BACKGROUND: Single-cell chromatin accessibility assays, such as scATAC-seq, are increasingly employed in individual and joint multi-omic profiling of single cells. As the accumulation of scATAC-seq and multi-omics datasets continue, challenges in analyzing such sparse, noisy, and high-dimensional data become pressing. Specifically, one challenge relates to optimizing the processing of chromatin-level measurements and efficiently extracting information to discern cellular heterogeneity. This is of critical importance, since the identification of cell types is a fundamental step in current single-cell data analysis practices.
RESULTS: We benchmark 8 feature engineering pipelines derived from 5 recent methods to assess their ability to discover and discriminate cell types. By using 10 metrics calculated at the cell embedding, shared nearest neighbor graph, or partition levels, we evaluate the performance of each method at different data processing stages. This comprehensive approach allows us to thoroughly understand the strengths and weaknesses of each method and the influence of parameter selection.
CONCLUSIONS: Our analysis provides guidelines for choosing analysis methods for different datasets. Overall, feature aggregation, SnapATAC, and SnapATAC2 outperform latent semantic indexing-based methods. For datasets with complex cell-type structures, SnapATAC and SnapATAC2 are preferred. With large datasets, SnapATAC2 and ArchR are most scalable.

This cross-sectional study assesses the associations between patient and clinical factors and variations in time emergency department physicians spend using electronic health record (EHR) systems.

Molecular Property Prediction (MPP) is vital for drug discovery, crop protection, and environmental science. Over the last decades, diverse computational techniques have been developed, from using simple physical and chemical properties and molecular fingerprints in statistical models and classical machine learning to advanced deep learning approaches. In this review, we aim to distill insights from current research on employing transformer models for MPP. We analyze the currently available models and explore key questions that arise when training and fine-tuning a transformer model for MPP. These questions encompass the choice and scale of the pretraining data, optimal architecture selections, and promising pretraining objectives. Our analysis highlights areas not yet covered in current research, inviting further exploration to enhance the field\'s understanding. Additionally, we address the challenges in comparing different models, emphasizing the need for standardized data splitting and robust statistical analysis.

Background Prostate MRI for the detection of clinically significant prostate cancer (csPCa) is standardized by the Prostate Imaging Reporting and Data System (PI-RADS), currently in version 2.1. A systematic review and meta-analysis infrastructure with a 12-month update cycle was established to evaluate the diagnostic performance of PI-RADS over time. Purpose To provide estimates of diagnostic accuracy and cancer detection rates (CDRs) of PI-RADS version 2.1 categories for prostate MRI, which is required for further evidence-based patient management. Materials and Methods A systematic search of PubMed, Embase, Cochrane Library, and multiple trial registers (English-language studies published from March 1, 2019, to August 30, 2022) was performed. Studies that reported data on diagnostic accuracy or CDRs of PI-RADS version 2.1 with csPCa as the primary outcome were included. For the meta-analysis, pooled estimates for sensitivity, specificity, and CDRs were derived from extracted data at the lesion level and patient level. Sensitivity and specificity for PI-RADS greater than or equal to 3 and PI-RADS greater than or equal to 4 considered as test positive were investigated. In addition to individual PI-RADS categories 1-5, subgroup analyses of subcategories (ie, 2+1, 3+0) were performed. Results A total of 70 studies (11 686 lesions, 13 330 patients) were included. At the patient level, with PI-RADS greater than or equal to 3 considered positive, meta-analysis found a 96% summary sensitivity (95% CI: 95, 98) and 43% specificity (95% CI: 33, 54), with an area under the summary receiver operating characteristic (SROC) curve of 0.86 (95% CI: 0.75, 0.93). For PI-RADS greater than or equal to 4, meta-analysis found an 89% sensitivity (95% CI: 85, 92) and 66% specificity (95% CI: 58, 74), with an area under the SROC curve of 0.89 (95% CI: 0.85, 0.92). CDRs were as follows: PI-RADS 1, 6%; PI-RADS 2, 5%; PI-RADS 3, 19%; PI-RADS 4, 54%; and PI-RADS 5, 84%. The CDR was 12% (95% CI: 7, 19) for transition zone 2+1 lesions and 19% (95% CI: 12, 29) for 3+0 lesions (P = .12). Conclusion Estimates of diagnostic accuracy and CDRs for PI-RADS version 2.1 categories are provided for quality benchmarking and to guide further evidence-based patient management. © RSNA, 2024 Supplemental material is available for this article. See also the editorial by Tammisetti and Jacobs in this issue.

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Microsatellite instability (MSI) is a phenomenon seen in several cancer types, which can be used as a biomarker to help guide immune checkpoint inhibitor treatment. To facilitate this, researchers have developed computational tools to categorize samples as having high microsatellite instability, or as being microsatellite stable using next-generation sequencing data. Most of these tools were published with unclear scope and usage, and they have yet to be independently benchmarked. To address these issues, we assessed the performance of eight leading MSI tools across several unique datasets that encompass a wide variety of sequencing methods. While we were able to replicate the original findings of each tool on whole exome sequencing data, most tools had worse receiver operating characteristic and precision-recall area under the curve values on whole genome sequencing data. We also found that they lacked agreement with one another and with commercial MSI software on gene panel data, and that optimal threshold cut-offs vary by sequencing type. Lastly, we tested tools made specifically for RNA sequencing data and found they were outperformed by tools designed for use with DNA sequencing data. Out of all, two tools (MSIsensor2, MANTIS) performed well across nearly all datasets, but when all datasets were combined, their precision decreased. Our results caution that MSI tools can have much lower performance on datasets other than those on which they were originally evaluated, and in the case of RNA sequencing tools, can even perform poorly on the type of data for which they were created.

