Graph structured data has wide applicability in various domains such as physics, chemistry, biology, computer vision, and social networks, to name a few. Recently, graph neural networks (GNN) were shown to be successful in effectively representing graph structured data because of their good performance and generalization ability. However, explaining the effectiveness of GNN models is a challenging task because of the complex nonlinear transformations made over the iterations. In this paper, we propose GraphLIME, a local interpretable model explanation for graphs using the Hilbert-Schmidt Independence Criterion (HSIC) Lasso, which is a nonlinear feature selection method. GraphLIME is a generic GNN-model explanation framework that learns a nonlinear interpretable model locally in the subgraph of the node being explained. Through experiments on two real-world datasets, the explanations of GraphLIME are found to be of extraordinary degree and more descriptive in comparison to the existing explanation methods.

Finding non-linear relationships between biomolecules and a biological outcome is computationally expensive and statistically challenging. Existing methods have important drawbacks, including among others lack of parsimony, non-convexity and computational overhead. Here we propose block HSIC Lasso, a non-linear feature selector that does not present the previous drawbacks. We compare block HSIC Lasso to other state-of-the-art feature selection techniques in both synthetic and real data, including experiments over three common types of genomic data: gene-expression microarrays, single-cell RNA sequencing and genome-wide association studies. In all cases, we observe that features selected by block HSIC Lasso retain more information about the underlying biology than those selected by other techniques. As a proof of concept, we applied block HSIC Lasso to a single-cell RNA sequencing experiment on mouse hippocampus. We discovered that many genes linked in the past to brain development and function are involved in the biological differences between the types of neurons. Block HSIC Lasso is implemented in the Python 2/3 package pyHSICLasso, available on PyPI. Source code is available on GitHub (https://github.com/riken-aip/pyHSICLasso). Supplementary data are available at Bioinformatics online.

Machine learning methods are used to discover complex nonlinear relationships in biological and medical data. However, sophisticated learning models are computationally unfeasible for data with millions of features. Here we introduce the first feature selection method for nonlinear learning problems that can scale up to large, ultra-high dimensional biological data. More specifically, we scale up the novel Hilbert-Schmidt Independence Criterion Lasso (HSIC Lasso) to handle millions of features with tens of thousand samples. The proposed method is guaranteed to find an optimal subset of maximally predictive features with minimal redundancy, yielding higher predictive power and improved interpretability. Its effectiveness is demonstrated through applications to classify phenotypes based on module expression in human prostate cancer patients and to detect enzymes among protein structures. We achieve high accuracy with as few as 20 out of one million features --- a dimensionality reduction of 99.998%. Our algorithm can be implemented on commodity cloud computing platforms. The dramatic reduction of features may lead to the ubiquitous deployment of sophisticated prediction models in mobile health care applications.

Yuping Lin, Pengfei He, Han Xu, Yue Xing, Makoto Yamada, Hui Liu, Jiliang Tang. Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing. 2024.

Few-shot image classification aims at exploring transferable features from base classes to recognize images of the unseen novel classes with only a few labeled images. Existing methods usually compare the support features and query features, which are implemented by either matching the global feature vectors or matching the local feature maps at the same position. However, few labeled images fail to capture all the diverse context and intraclass variations, leading to mismatch issues for existing methods. On one hand, due to the misaligned position and cluttered background, existing methods suffer from the object mismatch issue. On the other hand, due to the scale inconsistency between images, existing methods suffer from the scale mismatch issue. In this article, we propose the bilaterally normalized scale-consistent Sinkhorn distance (BSSD) to solve these issues. First, instead of same-position matching, we use the Sinkhorn distance to find an optimal matching between images, mitigating the object mismatch caused by misaligned position. Meanwhile, we propose the intraimage and interimage attentions as the bilateral normalization on the Sinkhorn distance to suppress the object mismatch caused by background clutter. Second, local feature maps are enhanced with the multiscale pooling strategy, making the Sinkhorn distance possible to find a consistent matching scale between images. Experimental results show the effectiveness of the proposed approach, and we achieve the state-of-the-art on three few-shot benchmarks.