DNA methylation plays a crucial role in human diseases pathogenesis. Substantial experimental evidence from clinical and biological studies has confirmed numerous methylation-disease associations, which provide valuable prior knowledge for advancing precision medicine through biomarker discovery and disease subtyping. To systematically mine reliable methylation prior knowledge from known DNA methylation-disease associations and develop robust computational methods for precision medicine applications, we propose MethPriorGCN. By integrating layer attention mechanisms and feature weighting mechanisms, MethPriorGCN not only identified reliable methylation digital biomarkers but also achieved superior disease subtype classification accuracy.

Cancer classification and biomarker identification are crucial for guiding personalized treatment. To make effective use of miRNA associations and expression data, we have developed a deep learning model for cancer classification and biomarker identification. We propose an approach for cancer classification called MiRNA Selection and Hybrid Fusion (MiRS-HF), which consists of early fusion and intermediate fusion. The early fusion involves applying a Layer Attention Graph Convolutional Network (LAGCN) to a miRNA-disease heterogeneous network, resulting in a miRNA-disease association degree score matrix. The intermediate fusion employs a Graph Convolutional Network (GCN) in the classification tasks, weighting the expression data based on the miRNA-disease association degree score. Furthermore, MiRS-HF can identify the important miRNA biomarkers and their expression patterns. The proposed method demonstrates superior performance in the classification tasks of six cancers compared to other methods. Simultaneously, we incorporated the feature weighting strategy into the comparison algorithm, leading to a significant improvement in the algorithm's results, highlighting the extreme importance of this strategy.

Abstract GPT-3 is a large-scale natural language model developed by OpenAI that can perform many different tasks, including topic classification. Although researchers claim that it requires only a small number of in-context examples to learn a task, in practice GPT-3 requires these training examples to be either of exceptional quality or a higher quantity than easily created by hand. To address this issue, this study teaches GPT-3 to classify whether a question is related to data science by augmenting a small training set with additional examples generated by GPT-3 itself. This study compares two augmented classifiers: the Classification Endpoint with an increased training set size and the Completion Endpoint with an augmented prompt optimized using a genetic algorithm. We find that data augmentation significantly increases the accuracy of both classifiers, and that the embedding-based Classification Endpoint achieves the best accuracy of about 76%, compared to human accuracy of 85%. In this way, giving large language models like GPT-3 the ability to propose their own training examples can improve short text classification performance.

Microbial natural products represent a major source of bioactive compounds for drug discovery. Among these molecules, nonribosomal peptides (NRPs) represent a diverse class that include antibiotics, immunosuppressants, anticancer agents, toxins, siderophores, pigments, and cytostatics. The discovery of novel NRPs remains a laborious process because many NRPs consist of nonstandard amino acids that are assembled by nonribosomal peptide synthetases (NRPSs). Adenylation domains (A-domains) in NRPSs are responsible for selection and activation of monomers appearing in NRPs. During the past decade, several support vector machine-based algorithms have been developed for predicting the specificity of the monomers present in NRPs. These algorithms utilize physiochemical features of the amino acids present in the A-domains of NRPSs. In this article, we benchmarked the performance of various machine learning algorithms and features for predicting specificities of NRPSs and we showed that the extra trees model paired with one-hot encoding features outperforms the existing approaches. Moreover, we show that unsupervised clustering of 453 560 A-domains reveals many clusters that correspond to potentially novel amino acids. While it is challenging to predict the chemical structure of these amino acids, we developed novel techniques to predict their various properties, including polarity, hydrophobicity, charge, and presence of aromatic rings, carboxyl, and hydroxyl groups.

K-nearest neighbor (kNN) search is an important problem in data mining and knowledge discovery. Inspired by the huge success of tree-based methodology and ensemble methods over the last decades, we propose a new method for kNN search, random projection forests (rpForests). rpForests finds nearest neighbors by combining multiple kNN-sensitive trees with each constructed recursively through a series of random projections. As demonstrated by experiments on a wide collection of real datasets, our method achieves a remarkable accuracy in terms of fast decaying missing rate of kNNs and that of discrepancy in the k-th nearest neighbor distances. rpForests has a very low computational complexity as a tree-based methodology. The ensemble nature of rpForests makes it easily parallelized to run on clustered or multicore computers; the running time is expected to be nearly inversely proportional to the number of cores or machines. We give theoretical insights on rpForests by showing the exponential decay of neighboring points being separated by ensemble random projection trees when the ensemble size increases. Our theory can also be used to refine the choice of random projections in the growth of rpForests; experiments show that the effect is remarkable.

