arXiv subjects

Qingpeng Zhang

Publications and source records attributed to Qingpeng Zhang.

24 records · Page 2Linked to original sources

arXiv2019

Unsupervised Euclidean Distance Attack on Network Embedding

Considering the wide application of network embedding methods in graph data mining, inspired by the adversarial attack in deep learning, this paper proposes a Genetic Algorithm (GA) based Euclidean Distance Attack strategy (EDA) to attack the network embedding, so as to prevent certain structural information from being discovered. EDA focuses on disturbing the Euclidean distance between a pair of nodes in the embedding space as much as possible through minimal modifications of the network structure. Since a large number of downstream network algorithms, such as community detection and node classification, rely on the Euclidean distance between nodes to evaluate the similarity between them in the embedding space, EDA can be considered as a universal attack on a variety of network algorithms. Different from traditional supervised attack strategies, EDA does not need labeling information, and, in other words, is an unsupervised network embedding attack method.

cs.SI↗

arXiv2019

A hybrid machine learning framework for analyzing human decision making through learning preferences

Machine learning has recently been widely adopted to address the managerial decision making problems, in which the decision maker needs to be able to interpret the contributions of individual attributes in an explicit form. However, there is a trade-off between performance and interpretability. Full complexity models are non-traceable black-box, whereas classic interpretable models are usually simplified with lower accuracy. This trade-off limits the application of state-of-the-art machine learning models in management problems, which requires high prediction performance, as well as the understanding of individual attributes' contributions to the model outcome. Multiple criteria decision aiding (MCDA) is a family of analytic approaches to depicting the rationale of human decision. It is also limited by strong assumptions. To meet the decision maker's demand for more interpretable machine learning models, we propose a novel hybrid method, namely Neural Network-based Multiple Criteria Decision Aiding, which combines an additive value model and a fully-connected multilayer perceptron (MLP) to achieve good performance while capturing the explicit relationships between individual attributes and the prediction. NN-MCDA has a linear component to characterize such relationships through providing explicit marginal value functions, and a nonlinear component to capture the implicit high-order interactions between attributes and their complex nonlinear transformations. We demonstrate the effectiveness of NN-MCDA with extensive simulation studies and three real-world datasets. To the best of our knowledge, this research is the first to enhance the interpretability of machine learning models with MCDA techniques. The proposed framework also sheds light on how to use machine learning techniques to free MCDA from strong assumptions.

cs.LG↗

arXiv2019

Analysing Motifs in Multilayer Networks

Network motifs can capture basic interaction patterns and inform the functional properties of networks. However, real-world complex systems often have multiple types of relationships, which cannot be represented by a monolayer network. The multilayer nature of complex systems demands research on extending the notion of motifs to multilayer networks, thereby exploring the interaction patterns with a higher resolution. In this paper, we propose a formal definition of multilayer motifs, and analyse the occurrence of three-node multilayer motifs in a set of real-world multilayer networks. We find that multilayer motifs in social networks are more homogeneous across layers, indicating that different types of social relationships are reinforcing each other, while those in the transportation network are more complementary across layers. We find that biological networks are often associated with heterogeneous functions. This research sheds light on how multilayer network framework enables the capture of the hidden multi-aspect relationships among the nodes.

physics.soc-ph↗

arXiv2019

E-LSTM-D: A Deep Learning Framework for Dynamic Network Link Prediction

Predicting the potential relations between nodes in networks, known as link prediction, has long been a challenge in network science. However, most studies just focused on link prediction of static network, while real-world networks always evolve over time with the occurrence and vanishing of nodes and links. Dynamic network link prediction thus has been attracting more and more attention since it can better capture the evolution nature of networks, but still most algorithms fail to achieve satisfied prediction accuracy. Motivated by the excellent performance of Long Short-Term Memory (LSTM) in processing time series, in this paper, we propose a novel Encoder-LSTM-Decoder (E-LSTM-D) deep learning model to predict dynamic links end to end. It could handle long term prediction problems, and suits the networks of different scales with fine-tuned structure. To the best of our knowledge, it is the first time that LSTM, together with an encoder-decoder architecture, is applied to link prediction in dynamic networks. This new model is able to automatically learn structural and temporal features in a unified framework, which can predict the links that never appear in the network before. The extensive experiments show that our E-LSTM-D model significantly outperforms newly proposed dynamic network link prediction methods and obtain the state-of-the-art results.

cs.SI↗

arXiv2014

These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure

K-mer abundance analysis is widely used for many purposes in nucleotide sequence analysis, including data preprocessing for de novo assembly, repeat detection, and sequencing coverage estimation. We present the khmer software package for fast and memory efficient online counting of k-mers in sequencing data sets. Unlike previous methods based on data structures such as hash tables, suffix arrays, and trie structures, khmer relies entirely on a simple probabilistic data structure, a Count-Min Sketch. The Count-Min Sketch permits online updating and retrieval of k-mer counts in memory which is necessary to support online k-mer analysis algorithms. On sparse data sets this data structure is considerably more memory efficient than any exact data structure. In exchange, the use of a Count-Min Sketch introduces a systematic overcount for k-mers; moreover, only the counts, and not the k-mers, are stored. Here we analyze the speed, the memory usage, and the miscount rate of khmer for generating k-mer frequency distributions and retrieving k-mer counts for individual k-mers. We also compare the performance of khmer to several other k-mer counting packages, including Tallymer, Jellyfish, BFCounter, DSK, KMC, Turtle and KAnalyze. Finally, we examine the effectiveness of profiling sequencing error, k-mer abundance trimming, and digital normalization of reads in the context of high khmer false positive rates. khmer is implemented in C++ wrapped in a Python interface, offers a tested and robust API, and is freely available under the BSD license at github.com/ged-lab/khmer.

q-bio.GN↗

arXiv2012

A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data

Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and high sequencing error rates of modern sequencers present many new computational challenges in data interpretation. These challenges have led to the development of new classes of mapping tools and {\em de novo} assemblers. These algorithms are challenged by the continued improvement in sequencing throughput. We here describe digital normalization, a single-pass computational algorithm that systematizes coverage in shotgun sequencing data sets, thereby decreasing sampling variation, discarding redundant data, and removing the majority of errors. Digital normalization substantially reduces the size of shotgun data sets and decreases the memory and time requirements for {\em de novo} sequence assembly, all without significantly impacting content of the generated contigs. We apply digital normalization to the assembly of microbial genomic data, amplified single-cell genomic data, and transcriptomic data. Our implementation is freely available for use and modification.

q-bio.GN↗