Gang Fu

Kyriakos Axiotis, Sami Abu-al-haija, Lin Chen et al.

Deep learning has become the standard approach for most machine learning tasks. While its impact is undeniable, interpreting the predictions of deep learning models from a human perspective remains a challenge. In contrast to model training, model interpretability is harder to quantify and pose as an explicit optimization problem. Inspired by the AUC softmax information curve (AUC SIC) metric for evaluating feature attribution methods, we propose a unified discrete optimization framework for feature attribution and feature selection based on subset selection. This leads to a natural adaptive generalization of the path integrated gradients (PIG) method for feature attribution, which we call Greedy PIG. We demonstrate the success of Greedy PIG on a wide variety of tasks, including image feature attribution, graph compression/explanation, and post-hoc feature selection on tabular data. Our results show that introducing adaptivity is a powerful and versatile method for making attribution methods more powerful.

Zheng Gao, Gang Fu, Chunping Ouyang et al.

Representation learning provides new and powerful graph analytical approaches and tools for the highly valued data science challenge of mining knowledge graphs. Since previous graph analytical methods have mostly focused on homogeneous graphs, an important current challenge is extending this methodology for richly heterogeneous graphs and knowledge domains. The biomedical sciences are such a domain, reflecting the complexity of biology, with entities such as genes, proteins, drugs, diseases, and phenotypes, and relationships such as gene co-expression, biochemical regulation, and biomolecular inhibition or activation. Therefore, the semantics of edges and nodes are critical for representation learning and knowledge discovery in real world biomedical problems. In this paper, we propose the edge2vec model, which represents graphs considering edge semantics. An edge-type transition matrix is trained by an Expectation-Maximization approach, and a stochastic gradient descent model is employed to learn node embedding on a heterogeneous graph via the trained transition matrix. edge2vec is validated on three biomedical domain tasks: biomedical entity classification, compound-gene bioactivity prediction, and biomedical information retrieval. Results show that by considering edge-types into node embedding learning in heterogeneous graphs, \textbf{edge2vec}\ significantly outperforms state-of-the-art models on all three tasks. We propose this method for its added value relative to existing graph analytical methodology, and in the real world context of biomedical knowledge discovery applicability.

Vinh Nguyen, Olivier Bodenreider, Krishnaprasad Thirunarayan et al.

The Singleton Property (SP) approach has been proposed for representing and querying metadata about RDF triples such as provenance, time, location, and evidence. In this approach, one singleton property is created to uniquely represent a relationship in a particular context, and in general, generates a large property hierarchy in the schema. It has become the subject of important questions from Semantic Web practitioners. Can an existing reasoner recognize the singleton property triples? And how? If the singleton property triples describe a data triple, then how can a reasoner infer this data triple from the singleton property triples? Or would the large property hierarchy affect the reasoners in some way? We address these questions in this paper and present our study about the reasoning aspects of the singleton properties. We propose a simple mechanism to enable existing reasoners to recognize the singleton property triples, as well as to infer the data triples described by the singleton property triples. We evaluate the effect of the singleton property triples in the reasoning processes by comparing the performance on RDF datasets with and without singleton properties. Our evaluation uses as benchmark the LUBM datasets and the LUBM-SP datasets derived from LUBM with temporal information added through singleton properties.