Akshay S. Chaudhari

Bio: Akshay S. Chaudhari is an academic researcher from Stanford University. The author has contributed to research in topics: Medicine & Computer science. The author has an hindex of 14, co-authored 54 publications receiving 604 citations. Previous affiliations of Akshay S. Chaudhari include University of California, San Diego.

TorchXRayVision: A library of chest X-ray datasets and models.

Abstract: TorchXRayVision is an open source software library for working with chest X-ray datasets and deep learning models. It provides a common interface and common pre-processing chain for a wide set of publicly available chest X-ray datasets. In addition, a number of classification and representation learning models with different architectures, trained on different data combinations, are available through the library to serve as baselines or feature extractors.

A Deep Learning Automated Segmentation Algorithm Accurately Detects Differences in Longitudinal Cartilage Thickness Loss – Data from the FNIH Biomarkers Study of the Osteoarthritis Initiative

Abstract: OBJECTIVE To study the longitudinal performance of fully automated cartilage segmentation in knees with radiographic osteoarthritis (ROA). We evaluate the sensitivity to change in progressor knees from the Foundation National Institutes of Health OA Biomarkers Consortium between the automated and previously reported manual expert segmentation, and whether differences in progression rates between predefined cohorts can be detected by the fully automated approach. METHODS The Osteoarthritis Initiative Biomarker Consortium was a nested case-control study. Progressor knees had both medial tibiofemoral radiographic joint space width loss (≥0.7 mm) and a persistent increase in WOMAC pain (≥9 on a 0-100 scale) after two years from baseline (n=194), whereas non-progressor knees did not have either of both (n=200). Deep learning automated algorithms trained on ROA or healthy reference (HRC) knees were used to automatically segment medial (MFTC) and lateral femorotibial cartilage on baseline and two-year follow-up MRIs. Findings were compared with previously published manual expert segmentation. RESULTS The MFTC cartilage loss in the progressor cohort was -181±245µm by manual (SRM=-0.74), -144±200µm by ROA-based model (SRM=-0.72), and -69±231µm by HRC-based model segmentation (SRM=-0.30). The Cohen's D for rates of progression between progressor vs. non-progressor cohort was -0.84 (p<0.001) for manual, -0.68 (p<0.001) for automated ROA-model, and -0.14 (p=0.18) for automated HRC-model segmentation. CONCLUSIONS A fully automated deep learning segmentation approach not only displayed similar sensitivity to change of longitudinal cartilage thickness loss in knee OA as manual expert segmentation, but also effectively differentiates longitudinal rates of cartilage thickness loss between cohorts with different progression profiles.

Challenges in ensuring the generalizability of image quantitation methods for MRI

Abstract: Image quantitation methods including quantitative MRI, multiparametric MRI, and radiomics offer great promise for clinical use. However, many of these methods have limited clinical adoption, in part due to issues of generalizability, that is, the ability to translate methods and models across institutions. Researchers can assess generalizability through measurement of repeatability and reproducibility, thus quantifying different aspects of measurement variance. In this article, we review the challenges to ensuring repeatability and reproducibility of image quantitation methods as well as present strategies to minimize their variance to enable wider clinical implementation. We present possible solutions for achieving clinically acceptable performance of image quantitation methods and briefly discuss the impact of minimizing variance and achieving generalizability towards clinical implementation and adoption.

Self-supervised learning for medical image classification: a systematic review and implementation guidelines

Abstract: Abstract Advancements in deep learning and computer vision provide promising solutions for medical image analysis, potentially improving healthcare and patient outcomes. However, the prevailing paradigm of training deep learning models requires large quantities of labeled training data, which is both time-consuming and cost-prohibitive to curate for medical images. Self-supervised learning has the potential to make significant contributions to the development of robust medical imaging models through its ability to learn useful insights from copious medical datasets without labels. In this review, we provide consistent descriptions of different self-supervised learning strategies and compose a systematic review of papers published between 2012 and 2022 on PubMed, Scopus, and ArXiv that applied self-supervised learning to medical imaging classification. We screened a total of 412 relevant studies and included 79 papers for data extraction and analysis. With this comprehensive effort, we synthesize the collective knowledge of prior work and provide implementation guidelines for future researchers interested in applying self-supervised learning to their development of medical imaging classification models.

Improved Parameters for the Martini Coarse-Grained Protein Force Field

Abstract: The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too hydrophobic, and dimers formed by polar residues in apolar solvents did not bind strongly enough. Here, we reparametrize these residues either through reassignment of particle types or by introducing embedded charges. The new parameters are tested with respect to partitioning across a lipid bilayer, membrane binding of Wimley–White peptides, and dimerization free energy in solvents of different polarity. In addition, we improve some of the bonded terms in the Martini protein force field that lead to a more realistic length of α-helices and to improved numerical stability for polyalanine and glycine repeats. The new parameter set is denoted Martini version 2.2.

Perspective on the Martini model.

Abstract: The Martini model, a coarse-grained force field for biomolecular simulations, has found a broad range of applications since its release a decade ago. Based on a building block principle, the model combines speed and versatility while maintaining chemical specificity. Here we review the current state of the model. We describe recent highlights as well as shortcomings, and our ideas on the further development of the model.