Tetsuya Sakurai

Akihiro Mizoguchi, Anna Bogdanova, Akira Imakura et al.

Given the time and expense associated with bringing a drug to market, numerous studies have been conducted to predict the properties of compounds based on their structure using machine learning. Federated learning has been applied to compound datasets to increase their prediction accuracy while safeguarding potentially proprietary information. However, federated learning is encumbered by low accuracy in not identically and independently distributed (non-IID) settings, i.e., data partitioning has a large label bias, and is considered unsuitable for compound datasets, which tend to have large label bias. To address this limitation, we utilized an alternative method of distributed machine learning to chemical compound data from open sources, called data collaboration analysis (DC). We also proposed data collaboration analysis using projection data (DCPd), which is an improved method that utilizes auxiliary PubChem data. This improves the quality of individual user-side data transformations for the projection data for the creation of intermediate representations. The classification accuracy, i.e., area under the curve in the receiver operating characteristic curve (ROC-AUC) and AUC in the precision-recall curve (PR-AUC), of federated averaging (FedAvg), DC, and DCPd was compared for five compound datasets. We determined that the machine learning performance for non-IID settings was in the order of DCPd, DC, and FedAvg, although they were almost the same in identically and independently distributed (IID) settings. Moreover, the results showed that compared to other methods, DCPd exhibited a negligible decline in classification accuracy in experiments with different degrees of label bias. Thus, DCPd can address the low performance in non-IID settings, which is one of the challenges of federated learning.

Yuji Kawamata, Ryoki Motai, Yukihiko Okada et al.

In recent years, the development of technologies for causal inference with privacy preservation of distributed data has gained considerable attention. Many existing methods for distributed data focus on resolving the lack of subjects (samples) and can only reduce random errors in estimating treatment effects. In this study, we propose a data collaboration quasi-experiment (DC-QE) that resolves the lack of both subjects and covariates, reducing random errors and biases in the estimation. Our method involves constructing dimensionality-reduced intermediate representations from private data from local parties, sharing intermediate representations instead of private data for privacy preservation, estimating propensity scores from the shared intermediate representations, and finally, estimating the treatment effects from propensity scores. Through numerical experiments on both artificial and real-world data, we confirm that our method leads to better estimation results than individual analyses. While dimensionality reduction loses some information in the private data and causes performance degradation, we observe that sharing intermediate representations with many parties to resolve the lack of subjects and covariates sufficiently improves performance to overcome the degradation caused by dimensionality reduction. Although external validity is not necessarily guaranteed, our results suggest that DC-QE is a promising method. With the widespread use of our method, intermediate representations can be published as open data to help researchers find causalities and accumulate a knowledge base.

Dai Hai Nguyen, Tetsuya Sakurai, Hiroshi Mamitsuka

Variational inference (VI) can be cast as an optimization problem in which the variational parameters are tuned to closely align a variational distribution with the true posterior. The optimization task can be approached through vanilla gradient descent in black-box VI or natural-gradient descent in natural-gradient VI. In this work, we reframe VI as the optimization of an objective that concerns probability distributions defined over a \textit{variational parameter space}. Subsequently, we propose Wasserstein gradient descent for tackling this optimization problem. Notably, the optimization techniques, namely black-box VI and natural-gradient VI, can be reinterpreted as specific instances of the proposed Wasserstein gradient descent. To enhance the efficiency of optimization, we develop practical methods for numerically solving the discrete gradient flows. We validate the effectiveness of the proposed methods through empirical experiments on a synthetic dataset, supplemented by theoretical analyses.

Akira Imakura, Masateru Kihira, Yukihiko Okada et al.

