arXiv subjects

Tetsuya Sakurai

Publications and source records attributed to Tetsuya Sakurai.

At least 19 recordsLinked to original sources

arXiv2025

A new type of federated clustering: A non-model-sharing approach

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.

cs.LG↗

arXiv2025

Estimating Covariate-balanced Survival Curve in Distributed Data Environment using Data Collaboration Quasi-Experiment

The sharing of patient-level data necessary for covariate-adjusted survival analysis between medical institutions is difficult due to privacy protection restrictions. We propose a privacy-preserving framework that estimates balanced Kaplan-Meier curves from distributed observational data without exchanging raw data. Each institution sends only the low-dimensional representation obtained through dimensionality reduction of the covariate matrix. Analysts reconstruct the aggregated dataset, perform propensity score matching, and estimate survival curves. Experiments using simulation datasets and five publicly available medical datasets showed that the proposed method consistently outperformed single-site analyses. This method can handle both horizontal and vertical data distribution scenarios and enables the collaborative acquisition of reliable survival curves with minimal communication and no disclosure of raw data.

stat.ME↗

arXiv2025

Anomaly Detection in Double-entry Bookkeeping Data by Federated Learning System with Non-model Sharing Approach

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.

cs.LG↗

arXiv2025

Data collaboration for causal inference from limited medical testing and medication data

Observational studies enable causal inferences when randomized controlled trials (RCTs) are not feasible. However, integrating sensitive medical data across multiple institutions introduces significant privacy challenges. The data collaboration quasi-experiment (DC-QE) framework addresses these concerns by sharing "intermediate representations" -- dimensionality-reduced data derived from raw data -- instead of the raw data. While the DC-QE can estimate treatment effects, its application to medical data remains unexplored. This study applied the DC-QE framework to medical data from a single institution to simulate distributed data environments under independent and identically distributed (IID) and non-IID conditions. We propose a novel method for generating intermediate representations within the DC-QE framework. Experimental results demonstrated that DC-QE consistently outperformed individual analyses across various accuracy metrics, closely approximating the performance of centralized analysis. The proposed method further improved performance, particularly under non-IID conditions. These outcomes highlight the potential of the DC-QE framework as a robust approach for privacy-preserving causal inferences in healthcare. Broader adoption of this framework and increased use of intermediate representations could grant researchers access to larger, more diverse datasets while safeguarding patient confidentiality. This approach may ultimately aid in identifying previously unrecognized causal relationships, support drug repurposing efforts, and enhance therapeutic interventions for rare diseases.

stat.ME↗

arXiv2024

FedDCL: a federated data collaboration learning as a hybrid-type privacy-preserving framework based on federated learning and data collaboration

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.

cs.LG↗

arXiv2024

Moreau-Yoshida Variational Transport: A General Framework For Solving Regularized Distributional Optimization Problems

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.

cs.LG↗

arXiv2024

MoFormer: Multi-objective Antimicrobial Peptide Generation Based on Conditional Transformer Joint Multi-modal Fusion Descriptor

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

q-bio.QM↗

arXiv2024

Estimation of conditional average treatment effects on distributed confidential data

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.

stat.ME↗

arXiv2024

Collaborative causal inference on distributed data

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.

stat.ME↗

arXiv2023

Wasserstein Gradient Flow over Variational Parameter Space for Variational Inference

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.

cs.LG↗

arXiv2023

Data Collaboration Analysis applied to Compound Datasets and the Introduction of Projection data to Non-IID settings

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.

cs.LG↗

arXiv2023

Top to random shuffles on colored permutations

A deck of $n$ cards are shuffled by repeatedly taking off the top card, flipping it with probability $1/2$, and inserting it back into the deck at a random position. This process can be considered as a Markov chain on the group $B_n$ of signed permutations. We show that the eigenvalues of the transition probability matrix are $0,1/n,2/n,\ldots,(n-1)/n,1$ and the multiplicity of the eigenvalue $i/n$ is equal to the number of the {\em signed} permutation having exactly $i$ fixed points. We show the similar results also for the colored permutations. Further, we show that the mixing time of this Markov chain is $n\log n$, same as the ordinary 'top-to-random' shuffles without flipping the cards. The cut-off is also analyzed by using the asymptotic behavior of the Stirling numbers of the second kind.

math.CO↗

arXiv2022

Achieving Transparency in Distributed Machine Learning with Explainable Data Collaboration

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.

cs.LG↗

arXiv2022

Inferring cell-specific lncRNA regulation with single-cell RNA-sequencing data in the developing human neocortex

Long non-coding RNAs (lncRNAs) are important regulators to modulate gene expression and cell proliferation in the developing human brain. Previous methods mainly use bulk lncRNA and mRNA expression data to study lncRNA regulation. However, to analyze lncRNA regulation regarding individual cells, we focus on single-cell RNA-sequencing (scRNA-seq) data instead of bulk data. Recent advance in scRNA-seq has provided a way to investigate lncRNA regulation at single-cell level. We will propose a novel computational method, CSlncR (cell-specific lncRNA regulation), which combines putative lncRNA-mRNA binding information with scRNA-seq data including lncRNAs and mRNAs to identify cell-specific lncRNA-mRNA regulation networks at individual cells. To understand lncRNA regulation at different development stages, we apply CSlncR to the scRNA-seq data of human neocortex. Network analysis shows that the lncRNA regulation is unique in each cell from the different human neocortex development stages. The comparison results indicate that CSlncR is also an effective tool for predicting cell-specific lncRNA targets and clustering single cells, which helps understand cell-cell communication.

q-bio.MN↗

arXiv2022

Unveiling interpretable development-specific gene signatures in the developing human prefrontal cortex with ICGS

In this paper, to unveil interpretable development-specific gene signatures in human PFC, we propose a novel gene selection method, named Interpretable Causality Gene Selection (ICGS), which adopts a Bayesian Network (BN) to represent causality between multiple gene variables and a development variable. The proposed ICGS method combines the positive instances-based contrastive learning with a Variational AutoEncoder (VAE) to obtain this optimal BN structure and use a Markov Blanket (MB) to identify gene signatures causally related to the development variable. Moreover, the differential expression genes (DEGs) are used to filter redundant genes before gene selection. In order to identify gene signatures, we apply the proposed ICGS to the human PFC single-cell transcriptomics data. The experimental results demonstrate that the proposed method can effectively identify interpretable development-specific gene signatures in human PFC. Gene ontology enrichment analysis and ASD-related gene analysis show that these identified gene signatures reveal the key biological processes and pathways in human PFC and have more potential for neurodevelopment disorder cure. These gene signatures are expected to bring important implications for understanding PFC development heterogeneity and function in humans.

q-bio.NC↗

arXiv2022

Knowledge-Driven Program Synthesis via Adaptive Replacement Mutation and Auto-constructed Subprogram Archives

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.

cs.NE↗

arXiv2022

Non-readily identifiable data collaboration analysis for multiple datasets including personal information

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.

cs.LG↗

arXiv2022

Another Use of SMOTE for Interpretable Data Collaboration Analysis

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.

cs.LG↗