Classical Machine Learning (ML) pipelines often comprise of multiple ML models where models, within a pipeline, are trained in isolation. Conversely, when training neural network models, layers composing the neural models are simultaneously trained using backpropagation. We argue that the isolated training scheme of ML pipelines is sub-optimal, since it cannot jointly optimize multiple components. To this end, we propose a framework that translates a pre-trained ML pipeline into a neural network and fine-tunes the ML models within the pipeline jointly using backpropagation. Our experiments show that fine-tuning of the translated pipelines is a promising technique able to increase the final accuracy.

The authors use a classic Armijo line-search approach in the context of SGD to automatically tune the line search parameter in training the neural networks. They're also able to prove convergence results on minimizing convex and non-convex objective functions satisfying certain growth conditions. An aside, but as an optimization-head myself, it's nice to see some of the traditional optimization ideas make their way into an ML context.

Network representation learning, as an approach to learn low dimensional representations of vertices, has attracted considerable research attention recently. It has been proven extremely useful in many machine learning tasks over large graph. Most existing methods focus on learning the structural representations of vertices in a static network, but cannot guarantee an accurate and efficient embedding in a dynamic network scenario. To address this issue, we present an efficient incremental skip-gram algorithm with negative sampling for dynamic network embedding, and provide a set of theoretical analyses to characterize the performance guarantee. Specifically, we first partition a dynamic network into the updated, including addition/deletion of links and vertices, and the retained networks over time. Then we factorize the objective function of network embedding into the added, vanished and retained parts of the network. Next we provide a new stochastic gradient-based method, guided by the partitions of the network, to update the nodes and the parameter vectors. The proposed algorithm is proven to yield an objective function value with a bounded difference to that of the original objective function. Experimental results show that our proposal can significantly reduce the training time while preserving the comparable performance. We also demonstrate the correctness of the theoretical analysis and the practical usefulness of the dynamic network embedding. We perform extensive experiments on multiple real-world large network datasets over multi-label classification and link prediction tasks to evaluate the effectiveness and efficiency of the proposed framework, and up to 22 times speedup has been achieved.

Machine learning methods may have the potential to significantly accelerate drug discovery. However, the increasing rate of new methodological approaches being published in the literature raises the fundamental question of how models should be benchmarked and validated. We reanalyze the data generated by a recently published large-scale comparison of machine learning models for bioactivity prediction and arrive at a somewhat different conclusion. We show that the performance of support vector machines is competitive with that of deep learning methods. Additionally, using a series of numerical experiments, we question the relevance of area under the receiver operating characteristic curve as a metric in virtual screening, and instead suggest that area under the precision-recall curve should be used in conjunction with the receiver operating characteristic. Our numerical experiments also highlight challenges in estimating the uncertainty in model performance via scaffold-split nested cross validation.

Advances in molecular "omics'" technologies have motivated new methodology for the integration of multiple sources of high-content biomedical data. However, most statistical methods for integrating multiple data matrices only consider data shared vertically (one cohort on multiple platforms) or horizontally (different cohorts on a single platform). This is limiting for data that take the form of bidimensionally linked matrices (e.g., multiple cohorts measured on multiple platforms), which are increasingly common in large-scale biomedical studies. In this paper, we propose BIDIFAC (Bidimensional Integrative Factorization) for integrative dimension reduction and signal approximation of bidimensionally linked data matrices. Our method factorizes the data into (i) globally shared, (ii) row-shared, (iii) column-shared, and (iv) single-matrix structural components, facilitating the investigation of shared and unique patterns of variability. For estimation we use a penalized objective function that extends the nuclear norm penalization for a single matrix. As an alternative to the complicated rank selection problem, we use results from random matrix theory to choose tuning parameters. We apply our method to integrate two genomics platforms (mRNA and miRNA expression) across two sample cohorts (tumor samples and normal tissue samples) using the breast cancer data from TCGA. We provide R code for fitting BIDIFAC, imputing missing values, and generating simulated data.

