ArXiv最新文献

{"title":"Impact of Stain Variation and Color Normalization for Prognostic Predictions in Pathology.","authors":"Siyu Steven Lin, Haowen Zhou, Richard J Cote, Mark Watson, Ramaswamy Govindan, Changhuei Yang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>In recent years, deep neural networks (DNNs) have demonstrated remarkable performance in pathology applications, potentially even outperforming expert pathologists due to their ability to learn subtle features from large datasets. One complication in preparing digital pathology datasets for DNN tasks is variation in tinctorial qualities. A common way to address this is to perform stain normalization on the images. In this study, we show that a well-trained DNN model trained on one batch of histological slides failed to generalize to another batch prepared at a different time from the same tissue blocks, even when stain normalization methods were applied. This study used sample data from a previously reported DNN that was able to identify patients with early stage non-small cell lung cancer (NSCLC) whose tumors did and did not metastasize, with high accuracy, based on training and then testing of digital images from H&E stained primary tumor tissue sections processed at the same time. In this study we obtained a new series of histologic slides from the adjacent recuts of same tissue blocks processed in the same lab but at a different time. We found that the DNN trained on the either batch of slides/images was unable to generalize and failed to predict progression in the other batch of slides/images (AUC_cross-batch = 0.52 - 0.53 compared to AUC_same-batch = 0.74 - 0.81). The failure to generalize did not improve even when the tinctorial difference correction were made through either traditional color-tuning or stain normalization with the help of a Cycle Generative Adversarial Network (CycleGAN) process. This highlights the need to develop an entirely new way to process and collect consistent microscopy images from histologic slides that can be used to both train and allow for the general application of predictive DNN algorithms.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419173/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Digital Volumetric Biopsy Cores Improve Gleason Grading of Prostate Cancer Using Deep Learning.","authors":"Ekaterina Redekop, Mara Pleasure, Zichen Wang, Anthony Sisk, Yang Zong, Kimberly Flores, William Speier, Corey W Arnold","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Prostate cancer (PCa) was the most frequently diagnosed cancer among American men in 2023 [1]. The histological grading of biopsies is essential for diagnosis, and various deep learning-based solutions have been developed to assist with this task. Existing deep learning frameworks are typically applied to individual 2D cross-sections sliced from 3D biopsy tissue specimens. This process impedes the analysis of complex tissue structures such as glands, which can vary depending on the tissue slice examined. We propose a novel digital pathology data source called a \"volumetric core,\" obtained via the extraction and co-alignment of serially sectioned tissue sections using a novel morphology-preserving alignment framework. We trained an attention-based multiple-instance learning (ABMIL) framework on deep features extracted from volumetric patches to automatically classify the Gleason Grade Group (GGG). To handle volumetric patches, we used a modified video transformer with a deep feature extractor pretrained using self-supervised learning. We ran our morphology preserving alignment framework to construct 10,210 volumetric cores, leaving out 30% for pretraining. The rest of the dataset was used to train ABMIL, which resulted in a 0.958 macro-average AUC, 0.671 F1 score, 0.661 precision, and 0.695 recall averaged across all five GGG significantly outperforming the 2D baselines.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detailed delineation of the fetal brain in diffusion MRI via multi-task learning.","authors":"Davood Karimi, Camilo Calixto, Haykel Snoussi, Maria Camila Cortes-Albornoz, Clemente Velasco-Annis, Caitlin Rollins, Camilo Jaimes, Ali Gholipour, Simon K Warfield","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Diffusion-weighted MRI is increasingly used to study the normal and abnormal development of fetal brain inutero. Recent studies have shown that dMRI can offer invaluable insights into the neurodevelopmental processes in the fetal stage. However, because of the low data quality and rapid brain development, reliable analysis of fetal dMRI data requires