Recently, data collaboration (DC) analysis has been developed for privacy-preserving integrated analysis across multiple institutions. DC analysis centralizes individually constructed dimensionality-reduced intermediate representations and realizes integrated analysis via collaboration representations without sharing the original data. To construct the collaboration representations, each institution generates and shares a shareable anchor dataset and centralizes its intermediate representation. Although, random anchor dataset functions well for DC analysis in general, using an anchor dataset whose distribution is close to that of the raw dataset is expected to improve the recognition performance, particularly for the interpretable DC analysis. Based on an extension of the synthetic minority over-sampling technique (SMOTE), this study proposes an anchor data construction technique to improve the recognition performance without increasing the risk of data leakage. Numerical results demonstrate the efficiency of the proposed SMOTE-based method over the existing anchor data constructions for artificial and real-world datasets. Specifically, the proposed method achieves 9 percentage point and 38 percentage point performance improvements regarding accuracy and essential feature selection, respectively, over existing methods for an income dataset. The proposed method provides another use of SMOTE not for imbalanced data classifications but for a key technology of privacy-preserving integrated analysis.

Jinyou Xiao, Chuanzeng Zhang, Tsung-Ming Huang et al.

Numerical solution of nonlinear eigenvalue problems (NEPs) is frequently encountered in computational science and engineering. The applicability of most existing methods is limited by matrix structures, property of eigen-solutions, size of the problem, etc. This paper aims to break those limitations and to develop robust and universal NEP solvers for large-scale engineering applications. The novelty lies in two aspects. First, a rational interpolation approach (RIA) is proposed based on the Keldysh theorem for holomorphic matrix functions. Comparing with the existing contour integral approach (CIA), the RIA provides the possibility to select sampling points in more general regions and has advantages in improving accuracy and reducing computational cost. Second, a resolvent sampling scheme using the RIA is proposed for constructing reliable search spaces for the Rayleigh-Ritz procedure, based on which a robust eigen-solver, denoted by RSRR, is developed for solving general NEPs. RSRR can be easily implemented and parallelized. The advantages of the RIA and the performance of RSRR are demonstrated by a variety of benchmark and practical problems.

Akira Imakura, Tetsuya Sakurai, Yukihiko Okada et al.

Multi-source data fusion, in which multiple data sources are jointly analyzed to obtain improved information, has considerable research attention. For the datasets of multiple medical institutions, data confidentiality and cross-institutional communication are critical. In such cases, data collaboration (DC) analysis by sharing dimensionality-reduced intermediate representations without iterative cross-institutional communications may be appropriate. Identifiability of the shared data is essential when analyzing data including personal information. In this study, the identifiability of the DC analysis is investigated. The results reveals that the shared intermediate representations are readily identifiable to the original data for supervised learning. This study then proposes a non-readily identifiable DC analysis only sharing non-readily identifiable data for multiple medical datasets including personal information. The proposed method solves identifiability concerns based on a random sample permutation, the concept of interpretable DC analysis, and usage of functions that cannot be reconstructed. In numerical experiments on medical datasets, the proposed method exhibits a non-readily identifiability while maintaining a high recognition performance of the conventional DC analysis. For a hospital dataset, the proposed method exhibits a nine percentage point improvement regarding the recognition performance over the local analysis that uses only local dataset.

Dai Hai Nguyen, Tetsuya Sakurai

We consider a general optimization problem of minimizing a composite objective functional defined over a class of probability distributions. The objective is composed of two functionals: one is assumed to possess the variational representation and the other is expressed in terms of the expectation operator of a possibly nonsmooth convex regularizer function. Such a regularized distributional optimization problem widely appears in machine learning and statistics, such as proximal Monte-Carlo sampling, Bayesian inference and generative modeling, for regularized estimation and generation. We propose a novel method, dubbed as Moreau-Yoshida Variational Transport (MYVT), for solving the regularized distributional optimization problem. First, as the name suggests, our method employs the Moreau-Yoshida envelope for a smooth approximation of the nonsmooth function in the objective. Second, we reformulate the approximate problem as a concave-convex saddle point problem by leveraging the variational representation, and then develope an efficient primal-dual algorithm to approximate the saddle point. Furthermore, we provide theoretical analyses and report experimental results to demonstrate the effectiveness of the proposed method.

Akira Imakura, Lei Du, Tetsuya Sakurai

Recently, contour integral-based methods have been actively studied for solving interior eigenvalue problems that find all eigenvalues located in a certain region and their corresponding eigenvectors. In this paper, we reconsider the algorithms of the five typical contour integral-based eigensolvers from the viewpoint of projection methods, and then map the relationships among these methods. From the analysis, we conclude that all contour integral-based eigensolvers can be regarded as projection methods and can be categorized based on their subspace used, the type of projection and the problem to which they are applied implicitly.

