19 papers · ranked by Valyu relevance
Daniel E. Schäffer, Helen Kang, Ekin Deniz Aksu, Daniel Edelman + 1 more
Data from single-cell RNA sequencing (scRNA-seq) and the Assay for Transposase-Accessible Chromatin (scATAC-seq) are high-dimensional, sparse, and undesirably capture technical variability between experiments or batches. Many analysis methods thus seek to produce a low-dimensional cell-by-feature embedding space that…
Yannis Schumann, Simon Schlumbohm, Julia E. Neumann, Philipp Neumann
Data from high-throughput technologies assessing global patterns of biomolecules (omic data), is often afflicted with missing values and with measurement-specific biases (batch-effects), that hinder the quantitative comparison of independently acquired datasets. This work introduces batch-effect reduction trees (BERT)…
Mekan Myradov, Aissa Houdjedj, Oznur Tastan, Hilal Kazan
Single-cell RNA sequencing (scRNA-seq) datasets generated across laboratories and experimental conditions often exhibit batch effects that obscure biological variation. Numerous computational methods have been developed to integrate such datasets, making robust benchmarking essential. Evaluation metrics play a central…
Han Xu, Yusen Ye, Ran Duan, Yong Gao + 2 more
Integrating multiple single-cell datasets is essential for the comprehensive understanding of cell heterogeneity. Batch effect is the undesired systematic variations among technologies or experimental laboratories that distort biological signals and hinder the integration of single-cell datasets. However, existing…
Yuan Wang, William Thistlethwaite, Alicja Tadych, Frederique Ruf-Zamojski + 6 more
To facilitate single cell multi-omics analysis and improve reproducibility, we present SPEEDI (Single-cell Pipeline for End to End Data Integration), a fully automated end-to-end framework for batch inference, data integration, and cell type labeling. SPEEDI introduces data-driven batch inference and transforms the…
Karin Hrovatin, Amir Ali Moinfar, Luke Zappia, Shrey Parikh + 4 more
Integration of single-cell RNA-sequencing (scRNA-seq) datasets is standard in scRNA-seq analysis. Nevertheless, current computational methods struggle to harmonize datasets across systems such as species, organoids and primary tissue, or different scRNA-seq protocols, including single-cell and single-nuclei.…
Yingxin Zhang, Qingzhen Hou
Spatial transcriptomics (ST) enables high-resolution mapping of gene expression within tissue slices, providing detailed insights into tissue architecture and cellular interactions. However, batch effects, arising from non-biological variations in sample collection, processing, sequencing platforms, or experimental…
Mark Messner, Tianchen Hu, Tianju Chen
Stiff systems of ordinary differential equations (ODEs) and sparse training data are common in scientific problems. This paper describes efficient, implicit, vectorized methods for integrating stiff systems of ordinary differential equations through time and calculating parameter gradients with the adjoint method. The…
Bowen Zhao, Dong-Qing Wei, Yi Xiong, Jun Ding
The rapid development of single-cell technologies has underscored the need for more effective methods in the integration and harmonization of single-cell sequencing data. The prevalent challenge of batch effects, resulting from technical and biological variations across studies, demands accurate and reliable solutions…
Bowen Zhao, Kailu Song, Dong-Qing Wei, Yi Xiong + 1 more
The rapid advancement of single-cell technologies has created an urgent need for effective methods to integrate and harmonize single-cell data. Technical and biological variations across studies complicate data integration, while conventional tools often struggle with reliance on gene expression distribution…
Zhiqian Zhai, Changhu Wang, Chengfeng Jiang, Ziqi Rong + 1 more
Integrating single-cell and spatial transcriptomics data across batches is essential for recovering comparable cell identities—including cell types, subtypes, and states—as a prerequisite for downstream analyses in multi-condition and large-scale studies. This task remains challenging because between-batch variation…
Reut Danino, Iftach Nachman, Roded Sharan, Thomas Lengauer
The decreasing cost of sequencing techniques, as well as the important insights achieved by the analysis of gene expression data, have led to the generation of enormous single-cell RNA sequencing atlas projects, such as the Human Cell Atlas (), which contain datasets generated by multiple laboratories under different…
Emad Fallahzadeh, Amir Hossein Bavand, Peter C. Rigby
Continuous integration at scale is costly but essential to software development. Various test optimization techniques including test selection and prioritization aim to reduce the cost. Test batching is an effective alternative, but overlooked technique. This study evaluates parallelization's effect by adjusting…
Shunmukha Sagar Puppala
Hybrid and multi cloud adoption has made enterprise integration a strategic architecture problem rather than a narrow middleware concern. Large organizations frequently operate SAP S4HANA, SAP ECC, SaaS business applications, partner portals, data lakes, and hyper scaler services across heterogeneous environments.…
Elfried Salanon, Blandine Comte, Delphine Centeno, Stéphanie Durand + 2 more
Introduction Assessing batch correction methods remains a major challenge in metabolomics, as no consensus currently exists for a generic and reliable evaluation strategy. Given the strong influence of batch effects on downstream statistical analyses, establishing a robust framework for their assessment is crucial to…
Matteo Turilli, Mihael Hategan, М. И. Титов, Ketan Maheshwari + 12 more
Interoperable Workflow Technologies Authors: ['Matteo Turilli' 'Mihael Hategan' 'М. И. Титов' 'Ketan Maheshwari' 'Aymen Al-Saadi' 'Andre Merzky' 'Ramon Arambula' 'Mikhail Zakharchanka' 'Matt Cowan' 'Justin M. Wozniak' 'Andreas Wilke' 'Ozgur O. Kilic' 'Kyle Chard' 'Rafael Ferreira da Silva' 'Shantenu Jha' 'Daniel…
Tibor Horak, Peter Strelec, Michal Kebisek, Pavol Tanuska + 5 more
'Andrea Vaclavova' 'Arslan Musaddiq' 'Fredrik Ahlgren' 'Neda Maleki' 'Jorge L. Zapico'] Small- and medium-sized manufacturing companies must adapt their production processes more quickly. The speed with which enterprises can apply a change in the context of data integration and historicization affects their business.…
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The pressure-swing distillation process with high-pressurized batch columns (HHP), with and without a recycling stream, in double stripper configuration for separating ethylacetate-ethanol is under investigation. With the aim of productivity maximization, the optimal control patterns are found for both ethanol and…
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This comprehensive review examines the evolution of autonomous materials synthesis laboratories that integrate artificial intelligence with advanced robotics to accelerate discovery. Traditional materials development pipelines typically require 10-20 years, but self-driving laboratories (SDLs) and Materials…