Koji Maruhashi

Meng Liu, Youzhi Luo, Kanji Uchino et al.

A fundamental problem in drug discovery is to design molecules that bind to specific proteins. To tackle this problem using machine learning methods, here we propose a novel and effective framework, known as GraphBP, to generate 3D molecules that bind to given proteins by placing atoms of specific types and locations to the given binding site one by one. In particular, at each step, we first employ a 3D graph neural network to obtain geometry-aware and chemically informative representations from the intermediate contextual information. Such context includes the given binding site and atoms placed in the previous steps. Second, to preserve the desirable equivariance property, we select a local reference atom according to the designed auxiliary classifiers and then construct a local spherical coordinate system. Finally, to place a new atom, we generate its atom type and relative location w.r.t. the constructed local coordinate system via a flow model. We also consider generating the variables of interest sequentially to capture the underlying dependencies among them. Experiments demonstrate that our GraphBP is effective to generate 3D molecules with binding ability to target protein binding sites. Our implementation is available at https://github.com/divelab/GraphBP.

Shuyu Dong, Kento Uemura, Akito Fujii et al.

Learning causal structures from observational data is a fundamental problem facing important computational challenges when the number of variables is large. In the context of linear structural equation models (SEMs), this paper focuses on learning causal structures from the inverse covariance matrix. The proposed method, called ICID for Independence-preserving Decomposition from Inverse Covariance matrix, is based on continuous optimization of a matrix decomposition model that preserves the nonzero patterns of the inverse covariance matrix. Through theoretical and empirical evidences, we show that ICID efficiently identifies the sought directed acyclic graph (DAG) assuming the knowledge of noise variances. Moreover, ICID is shown empirically to be robust under bounded misspecification of noise variances in the case where the noise variances are non-equal. The proposed method enjoys a low complexity, as reflected by its time efficiency in the experiments, and also enables a novel regularization scheme that yields highly accurate solutions on the Simulated fMRI data (Smith et al., 2011) in comparison with state-of-the-art algorithms.

Cong Fu, Keqiang Yan, Limei Wang et al.

Proteins are complex biomolecules that perform a variety of crucial functions within living organisms. Designing and generating novel proteins can pave the way for many future synthetic biology applications, including drug discovery. However, it remains a challenging computational task due to the large modeling space of protein structures. In this study, we propose a latent diffusion model that can reduce the complexity of protein modeling while flexibly capturing the distribution of natural protein structures in a condensed latent space. Specifically, we propose an equivariant protein autoencoder that embeds proteins into a latent space and then uses an equivariant diffusion model to learn the distribution of the latent protein representations. Experimental results demonstrate that our method can effectively generate novel protein backbone structures with high designability and efficiency. The code will be made publicly available at https://github.com/divelab/AIRS/tree/main/OpenProt/LatentDiff

Arseny Tolmachev, Akira Sakai, Masaru Todoriki et al.

Most graph neural network architectures work by message-passing node vector embeddings over the adjacency matrix, and it is assumed that they capture graph topology by doing that. We design two synthetic tasks, focusing purely on topological problems -- triangle detection and clique distance -- on which graph neural networks perform surprisingly badly, failing to detect those "bermuda" triangles. Datasets and their generation scripts are publicly available on github.com/FujitsuLaboratories/bermudatriangles and dataset.labs.fujitsu.com.

Shuyu Dong, Michèle Sebag, Kento Uemura et al.

Causal learning tackles the computationally demanding task of estimating causal graphs. This paper introduces a new divide-and-conquer approach for causal graph learning, called DCILP. In the divide phase, the Markov blanket MB($X_i$) of each variable $X_i$ is identified, and causal learning subproblems associated with each MB($X_i$) are independently addressed in parallel. This approach benefits from a more favorable ratio between the number of data samples and the number of variables considered. In counterpart, it can be adversely affected by the presence of hidden confounders, as variables external to MB($X_i$) might influence those within it. The reconciliation of the local causal graphs generated during the divide phase is a challenging combinatorial optimization problem, especially in large-scale applications. The main novelty of DCILP is an original formulation of this reconciliation as an integer linear programming (ILP) problem, which can be delegated and efficiently handled by an ILP solver. Through experiments on medium to large scale graphs, and comparisons with state-of-the-art methods, DCILP demonstrates significant improvements in terms of computational complexity, while preserving the learning accuracy on real-world problem and suffering at most a slight loss of accuracy on synthetic problems.