Akira Imakura, Tetsuya Sakurai

Recently, federated learning has attracted much attention as a privacy-preserving integrated analysis that enables integrated analysis of data held by multiple institutions without sharing raw data. On the other hand, federated learning requires iterative communication across institutions and has a big challenge for implementation in situations where continuous communication with the outside world is extremely difficult. In this study, we propose a federated data collaboration learning (FedDCL), which solves such communication issues by combining federated learning with recently proposed non-model share-type federated learning named as data collaboration analysis. In the proposed FedDCL framework, each user institution independently constructs dimensionality-reduced intermediate representations and shares them with neighboring institutions on intra-group DC servers. On each intra-group DC server, intermediate representations are transformed to incorporable forms called collaboration representations. Federated learning is then conducted between intra-group DC servers. The proposed FedDCL framework does not require iterative communication by user institutions and can be implemented in situations where continuous communication with the outside world is extremely difficult. The experimental results show that the performance of the proposed FedDCL is comparable to that of existing federated learning.

Anna Bogdanova, Akira Imakura, Tetsuya Sakurai et al.

Transparency of Machine Learning models used for decision support in various industries becomes essential for ensuring their ethical use. To that end, feature attribution methods such as SHAP (SHapley Additive exPlanations) are widely used to explain the predictions of black-box machine learning models to customers and developers. However, a parallel trend has been to train machine learning models in collaboration with other data holders without accessing their data. Such models, trained over horizontally or vertically partitioned data, present a challenge for explainable AI because the explaining party may have a biased view of background data or a partial view of the feature space. As a result, explanations obtained from different participants of distributed machine learning might not be consistent with one another, undermining trust in the product. This paper presents an Explainable Data Collaboration Framework based on a model-agnostic additive feature attribution algorithm (KernelSHAP) and Data Collaboration method of privacy-preserving distributed machine learning. In particular, we present three algorithms for different scenarios of explainability in Data Collaboration and verify their consistency with experiments on open-access datasets. Our results demonstrated a significant (by at least a factor of 1.75) decrease in feature attribution discrepancies among the users of distributed machine learning.

Yifan He, Claus Aranha, Tetsuya Sakurai

We introduce Knowledge-Driven Program Synthesis (KDPS) as a variant of the program synthesis task that requires the agent to solve a sequence of program synthesis problems. In KDPS, the agent should use knowledge from the earlier problems to solve the later ones. We propose a novel method based on PushGP to solve the KDPS problem, which takes subprograms as knowledge. The proposed method extracts subprograms from the solution of previously solved problems by the Even Partitioning (EP) method and uses these subprograms to solve the upcoming programming task using Adaptive Replacement Mutation (ARM). We call this method PushGP+EP+ARM. With PushGP+EP+ARM, no human effort is required in the knowledge extraction and utilization processes. We compare the proposed method with PushGP, as well as a method using subprograms manually extracted by a human. Our PushGP+EP+ARM achieves better train error, success count, and faster convergence than PushGP. Additionally, we demonstrate the superiority of PushGP+EP+ARM when consecutively solving a sequence of six program synthesis problems.

Hongmin Li, Xiucai Ye, Akira Imakura et al.

Spectral clustering is one of the most popular clustering methods. However, how to balance the efficiency and effectiveness of the large-scale spectral clustering with limited computing resources has not been properly solved for a long time. In this paper, we propose a divide-and-conquer based large-scale spectral clustering method to strike a good balance between efficiency and effectiveness. In the proposed method, a divide-and-conquer based landmark selection algorithm and a novel approximate similarity matrix approach are designed to construct a sparse similarity matrix within low computational complexities. Then clustering results can be computed quickly through a bipartite graph partition process. The proposed method achieves a lower computational complexity than most existing large-scale spectral clustering methods. Experimental results on ten large-scale datasets have demonstrated the efficiency and effectiveness of the proposed method. The MATLAB code of the proposed method and experimental datasets are available at https://github.com/Li-Hongmin/MyPaperWithCode.