The last decades have seen a surge of interests in distributed computing thanks to advances in clustered computing and big data technology. Existing distributed algorithms typically assume all the data are already in one place, and divide the data and conquer on multiple machines. However, it is increasingly often that the data are located at a number of distributed sites, and one wishes to compute over all the data with low communication overhead. For spectral clustering, we propose a novel framework that enables its computation over such distributed data, with “minimal” communications while a major speedup in computation. The loss in accuracy is negligible compared to the non-distributed setting. Our approach allows local parallel computing at where the data are located, thus turns the distributed nature of the data into a blessing; the speedup is most substantial when the data are evenly distributed across sites. Experiments on synthetic and large UC Irvine datasets show almost no loss in accuracy with our approach while a 2x speedup under various settings with two distributed sites. As the transmitted data need not be in their original form, our framework readily addresses the privacy concern for data sharing in distributed computing.

Divide-and-conquer is a general strategy to deal with large scale problems. It is typically applied to generate ensemble instances, which potentially limits the problem size it can handle. Additionally, the data are often divided by random sampling which may be suboptimal. To address these concerns, we propose the DC2algorithm. Instead of ensemble instances, we produce structure-preserving signature pieces to be assembled and conquered. DC2achieves the efficiency of sampling-based large scale kernel methods while enabling parallel multicore or clustered computation. The data partition and subsequent compression are unified by recursive random projections. Empirically dividing the data by random projections induces smaller mean squared approximation errors than conventional random sampling. The power of DC2is demonstrated by our clustering algorithm rpfCluster+, which is as accurate as some fastest approximate spectral clustering algorithms while maintaining a running time close to that of K-means clustering. Analysis on DC2when applied to spectral clustering shows that the loss in clustering accuracy due to data division and reduction is upper bounded by the data approximation error which would vanish with recursive random projections. Due to its easy implementation and flexibility, we expect DC2to be applicable to general large scale learning problems.

K-nearest neighbor (kNN) search has wide applications in many areas, including data mining, machine learning, statistics and many applied domains. Inspired by the success of ensemble methods and the flexibility of tree-based methodology, we propose random projection forests, rpForests, for kNN search. rpForests finds kNNs by aggregating results from an ensemble of random projection trees with each constructed recursively through a series of carefully chosen random projections. rpForests achieves a remarkable accuracy in terms of fast decay in the missing rate of kNNs and that of discrepancy in the kNN distances. rpForests has a very low computational complexity. The ensemble nature of rpForests makes it easily run in parallel on multicore or clustered computers; the running time is expected to be nearly inversely proportional to the number of cores or machines. We give theoretical insights by showing the exponential decay of the probability that neighboring points would be separated by ensemble random projection trees when the ensemble size increases. Our theory can be used to refine the choice of random projections in the growth of trees, and experiments show that the effect is remarkable.

Spectral clustering refers to a flexible class of clustering procedures that can produce high-quality clusterings on small data sets but which has limited applicability to large-scale problems due to its computational complexity of O(n^3), with n the number of data points. We extend the range of spectral clustering by developing a general framework for fast approximate spectral clustering in which a distortion-minimizing local transformation is first applied to the data. This framework is based on a theoretical analysis that provides a statistical characterization of the effect of local distortion on the mis-clustering rate. We develop two concrete instances of our general framework, one based on local k-means clustering (KASP) and one based on random projection trees (RASP). Extensive experiments show that these algorithms can achieve significant speedups with little degradation in clustering accuracy. Specifically, our algorithms outperform k-means by a large margin in terms of accuracy, and run several times faster than approximate spectral clustering based on the Nystrom method, with comparable accuracy and significantly smaller memory footprint. Remarkably, our algorithms make it possible for a single machine to spectral cluster data sets with a million observations within several minutes.

Spectral clustering is useful for a wide-ranging set of applications in areas such as biological data analysis, image processing and data mining. However, the computational and/or communication resources required by the method in processing large-scale data sets are often prohibitively high, and practitioners are often required to perturb the original data in various ways (quantization, downsampling, etc) before invoking a spectral algorithm. In this paper, we use stochastic perturbation theory to study the effects of data perturbation on the performance of spectral clustering. We show that the error under perturbation of spectral clustering is closely related to the perturbation of the eigenvectors of the Laplacian matrix. From this result we derive approximate upper bounds on the clustering error. We show that this bound is tight empirically across a wide range of problems, suggesting that it can be used in practical settings to determine the amount of data reduction allowed in order to meet a specification of permitted loss in clustering performance.

Gesture recognition techniques often suffer from being highly device-dependent and hard to extend. If a system is trained using data from a specific glove input device, that system is typically unusable with any other input device. The set of gestures that a system is trained to recognize is typically not extensible, without retraining the entire system. We propose a novel gesture recognition framework to address these problems. This framework is based on a multi-layered view of gesture recognition. Only the lowest layer is device dependent, it converts raw sensor values produced by the glove to a glove-independent semantic description of the hand. The higher layers of our framework can be reused across gloves, and are easily extensible to include new gestures. We have experimentally evaluated our framework and found that it yields comparable performance to conventional techniques, while substantiating our claims of device independence and extensibility.