dedicated computational methods that are currently unavailable. The lack of automated methods for fast, accurate, and reproducible data analysis has seriously limited our ability to tap the potential of fetal brain dMRI for medical and scientific applications. In this work, we developed and validated a unified computational framework to (1) segment the brain tissue into white matter, cortical/subcortical gray matter, and cerebrospinal fluid, (2) segment 31 distinct white matter tracts, and (3) parcellate the brain's cortex and delineate the deep gray nuclei and white matter structures into 96 anatomically meaningful regions. We utilized a set of manual, semi-automatic, and automatic approaches to annotate 97 fetal brains. Using these labels, we developed and validated a multi-task deep learning method to perform the three computations. Our evaluations show that the new method can accurately carry out all three tasks, achieving a mean Dice similarity coefficient of 0.865 on tissue segmentation, 0.825 on white matter tract segmentation, and 0.819 on parcellation. The proposed method can greatly advance the field of fetal neuroimaging as it can lead to substantial improvements in fetal brain tractography, tract-specific analysis, and structural connectivity assessment.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419175/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PRIME: Phase Reversed Interleaved Multi-Echo acquisition enables highly accelerated distortion-free diffusion MRI.","authors":"Yohan Jun, Qiang Liu, Ting Gong, Jaejin Cho, Shohei Fujita, Xingwang Yong, Susie Y Huang, Lipeng Ning, Anastasia Yendiki, Yogesh Rathi, Berkin Bilgic","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Purpose: </strong>To develop and evaluate a new pulse sequence for highly accelerated distortion-free diffusion MRI (dMRI) by inserting an additional echo without prolonging TR, when generalized slice dithered enhanced resolution (gSlider) radiofrequency encoding is used for volumetric acquisition.</p><p><strong>Methods: </strong>A phase-reversed interleaved multi-echo acquisition (PRIME) was developed for rapid, high-resolution, and distortion-free dMRI, which includes two echoes where the first echo is for target diffusion-weighted imaging (DWI) acquisition with high-resolution and the second echo is acquired with either 1) lower-resolution for high-fidelity field map estimation, or 2) matching resolution to enable efficient diffusion relaxometry acquisitions. The sequence was evaluated on in vivo data acquired from healthy volunteers on clinical and Connectome 2.0 scanners.</p><p><strong>Results: </strong>In vivo experiments demonstrated that 1) high in-plane acceleration (Rin-plane of 5-fold with 2D partial Fourier) was achieved using the high-fidelity field maps estimated from the second echo, which was made at a lower resolution/acceleration to increase its SNR while matching the effective echo spacing of the first readout, 2) high-resolution diffusion relaxometry parameters were estimated from dual-echo PRIME data using a white matter model of multi-TE spherical mean technique (MTE-SMT), and 3) high-fidelity mesoscale DWI at 550 um isotropic resolution could be obtained in vivo by capitalizing on the high-performance gradients of the Connectome 2.0 scanner.</p><p><strong>Conclusion: </strong>The proposed PRIME sequence enabled highly accelerated, high-resolution, and distortion-free dMRI using an additional echo without prolonging scan time when gSlider encoding is utilized.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419176/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimizing Sample Size for Supervised Machine Learning with Bulk Transcriptomic Sequencing: A Learning Curve Approach.","authors":"Yunhui Qi, Xinyi Wang, Li-Xuan Qin","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Accurate sample classification using transcriptomics data is crucial for advancing personalized medicine. Achieving this goal necessitates determining a suitable sample size that ensures adequate statistical power without undue resource allocation. Current sample size calculation methods rely on assumptions and algorithms that may not align with supervised machine learning techniques for sample classification. Addressing this critical methodological gap, we present a novel computational approach that establishes the power-versus-sample-size relationship by employing a data augmentation strategy followed by fitting a learning curve. We comprehensively evaluated its performance for microRNA and RNA sequencing data, considering diverse data characteristics and algorithm configurations, based on a spectrum of evaluation metrics. To foster accessibility and reproducibility, the Python and R code for implementing our approach is available on GitHub. Its deployment will significantly facilitate the adoption of machine learning in transcriptomics studies and accelerate their translation into clinically useful classifiers for personalized treatment.