Dai Hai Nguyen, Tetsuya Sakurai

We consider the optimization problem of minimizing an objective functional, which admits a variational form and is defined over probability distributions on the constrained domain, which poses challenges to both theoretical analysis and algorithmic design. Inspired by the mirror descent algorithm for constrained optimization, we propose an iterative particle-based algorithm, named Mirrored Variational Transport (mirrorVT), extended from the Variational Transport framework [7] for dealing with the constrained domain. In particular, for each iteration, mirrorVT maps particles to an unconstrained dual domain induced by a mirror map and then approximately perform Wasserstein gradient descent on the manifold of distributions defined over the dual space by pushing particles. At the end of iteration, particles are mapped back to the original constrained domain. Through simulated experiments, we demonstrate the effectiveness of mirrorVT for minimizing the functionals over probability distributions on the simplex- and Euclidean ball-constrained domains. We also analyze its theoretical properties and characterize its convergence to the global minimum of the objective functional.

Sota Mashiko, Yuji Kawamata, Tomoru Nakayama et al.

Anomaly detection is crucial in financial auditing, and effective detection requires large volumes of data from multiple organizations. However, journal entry data is highly sensitive, making it infeasible to share them directly across audit firms. To address this challenge, journal entry anomaly detection methods based on model share-type federated learning (FL) have been proposed. These methods require multiple rounds of communication with external servers to exchange model parameters, which necessitates connecting devices storing confidential data to external networks -- a practice not recommended for sensitive data such as journal entries. To overcome these limitations, a novel anomaly detection framework based on data collaboration (DC) analysis, a non-model share-type FL approach, is proposed. The method first transforms raw journal entry data into secure intermediate representations via dimensionality reduction and then constructs a collaboration representation used to train an anomaly detection autoencoder. Notably, the approach does not require raw data to be exposed or devices to be connected to external networks, and the entire process needs only a single round of communication. The proposed method was evaluated on both synthetic and real-world journal entry data collected from eight healthcare organizations. The experimental results demonstrated that the framework not only outperforms the baseline trained on individual data but also achieves higher detection performance than model-sharing FL methods such as FedAvg and FedProx, particularly under non-i.i.d. settings that simulate practical audit environments. This study addresses the critical need to integrate organizational knowledge while preserving data confidentiality, contributing to the development of practical intelligent auditing systems.

Yuji Kawamata, Kaoru Kamijo, Masateru Kihira et al.

In recent years, the growing need to leverage sensitive data across institutions has led to increased attention on federated learning (FL), a decentralized machine learning paradigm that enables model training without sharing raw data. However, existing FL-based clustering methods, known as federated clustering, typically assume simple data partitioning scenarios such as horizontal or vertical splits, and cannot handle more complex distributed structures. This study proposes data collaboration clustering (DC-Clustering), a novel federated clustering method that supports clustering over complex data partitioning scenarios where horizontal and vertical splits coexist. In DC-Clustering, each institution shares only intermediate representations instead of raw data, ensuring privacy preservation while enabling collaborative clustering. The method allows flexible selection between k-means and spectral clustering, and achieves final results with a single round of communication with the central server. We conducted extensive experiments using synthetic and open benchmark datasets. The results show that our method achieves clustering performance comparable to centralized clustering where all data are pooled. DC-Clustering addresses an important gap in current FL research by enabling effective knowledge discovery from distributed heterogeneous data. Its practical properties -- privacy preservation, communication efficiency, and flexibility -- make it a promising tool for privacy-sensitive domains such as healthcare and finance.

Li Wang, Xiangzheng Fu, Jiahao Yang et al.

