arXiv subjects

Amadou Barry

Publications and source records attributed to Amadou Barry.

5 recordsLinked to original sources

arXiv2026

CosMAP: Contrastive Manifold Approximation and Projection for Dimensionality Reduction of Omics and Genealogical Data

Omics datasets, particularly single-cell RNA sequencing data, are high-dimensional, sparse, noisy, and dominated by zero values, making faithful low-dimensional representation challenging. Existing dimensionality-reduction methods may distort local neighbourhoods, global organization, or the cohesion of meaningful populations, with similar limitations arising in genealogical data. We introduce Contrastive Manifold Approximation and Projection (CosMAP), a graph-based unsupervised dimensionality-reduction method for producing faithful and interpretable embeddings. CosMAP extends the graph-based framework of UMAP by combining cosine-similarity neighbourhoods with temperature-normalized contrastive affinities, which are optimized in the embedding space using an attractive--repulsive objective. It further employs a two-phase refinement strategy: an intermediate higher-dimensional representation is first learned and then used to reconstruct the neighbourhood graph and initialize the final low-dimensional embedding. We evaluate CosMAP on MNIST and USPS handwritten-digit datasets, mouse retina and cortex single-cell RNA-sequencing datasets, and a large genealogical kinship dataset derived from BALSAC-CARTaGENE. Compared with state-of-the-art dimensionality-reduction methods, CosMAP produces more coherent visual representations, improves neighbourhood preservation, and provides clearer global organization of digit classes, biological cell populations, and regional genealogical patterns. These results indicate that CosMAP offers a robust framework for exploratory analysis of complex, sparse, high-dimensional data. The implementation is publicly available at https://github.com/FenosoaRandrianjatovo/CosMAP-dr.

q-bio.GN↗

arXiv2025

AdapDISCOM: An Adaptive Sparse Regression Method for High-Dimensional Multimodal Data With Block-Wise Missingness and Measurement Errors

Multimodal high-dimensional data are increasingly prevalent in biomedical research, yet they are often compromised by block-wise missingness and measurement errors, posing significant challenges for statistical inference and prediction. We propose AdapDISCOM, a novel adaptive direct sparse regression method that simultaneously addresses these two pervasive issues. Building on the DISCOM framework, AdapDISCOM introduces modality-specific weighting schemes to account for heterogeneity in data structures and error magnitudes across modalities. We establish the theoretical properties of AdapDISCOM, including model selection consistency and convergence rates under sub-Gaussian and heavy-tailed settings, and develop robust and computationally efficient variants (AdapDISCOM-Huber and Fast-AdapDISCOM). Extensive simulations demonstrate that AdapDISCOM consistently outperforms existing methods such as DISCOM, SCOM, and CoCoLasso, particularly under heterogeneous contamination and heavy-tailed distributions. Finally, we apply AdapDISCOM to Alzheimers Disease Neuroimaging Initiative (ADNI) data, demonstrating improved prediction of cognitive scores and reliable selection of established biomarkers, even with substantial missingness and measurement errors. AdapDISCOM provides a flexible, robust, and scalable framework for high-dimensional multimodal data analysis under realistic data imperfections.

stat.ME↗

arXiv2021

Weighted asymmetric least squares regression with fixed-effects

The fixed-effects model estimates the regressor effects on the mean of the response, which is inadequate to summarize the variable relationships in the presence of heteroscedasticity. In this paper, we adapt the asymmetric least squares (expectile) regression to the fixed-effects model and propose a new model: expectile regression with fixed-effects $(\ERFE).$ The $\ERFE$ model applies the within transformation strategy to concentrate out the incidental parameter and estimates the regressor effects on the expectiles of the response distribution. The $\ERFE$ model captures the data heteroscedasticity and eliminates any bias resulting from the correlation between the regressors and the omitted factors. We derive the asymptotic properties of the $\ERFE$ estimators and suggest robust estimators of its covariance matrix. Our simulations show that the $\ERFE$ estimator is unbiased and outperforms its competitors. Our real data analysis shows its ability to capture data heteroscedasticity (see our R package, \url{github.com/AmBarry/erfe}).

econ.EM↗

arXiv2021

An algorithm-based multiple detection influence measure for high dimensional regression using expectile

The identification of influential observations is an important part of data analysis that can prevent erroneous conclusions drawn from biased estimators. However, in high dimensional data, this identification is challenging. Classical and recently-developed methods often perform poorly when there are multiple influential observations in the same dataset. In particular, current methods can fail when there is masking several influential observations with similar characteristics, or swamping when the influential observations are near the boundary of the space spanned by well-behaved observations. Therefore, we propose an algorithm-based, multi-step, multiple detection procedure to identify influential observations that addresses current limitations. Our three-step algorithm to identify and capture undesirable variability in the data, $\asymMIP,$ is based on two complementary statistics, inspired by asymmetric correlations, and built on expectiles. Simulations demonstrate higher detection power than competing methods. Use of the resulting asymptotic distribution leads to detection of influential observations without the need for computationally demanding procedures such as the bootstrap. The application of our method to the Autism Brain Imaging Data Exchange neuroimaging dataset resulted in a more balanced and accurate prediction of brain maturity based on cortical thickness. See our GitHub for a free R package that implements our algorithm: \texttt{asymMIP} (\url{github.com/AmBarry/hidetify}).

stat.ME↗

arXiv2020

A new GEE method to account for heteroscedasticity, using asymmetric least-square regressions

Generalized estimating equations (GEE) are widely used to analyze longitudinal data; however, they are not appropriate for heteroscedastic data, because they only estimate regressor effects on the mean response{\textemdash}and therefore do not account for data heterogeneity. Here, we combine the GEE with the asymmetric least squares (expectile) regression to derive a new class of estimators, which we call generalized expectile estimating equations (GEEE). The GEEE model estimates regressor effects on the expectiles of the response distribution, which provides a detailed view of regressor effects on the entire response distribution. In addition to capturing data heteroscedasticity, the GEEE extends the various working correlation structures to account for within-subject dependence. We derive the asymptotic properties of the GEEE estimators and propose a robust estimator of its covariance matrix for inference (see our R package, github.com/AmBarry/expectgee). Our simulations show that the GEEE estimator is non-biased and efficient, and our real data analysis shows it captures heteroscedasticity.

stat.ME↗