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Initial Experience of Metabolic Imaging with Hyperpolarized [1-¹³C]pyruvate MRI in Kidney Transplant Patients.","authors":"Xiaoxi Liu, Ying-Chieh Lai, Di Cui, Shiang-Cheng Kung, Meyeon Park, Laszik Zoltan, Peder E Z Larson, Zhen J Wang","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Background: </strong>Kidney transplant is the treatment of choice for patients with end-stage renal disease. Early detection of allograft injury is important to delay or prevent irreversible damage.</p><p><strong>Purpose: </strong>To investigate the feasibility of hyperpolarized (HP) [1-¹³C]pyruvate MRI for assessing kidney allograft metabolism.</p><p><strong>Study type: </strong>Prospective.</p><p><strong>Subjects: </strong>6 participants (mean age, 45.2 ± 12.4 years, 2 females) scheduled for kidney allograft biopsy and 5 patients (mean age, 59.6 ± 10.4 years, 2 females) with renal cell carcinoma (RCC).</p><p><strong>Field strength/sequence: </strong>3 Tesla, T2-weighted fast spin echo, multi-echo gradient echo, single shot diffusion-weighted echo-planar imaging, and time-resolved HP ¹³C metabolite-selective imaging.</p><p><strong>Assessment: </strong>Five of the six kidney allograft participants underwent biopsy after MRI. Estimated glomerular filtration rate (eGFR) and urine protein-to-creatine ratio (uPCR) were collected within 4 weeks of MRI. Kidney metabolism was quantified from HP [1-¹³C]pyruvate MRI using the lactate-to-pyruvate ratio in allograft kidneys and non-tumor bearing kidneys from RCC patients.</p><p><strong>Statistical tests: </strong>Descriptive statistics (mean ± standard deviation).</p><p><strong>Results: </strong>Biopsy was performed a mean of 9 days (range 5-19 days) after HP [1-¹³C]pyruvate MRI. Three biopsies were normal, one showed low-grade fibrosis and one showed moderate microvascular inflammation. All had stable functioning allografts with eGFR > 60 mL/min/1.73 m² and normal uPCR. One participant who did not undergo biopsy had reduced eGFR of 49 mL/min/1.73 m² and elevated uPCR. The mean lactate-to-pyruvate ratio was 0.373 in participants with normal findings (n = 3) and 0.552 in participants with abnormal findings (n = 2). The lactate-to-pyruvate ratio was highest (0.847) in the participant with reduced eGFR and elevated uPRC. Native non-tumor bearing kidneys had a mean lactate-to-pyruvate ratio of 0.309.</p><p><strong>Data conclusion: </strong>Stable allografts with normal findings at biopsy showed lactate-to-pyruvate ratios similar to native non-tumor bearing kidneys, whereas allografts with abnormal findings showed higher lactate-to-pyruvate ratios.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419194/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"1D Thermoembolization Model Using CT Imaging Data for Porcine Liver.","authors":"Rohan Amare, Danielle Stolley, Steve Parrish, Megan Jacobsen, Rick Layman, Chimamanda Santos, Beatrice Riviere, Natalie Fowlkes, David Fuentes, Erik Cressman","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Objective: </strong>Innovative therapies such as thermoembolization are expected to play an important role in improving care for patients with diseases such as hepatocellular carcinoma. Thermoembolization is a minimally invasive strategy that combines thermal ablation and embolization in a single procedure. This approach exploits an exothermic chemical reaction that occurs when an acid chloride is delivered via an endovascular route. However, comprehension of the complexities of the biophysics of thermoembolization is challenging. Mathematical models can aid in understanding such complex processes and assisting clinicians in making informed decisions. In this study, we used a Hagen-Poiseuille 1D blood flow model to predict the mass transport and possible embolization locations in a porcine hepatic artery.</p><p><strong>Method: </strong>The 1D flow model was used on imaging data of <i>in-vivo</i> embolization imaging data of three pigs. The hydrolysis time constant of acid chloride chemical reaction was optimized for each pig, and LOOCV method was used to test the model's predictive ability.