Deep learning holds a big promise for optimizing existing peptides with more desirable properties, a critical step towards accelerating new drug discovery. Despite the recent emergence of several optimized Antimicrobial peptides(AMP) generation methods, multi-objective optimizations remain still quite challenging for the idealism-realism tradeoff. Here, we establish a multi-objective AMP synthesis pipeline (MoFormer) for the simultaneous optimization of multi-attributes of AMPs. MoFormer improves the desired attributes of AMP sequences in a highly structured latent space, guided by conditional constraints and fine-grained multi-descriptor.We show that MoFormer outperforms existing methods in the generation task of enhanced antimicrobial activity and minimal hemolysis. We also utilize a Pareto-based non-dominated sorting algorithm and proxies based on large model fine-tuning to hierarchically rank the candidates. We demonstrate substantial property improvement using MoFormer from two perspectives: (1) employing molecular simulations and scoring interactions among amino acids to decipher the structure and functionality of AMPs; (2) visualizing latent space to examine the qualities and distribution features, verifying an effective means to facilitate multi-objective optimization AMPs with design constraints

Yuji Kawamata, Ryoki Motai, Yukihiko Okada et al.

The estimation of conditional average treatment effects (CATEs) is an important topic in many scientific fields. CATEs can be estimated with high accuracy if data distributed across multiple parties are centralized. However, it is difficult to aggregate such data owing to confidentiality or privacy concerns. To address this issue, we propose data collaboration double machine learning, a method for estimating CATE models using privacy-preserving fusion data constructed from distributed sources, and evaluate its performance through simulations. We make three main contributions. First, our method enables estimation and testing of semi-parametric CATE models without iterative communication on distributed data, providing robustness to model mis-specification compared to parametric approaches. Second, it enables collaborative estimation across different time points and parties by accumulating a knowledge base. Third, our method performs as well as or better than existing methods in simulations using synthetic, semi-synthetic, and real-world datasets.

Hongmin Li, Xiucai Ye, Akira Imakura et al.

Ensemble clustering is a fundamental problem in the machine learning field, combining multiple base clusterings into a better clustering result. However, most of the existing methods are unsuitable for large-scale ensemble clustering tasks due to the efficiency bottleneck. In this paper, we propose a large-scale spectral ensemble clustering (LSEC) method to strike a good balance between efficiency and effectiveness. In LSEC, a large-scale spectral clustering based efficient ensemble generation framework is designed to generate various base clusterings within a low computational complexity. Then all based clustering are combined through a bipartite graph partition based consensus function into a better consensus clustering result. The LSEC method achieves a lower computational complexity than most existing ensemble clustering methods. Experiments conducted on ten large-scale datasets show the efficiency and effectiveness of the LSEC method. The MATLAB code of the proposed method and experimental datasets are available at https://github.com/Li- Hongmin/MyPaperWithCode.

Akira Imakura, Anna Bogdanova, Takaya Yamazoe et al.

Distributed data analysis without revealing the individual data has recently attracted significant attention in several applications. A collaborative data analysis through sharing dimensionality reduced representations of data has been proposed as a non-model sharing-type federated learning. This paper analyzes the accuracy and privacy evaluations of this novel framework. In the accuracy analysis, we provided sufficient conditions for the equivalence of the collaborative data analysis and the centralized analysis with dimensionality reduction. In the privacy analysis, we proved that collaborative users' private datasets are protected with a double privacy layer against insider and external attacking scenarios.

Anna Bogdanova, Akie Nakai, Yukihiko Okada et al.

Dimensionality Reduction is a commonly used element in a machine learning pipeline that helps to extract important features from high-dimensional data. In this work, we explore an alternative federated learning system that enables integration of dimensionality reduced representations of distributed data prior to a supervised learning task, thus avoiding model sharing among the parties. We compare the performance of this approach on image classification tasks to three alternative frameworks: centralized machine learning, individual machine learning, and Federated Averaging, and analyze potential use cases for a federated learning system without model sharing. Our results show that our approach can achieve similar accuracy as Federated Averaging and performs better than Federated Averaging in a small-user setting.

Akira Imakura, Hiroaki Inaba, Yukihiko Okada et al.

This paper proposes an interpretable non-model sharing collaborative data analysis method as one of the federated learning systems, which is an emerging technology to analyze distributed data. Analyzing distributed data is essential in many applications such as medical, financial, and manufacturing data analyses due to privacy, and confidentiality concerns. In addition, interpretability of the obtained model has an important role for practical applications of the federated learning systems. By centralizing intermediate representations, which are individually constructed in each party, the proposed method obtains an interpretable model, achieving a collaborative analysis without revealing the individual data and learning model distributed over local parties. Numerical experiments indicate that the proposed method achieves better recognition performance for artificial and real-world problems than individual analysis.