Taxonomic classification is crucial in identifying organisms within diverse microbial communities when using metagenomics shotgun sequencing. While second-generation Illumina sequencing still dominates, third-generation nanopore sequencing promises improved classification through longer reads. However, extensive benchmarking studies on nanopore data are lacking. We systematically evaluated performance of bacterial taxonomic classification for metagenomics nanopore sequencing data for several commonly used classifiers, using standardized reference sequence databases, on the largest collection of publicly available data for defined mock communities thus far (nine samples), representing different research domains and application scopes. Our results categorize classifiers into three categories: low precision/high recall; medium precision/medium recall, and high precision/medium recall. Most fall into the first group, although precision can be improved without excessively penalizing recall with suitable abundance filtering. No definitive \'best\' classifier emerges, and classifier selection depends on application scope and practical requirements. Although few classifiers designed for long reads exist, they generally exhibit better performance. Our comprehensive benchmarking provides concrete recommendations, supported by publicly available code for reassessment and fine-tuning by other scientists.

Pharmacogenomics (PGx) investigates the influence of genetics on drug responses, enabling tailored treatments for personalized healthcare. This study assessed the accuracy of genotyping six genes using whole genome sequencing with four different computational tools and various sequencing depths. The effects of using different reference genomes (GRCh38 and GRCh37) and sequence aligners (BWA-MEM and Bowtie2) were also explored. The results showed generally minor variations in tool performance across most genes; however, more notable discrepancies were observed in the analysis of the complex CYP2D6 gene. Cyrius, a CYP2D6-specific tool, demonstrated the most robust performance, achieving the highest concordance rates for CYP2D6 in all instances, comparable to the consensus approach in most cases. There were rather small differences between the samples with 20× coverage depth and those with higher depth, but the decreased performance was more evident at lower depths, particularly at 5×. Additionally, variations in CYP2D6 results were observed when samples were aligned to different reference genomes using the same method, or to the same genome using different aligners, which led to reporting incorrect rare star alleles in several cases. These findings inform the selection of optimal PGx tools and methodologies as well as suggest that employing a consensus approach with two or more tools might be preferable for certain genes and tool combinations, especially at lower sequencing depths, to ensure accurate results. Additionally, we show how the upstream alignment can affect the performance of tools, an important factor to take into account.

BACKGROUND: Spatial transcriptomics (ST) is advancing our understanding of complex tissues and organisms. However, building a robust clustering algorithm to define spatially coherent regions in a single tissue slice and aligning or integrating multiple tissue slices originating from diverse sources for essential downstream analyses remains challenging. Numerous clustering, alignment, and integration methods have been specifically designed for ST data by leveraging its spatial information. The absence of comprehensive benchmark studies complicates the selection of methods and future method development.
RESULTS: In this study, we systematically benchmark a variety of state-of-the-art algorithms with a wide range of real and simulated datasets of varying sizes, technologies, species, and complexity. We analyze the strengths and weaknesses of each method using diverse quantitative and qualitative metrics and analyses, including eight metrics for spatial clustering accuracy and contiguity, uniform manifold approximation and projection visualization, layer-wise and spot-to-spot alignment accuracy, and 3D reconstruction, which are designed to assess method performance as well as data quality. The code used for evaluation is available on our GitHub. Additionally, we provide online notebook tutorials and documentation to facilitate the reproduction of all benchmarking results and to support the study of new methods and new datasets.
CONCLUSIONS: Our analyses lead to comprehensive recommendations that cover multiple aspects, helping users to select optimal tools for their specific needs and guide future method development.

The performance of molecular docking can be improved by comparing the shape similarity of the flexibly sampled poses against the target proteins\' inverted binding cavities. The effectiveness of these pseudo-ligands or negative image-based models in docking rescoring is boosted further by performing enrichment-driven optimization. Here, we introduce a novel shape-focused pharmacophore modeling algorithm O-LAP that generates a new class of cavity-filling models by clumping together overlapping atomic content via pairwise distance graph clustering. Top-ranked poses of flexibly docked active ligands were used as the modeling input and multiple alternative clustering settings were benchmark-tested thoroughly with five demanding drug targets using random training/test divisions. In docking rescoring, the O-LAP modeling typically improved massively on the default docking enrichment; furthermore, the results indicate that the clustered models work well in rigid docking. The C+ +/Qt5-based algorithm O-LAP is released under the GNU General Public License v3.0 via GitHub ( https://github.com/jvlehtonen/overlap-toolkit ). SCIENTIFIC CONTRIBUTION: This study introduces O-LAP, a C++/Qt5-based graph clustering software for generating new type of shape-focused pharmacophore models. In the O-LAP modeling, the target protein cavity is filled with flexibly docked active ligands, the overlapping ligand atoms are clustered, and the shape/electrostatic potential of the resulting model is compared against the flexibly sampled molecular docking poses. The O-LAP modeling is shown to ensure high enrichment in both docking rescoring and rigid docking based on comprehensive benchmark-testing.