Youzhi Luo, Michael McThrow, Wing Yee Au et al.

Data augmentations are effective in improving the invariance of learning machines. We argue that the core challenge of data augmentations lies in designing data transformations that preserve labels. This is relatively straightforward for images, but much more challenging for graphs. In this work, we propose GraphAug, a novel automated data augmentation method aiming at computing label-invariant augmentations for graph classification. Instead of using uniform transformations as in existing studies, GraphAug uses an automated augmentation model to avoid compromising critical label-related information of the graph, thereby producing label-invariant augmentations at most times. To ensure label-invariance, we develop a training method based on reinforcement learning to maximize an estimated label-invariance probability. Experiments show that GraphAug outperforms previous graph augmentation methods on various graph classification tasks.

Xiaotian Lu, Arseny Tolmachev, Tatsuya Yamamoto et al.

Understanding the reasons behind the predictions made by deep neural networks is critical for gaining human trust in many important applications, which is reflected in the increasing demand for explainability in AI (XAI) in recent years. Saliency-based feature attribution methods, which highlight important parts of images that contribute to decisions by classifiers, are often used as XAI methods, especially in the field of computer vision. In order to compare various saliency-based XAI methods quantitatively, several approaches for automated evaluation schemes have been proposed; however, there is no guarantee that such automated evaluation metrics correctly evaluate explainability, and a high rating by an automated evaluation scheme does not necessarily mean a high explainability for humans. In this study, instead of the automated evaluation, we propose a new human-based evaluation scheme using crowdsourcing to evaluate XAI methods. Our method is inspired by a human computation game, "Peek-a-boom", and can efficiently compare different XAI methods by exploiting the power of crowds. We evaluate the saliency maps of various XAI methods on two datasets with automated and crowd-based evaluation schemes. Our experiments show that the result of our crowd-based evaluation scheme is different from those of automated evaluation schemes. In addition, we regard the crowd-based evaluation results as ground truths and provide a quantitative performance measure to compare different automated evaluation schemes. We also discuss the impact of crowd workers on the results and show that the varying ability of crowd workers does not significantly impact the results.

Luu Huu Phuc, Koh Takeuchi, Seiji Okajima et al.

Multi-relational graph is a ubiquitous and important data structure, allowing flexible representation of multiple types of interactions and relations between entities. Similar to other graph-structured data, link prediction is one of the most important tasks on multi-relational graphs and is often used for knowledge completion. When related graphs coexist, it is of great benefit to build a larger graph via integrating the smaller ones. The integration requires predicting hidden relational connections between entities belonged to different graphs (inter-domain link prediction). However, this poses a real challenge to existing methods that are exclusively designed for link prediction between entities of the same graph only (intra-domain link prediction). In this study, we propose a new approach to tackle the inter-domain link prediction problem by softly aligning the entity distributions between different domains with optimal transport and maximum mean discrepancy regularizers. Experiments on real-world datasets show that optimal transport regularizer is beneficial and considerably improves the performance of baseline methods.

Koji Maruhashi, Heewon Park, Rui Yamaguchi et al.

Dimensionality reduction is an effective method for learning high-dimensional data, which can provide better understanding of decision boundaries in human-readable low-dimensional subspace. Linear methods, such as principal component analysis and linear discriminant analysis, make it possible to capture the correlation between many variables; however, there is no guarantee that the correlations that are important in predicting data can be captured. Moreover, if the decision boundary has strong nonlinearity, the guarantee becomes increasingly difficult. This problem is exacerbated when the data are matrices or tensors that represent relationships between variables. We propose a learning method that searches for a subspace that maximizes the prediction accuracy while retaining as much of the original data information as possible, even if the prediction model in the subspace has strong nonlinearity. This makes it easier to interpret the mechanism of the group of variables behind the prediction problem that the user wants to know. We show the effectiveness of our method by applying it to various types of data including matrices and tensors.