prostate, and colorectal).
The problem of missing values in multivariable time series is a key challenge in many applications such as clinical data mining. Although many imputation methods show their effectiveness in many applications, few of them are designed to accommodate clinical multivariable time series. In this work, we propose a multiple imputation model that capture both cross-sectional information and temporal correlations. We integrate Gaussian processes with mixture models and introduce individualized mixing weights to handle the variance of predictive confidence of Gaussian process models. The proposed model is compared with several state-of-the-art imputation algorithms on both real-world and synthetic datasets. Experiments show that our best model can provide more accurate imputation than the benchmarks on all of our datasets.
The problem of missing values in multivariable time series is a key challenge in many applications such as clinical data mining. Although many imputation methods show their effectiveness in many applications, few of them are designed to accommodate clinical multivariable time series. In this work, we propose multiple imputation models that capture both cross-sectional information and temporal correlations. We integrate Gaussian processes with mixture models and introduce individualized mixing weights to handle the variance of predictive confidence of Gaussian process models. The proposed models are compared with several state-of-the-art imputation algorithms on both real-world and synthetic datasets. Experiments show that our best model can provide more accurate imputation than the benchmarks on all of our datasets.
Automatic data extraction from charts is challenging for two reasons: there exist many relations among objects in a chart, which is not a common consideration in general computer vision problems; and different types of charts may not be processed by the same model. To address these problems, we propose a framework of a single deep neural network, which consists of object detection, text recognition and object matching modules. The framework handles both bar and pie charts, and it may also be extended to other types of charts by slight revisions and by augmenting the training data. Our model performs successfully on 79.4% of test simulated bar charts and 88.0% of test simulated pie charts, while for charts outside of the training domain it degrades for 57.5% and 62.3%, respectively.
In a recurrent setting, conventional approaches to neural architecture search find and fix a general model for all data samples and time steps. We propose a novel algorithm that can dynamically search for the structure of cells in a recurrent neural network model. Based on a combination of recurrent and recursive neural networks, our algorithm is able to construct customized cell structures for each data sample and time step, allowing for a more efficient architecture search than existing models. Experiments on three common datasets show that the algorithm discovers high-performance cell architectures and achieves better prediction accuracy compared to the GRU structure for language modelling and sentiment analysis.
Power iteration has been generalized to solve many interesting problems in machine learning and statistics. Despite its striking success, theoretical understanding of when and how such an algorithm enjoys good convergence property is limited. In this work, we introduce a new class of optimization problems called scale invariant problems and prove that they can be efficiently solved by scale invariant power iteration (SCI-PI) with a generalized convergence guarantee of power iteration. By deriving that a stationary point is an eigenvector of the Hessian evaluated at the point, we show that scale invariant problems indeed resemble the leading eigenvector problem near a local optimum. Also, based on a novel reformulation, we geometrically derive SCI-PI which has a general form of power iteration. The convergence analysis shows that SCI-PI attains local linear convergence with a rate being proportional to the top two eigenvalues of the Hessian at the optimum. Moreover, we discuss some extended settings of scale invariant problems and provide similar convergence results for them. In numerical experiments, we introduce applications to independent component analysis, Gaussian mixtures, and non-negative matrix factorization. Experimental results demonstrate that SCI-PI is competitive to state-of-the-art benchmark algorithms and often yield better solutions.
Nowadays, online learning is an appealing learning paradigm, which is of great interest in practice due to the recent emergence of large scale applications such as online advertising placement and online web ranking. Standard online learning assumes a finite number of samples while in practice data is streamed infinitely. In such a setting gradient descent with a diminishing learning rate does not work. We first introduce regret with rolling window, a new performance metric for online streaming learning, which measures the performance of an algorithm on every fixed number of contiguous samples. At the same time, we propose a family of algorithms based on gradient descent with a constant or adaptive learning rate and provide very technical analyses establishing regret bound properties of the algorithms. We cover the convex setting showing the regret of the order of the square root of the size of the window in the constant and dynamic learning rate scenarios. Our proof is applicable also to the standard online setting where we provide the first analysis of the same regret order (the previous proofs have flaws). We also study a two layer neural network setting with ReLU activation. In this case we establish that if initial weights are close to a stationary point, the same square root regret bound is attainable. We conduct computational experiments demonstrating a superior performance of the proposed algorithms.
Ontology learning is a critical task in industry, dealing with identifying and extracting concepts captured in text data such that these concepts can be used in different tasks, e.g. information retrieval. Ontology learning is non-trivial due to several reasons with limited amount of prior research work that automatically learns a domain specific ontology from data. In our work, we propose a two-stage classification system to automatically learn an ontology from unstructured text data. We first collect candidate concepts, which are classified into concepts and irrelevant collocates by our first classifier. The concepts from the first classifier are further classified by the second classifier into different concept types. The proposed system is deployed as a prototype at a company and its performance is validated by using complaint and repair verbatim data collected in automotive industry from different data sources.