We propose a new approach to address the text classification problems when learning with partial labels is beneficial. Instead of offering each training sample a set of candidate labels, we assign negative-oriented labels to the ambiguous training examples if they are unlikely fall into certain classes. We construct our new maximum likelihood estimators with self-correction property, and prove that under some conditions, our estimators converge faster. Also we discuss the advantages of applying one of our estimator to a fully supervised learning problem. The proposed method has potential applicability in many areas, such as crowdsourcing, natural language processing and medical image analysis.

Zero-shot learning (ZSL) is a framework to classify images belonging to unseen classes based on solely semantic information about these unseen classes. In this paper, we propose a new ZSL algorithm using coupled dictionary learning. The core idea is that the visual features and the semantic attributes of an image can share the same sparse representation in an intermediate space. We use images from seen classes and semantic attributes from seen and unseen classes to learn two dictionaries that can represent sparsely the visual and semantic feature vectors of an image. In the ZSL testing stage and in the absence of labeled data, images from unseen classes can be mapped into the attribute space by finding the joint sparse representation using solely the visual data. The image is then classified in the attribute space given semantic descriptions of unseen classes. We also provide an attribute-aware formulation to tackle domain shift and hubness problems in ZSL. Extensive experiments are provided to demonstrate the superior performance of our approach against the state of the art ZSL algorithms on benchmark ZSL datasets.

Extracting the underlying trend signal is a crucial step to facilitate time series analysis like forecasting and anomaly detection. Besides noise signal, time series can contain not only outliers but also abrupt trend changes in real-world scenarios. To deal with these challenges, we propose a robust trend filtering algorithm based on robust statistics and sparse learning. Specifically, we adopt the Huber loss to suppress outliers, and utilize a combination of the first order and second order difference on the trend component as regularization to capture both slow and abrupt trend changes. Furthermore, an efficient method is designed to solve the proposed robust trend filtering based on majorization minimization (MM) and alternative direction method of multipliers (ADMM). We compared our proposed robust trend filter with other nine state-of-the-art trend filtering algorithms on both synthetic and real-world datasets. The experiments demonstrate that our algorithm outperforms existing methods.

In recent years, implicit regularization from various optimization algorithms plays a crucial role in the generalizatiion abilities in training deep neural networks [Salakhutdinov and Srebro, 2015, Neyshabur et al., 2015, Keskar et al., 2016, Neyshabur et al., 2017, Zhang et al., 2017]. For example, in underdetermined problems where the number of parameters is larger than the number of training examples, many global optimum fail to exhibit good generalization properties, however, a specific optimization algorithm (such as gradient descent) does converge to a particular optimum that generalize well, although no explicit regularization is enforced when training the model.

CNNs, RNNs, GCNs, and CapsNets have shown significant insights in representation learning and are widely used in various text mining tasks such as large-scale multi-label text classification. However, most existing deep models for multi-label text classification consider either the non-consecutive and long-distance semantics or the sequential semantics, but how to consider them both coherently is less studied. In addition, most existing methods treat output labels as independent methods, but ignore the hierarchical relations among them, leading to useful semantic information loss. In this paper, we propose a novel hierarchical taxonomy-aware and attentional graph capsule recurrent CNNs framework for large-scale multi-label text classification. Specifically, we first propose to model each document as a word order preserved graph-of-words and normalize it as a corresponding words-matrix representation which preserves both the non-consecutive, long-distance and local sequential semantics. Then the words-matrix is input to the proposed attentional graph capsule recurrent CNNs for more effectively learning the semantic features. To leverage the hierarchical relations among the class labels, we propose a hierarchical taxonomy embedding method to learn their representations, and define a novel weighted margin loss by incorporating the label representation similarity. Extensive evaluations on three datasets show that our model significantly improves the performance of large-scale multi-label text classification by comparing with state-of-the-art approaches.