Workshop Notes of the Sixth International Workshop "What can FCA do for Artificial Intelligence?"

International audienc

Development of Biclustering Techniques for Gene Expression Data Modeling and Mining

The next-generation sequencing technologies can generate large-scale biological data with higher resolution, better accuracy, and lower technical variation than the arraybased counterparts. RNA sequencing (RNA-Seq) can generate genome-scale gene expression data in biological samples at a given moment, facilitating a better understanding of cell functions at genetic and cellular levels. The abundance of gene expression datasets provides an opportunity to identify genes with similar expression patterns across multiple conditions, i.e., co-expression gene modules (CEMs). Genomescale identification of CEMs can be modeled and solved by biclustering, a twodimensional data mining technique that allows clustering of rows and columns in a gene expression matrix, simultaneously. Compared with traditional clustering that targets global patterns, biclustering can predict local patterns. This unique feature makes biclustering very useful when applied to big gene expression data since genes that participate in a cellular process are only active in specific conditions, thus are usually coexpressed under a subset of all conditions. The combination of biclustering and large-scale gene expression data holds promising potential for condition-specific functional pathway/network analysis. However, existing biclustering tools do not have satisfied performance on high-resolution RNA-Seq data, majorly due to the lack of (i) a consideration of high sparsity of RNA-Seq data, especially for scRNA-Seq data, and (ii) an understanding of the underlying transcriptional regulation signals of the observed gene expression values. QUBIC2, a novel biclustering algorithm, is designed for large-scale bulk RNA-Seq and single-cell RNA-seq (scRNA-Seq) data analysis. Critical novelties of the algorithm include (i) used a truncated model to handle the unreliable quantification of genes with low or moderate expression; (ii) adopted the Gaussian mixture distribution and an information-divergency objective function to capture shared transcriptional regulation signals among a set of genes; (iii) utilized a Dual strategy to expand the core biclusters, aiming to save dropouts from the background; and (iv) developed a statistical framework to evaluate the significances of all the identified biclusters. Method validation on comprehensive data sets suggests that QUBIC2 had superior performance in functional modules detection and cell type classification. The applications of temporal and spatial data demonstrated that QUBIC2 could derive meaningful biological information from scRNA-Seq data. Also presented in this dissertation is QUBICR. This R package is characterized by an 82% average improved efficiency compared to the source C code of QUBIC. It provides a set of comprehensive functions to facilitate biclustering-based biological studies, including the discretization of expression data, query-based biclustering, bicluster expanding, biclusters comparison, heatmap visualization of any identified biclusters, and co-expression networks elucidation. In the end, a systematical summary is provided regarding the primary applications of biclustering for biological data and more advanced applications for biomedical data. It will assist researchers to effectively analyze their big data and generate valuable biological knowledge and novel insights with higher efficiency

Next Generation of Product Search and Discovery

Online shopping has become an important part of people’s daily life with the rapid development of e-commerce. In some domains such as books, electronics, and CD/DVDs, online shopping has surpassed or even replaced the traditional shopping method. Compared with traditional retailing, e-commerce is information intensive. One of the key factors to succeed in e-business is how to facilitate the consumers’ approaches to discover a product. Conventionally a product search engine based on a keyword search or category browser is provided to help users find the product information they need. The general goal of a product search system is to enable users to quickly locate information of interest and to minimize users’ efforts in search and navigation. In this process human factors play a significant role. Finding product information could be a tricky task and may require an intelligent use of search engines, and a non-trivial navigation of multilayer categories. Searching for useful product information can be frustrating for many users, especially those inexperienced users. This dissertation focuses on developing a new visual product search system that effectively extracts the properties of unstructured products, and presents the possible items of attraction to users so that the users can quickly locate the ones they would be most likely interested in. We designed and developed a feature extraction algorithm that retains product color and local pattern features, and the experimental evaluation on the benchmark dataset demonstrated that it is robust against common geometric and photometric visual distortions. Besides, instead of ignoring product text information, we investigated and developed a ranking model learned via a unified probabilistic hypergraph that is capable of capturing correlations among product visual content and textual content. Moreover, we proposed and designed a fuzzy hierarchical co-clustering algorithm for the collaborative filtering product recommendation. Via this method, users can be automatically grouped into different interest communities based on their behaviors. Then, a customized recommendation can be performed according to these implicitly detected relations. In summary, the developed search system performs much better in a visual unstructured product search when compared with state-of-art approaches. With the comprehensive ranking scheme and the collaborative filtering recommendation module, the user’s overhead in locating the information of value is reduced, and the user’s experience of seeking for useful product information is optimized

A Transformer-Based Substitute Recommendation Model Incorporating Weakly Supervised Customer Behavior Data

The substitute-based recommendation is widely used in E-commerce to provide better alternatives to customers. However, existing research typically uses the customer behavior signals like co-view and view-but-purchase-another to capture the substitute relationship. Despite its intuitive soundness, we find that such an approach might ignore the functionality and characteristics of products. In this paper, we adapt substitute recommendation into language matching problem by taking product title description as model input to consider product functionality. We design a new transformation method to de-noise the signals derived from production data. In addition, we consider multilingual support from the engineering point of view. Our proposed end-to-end transformer-based model achieves both successes from offline and online experiments. The proposed model has been deployed in a large-scale E-commerce website for 11 marketplaces in 6 languages. Our proposed model is demonstrated to increase revenue by 19% based on an online A/B experiment.Comment: 6 pages, 3 figures, 5 tables, accepted in 21st IEEE International Conference on Machine Learning and Application

Building emergent social networks and group profiles by semantic user preference clustering

This is an electronic version of the paper presented at the International Workshop on Semantic Network Analysis (SNA 2006) at the European Semantic Web Conference (ESWC 2006), held in Budva on 2006This paper presents a novel approach to automatic semantic social network construction based on semantic user preference clustering. Considering a number of users, each of them with an associated ontology-based profile, we propose a strategy that clusters the concepts of the reference ontology according to user preferences of these concepts, and then determines which clusters are more appropriate to the users. The resultant user clusters can be merged into individual group profiles, automatically defining a semantic social network suitable for use in collaborative and recommendation environments.This research was supported by the European Commission (FP6-027685 – MESH), and the Spanish Ministry of Science and Education (TIN2005-06885). The expressed content is the view of the authors but not necessarily the view of the MESH project as a whole