Momo Matsuda, Keiichi Morikuni, Akira Imakura et al.

Irregular features disrupt the desired classification. In this paper, we consider aggressively modifying scales of features in the original space according to the label information to form well-separated clusters in low-dimensional space. The proposed method exploits spectral clustering to derive scaling factors that are used to modify the features. Specifically, we reformulate the Laplacian eigenproblem of the spectral clustering as an eigenproblem of a linear matrix pencil whose eigenvector has the scaling factors. Numerical experiments show that the proposed method outperforms well-established supervised dimensionality reduction methods for toy problems with more samples than features and real-world problems with more features than samples.

Akira Imakura, Tetsuya Sakurai

In this paper, we propose a data collaboration analysis method for distributed datasets. The proposed method is a centralized machine learning while training datasets and models remain distributed over some institutions. Recently, data became large and distributed with decreasing costs of data collection. If we can centralize these distributed datasets and analyse them as one dataset, we expect to obtain novel insight and achieve a higher prediction performance compared with individual analyses on each distributed dataset. However, it is generally difficult to centralize the original datasets due to their huge data size or regarding a privacy-preserving problem. To avoid these difficulties, we propose a data collaboration analysis method for distributed datasets without sharing the original datasets. The proposed method centralizes only intermediate representation constructed individually instead of the original dataset.

Yusei Miura, Tetsuya Sakurai, Claus Aranha et al.

Recently, deep convolutional neural networks have shown good results for image recognition. In this paper, we use convolutional neural networks with a finder module, which discovers the important region for recognition and extracts that region. We propose applying our method to the recognition of protein crystals for X-ray structural analysis. In this analysis, it is necessary to recognize states of protein crystallization from a large number of images. There are several methods that realize protein crystallization recognition by using convolutional neural networks. In each method, large-scale data sets are required to recognize with high accuracy. In our data set, the number of images is not good enough for training CNN. The amount of data for CNN is a serious issue in various fields. Our method realizes high accuracy recognition with few images by discovering the region where the crystallization drop exists. We compared our crystallization image recognition method with a high precision method using Inception-V3. We demonstrate that our method is effective for crystallization images using several experiments. Our method gained the AUC value that is about 5% higher than the compared method.

Momo Matsuda, Keiichi Morikuni, Tetsuya Sakurai

Spectral dimensionality reduction methods enable linear separations of complex data with high-dimensional features in a reduced space. However, these methods do not always give the desired results due to irregularities or uncertainties of the data. Thus, we consider aggressively modifying the scales of the features to obtain the desired classification. Using prior knowledge on the labels of partial samples to specify the Fiedler vector, we formulate an eigenvalue problem of a linear matrix pencil whose eigenvector has the feature scaling factors. The resulting factors can modify the features of entire samples to form clusters in the reduced space, according to the known labels. In this study, we propose new dimensionality reduction methods supervised using the feature scaling associated with the spectral clustering. Numerical experiments show that the proposed methods outperform well-established supervised methods for toy problems with more samples than features, and are more robust regarding clustering than existing methods. Also, the proposed methods outperform existing methods regarding classification for real-world problems with more features than samples of gene expression profiles of cancer diseases. Furthermore, the feature scaling tends to improve the clustering and classification accuracies of existing unsupervised methods, as the proportion of training data increases.

Tetsuya Sakurai, Akira Imakura, Yuto Inoue et al.

The backpropagation algorithm for calculating gradients has been widely used in computation of weights for deep neural networks (DNNs). This method requires derivatives of objective functions and has some difficulties finding appropriate parameters such as learning rate. In this paper, we propose a novel approach for computing weight matrices of fully-connected DNNs by using two types of semi-nonnegative matrix factorizations (semi-NMFs). In this method, optimization processes are performed by calculating weight matrices alternately, and backpropagation (BP) is not used. We also present a method to calculate stacked autoencoder using a NMF. The output results of the autoencoder are used as pre-training data for DNNs. The experimental results show that our method using three types of NMFs attains similar error rates to the conventional DNNs with BP.