</p><p><strong>Conclusion: </strong>This basic model provided a balanced accuracy rate of 66.8% for identifying the possible locations of damage in the hepatic artery. Use of the model provides an initial understanding of the vascular transport phenomena that are predicted to occur as a result of thermoembolization.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419193/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Limits on the computational expressivity of non-equilibrium biophysical processes.","authors":"Carlos Floyd, Aaron R Dinner, Arvind Murugan, Suriyanarayanan Vaikuntanathan","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Many biological decision-making processes can be viewed as performing a classification task over a set of inputs, using various chemical and physical processes as \"biological hardware.\" In this context, it is important to understand the inherent limitations on the computational expressivity of classification functions instantiated in biophysical media. Here, we model biochemical networks as Markov jump processes and train them to perform classification tasks, allowing us to investigate their computational expressivity. We reveal several unanticipated limitations on the input-output functions of these systems, which we further show can be lifted using biochemical mechanisms like promiscuous binding. We analyze the flexibility and sharpness of decision boundaries as well as the classification capacity of these networks. Additionally, we identify distinctive signatures of networks trained for classification, including the emergence of correlated subsets of spanning trees and a creased \"energy landscape\" with multiple basins. Our findings have implications for understanding and designing physical computing systems in both biological and synthetic chemical settings.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<ArticleTitle xmlns:ns0=\"http://www.w3.org/1998/Math/MathML\">Magnetization transfer explains most of the <ns0:math> <ns0:mrow><ns0:msub><ns0:mi>T</ns0:mi> <ns0:mn>1</ns0:mn></ns0:msub> </ns0:mrow> </ns0:math> variability in the MRI literature.","authors":"Jakob Assländer","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Purpose: </strong>To identify the predominant source of the <math> <mrow><msub><mi>T</mi> <mn>1</mn></msub> </mrow> </math> variability described in the literature, which ranges from 0.6-1.1s for brain white matter at 3T.</p><p><strong>Methods: </strong>25 <math> <mrow><msub><mi>T</mi> <mn>1</mn></msub> </mrow> </math> -mapping methods from the literature were simulated with a mono-exponential and magnetization-transfer (MT) models, each followed by mono-exponential fitting. A single set of model parameters was assumed for the simulation of all methods, and these parameters were estimated by fitting the simulation-based to the corresponding literature <math> <mrow><msub><mi>T</mi> <mn>1</mn></msub> </mrow> </math> values of white matter at 3T.</p><p><strong>Results: </strong>Mono-exponential simulations suggest good inter-method reproducibility and fail to explain the highly variable <math> <mrow><msub><mi>T</mi> <mn>1</mn></msub> </mrow> </math> estimates in the literature. In contrast, MT simulations suggest that a mono-exponential fit results in a variable <math> <mrow><msub><mi>T</mi> <mn>1</mn></msub> </mrow> </math> and explain up to 62% of the literature's variability.</p><p><strong>Conclusion: </strong>The results suggest that a mono-exponential model does not adequately describe longitudinal relaxation in biological tissue. Therefore, <math> <mrow><msub><mi>T</mi> <mn>1</mn></msub> </mrow> </math> in biological tissue should be considered only a <i>semi-quantitative</i> metric that is inherently contingent upon the imaging methodology; and comparisons between different <math> <mrow><msub><mi>T</mi> <mn>1</mn></msub> </mrow> </math> -mapping methods and the use of simplistic spin systems-such as doped-water phantoms-for validation should be viewed with caution.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419191/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improving Tree Probability Estimation with Stochastic Optimization and Variance Reduction.","authors":"Tianyu Xie, Musu Yuan, Minghua Deng, Cheng Zhang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Probability estimation of tree topologies is one of the fundamental tasks in phylogenetic inference. The recently proposed subsplit Bayesian networks (SBNs) provide a powerful probabilistic graphical model for tree topology probability estimation by properly leveraging the hierarchical structure of phylogenetic trees. However, the expectation maximization (EM) method currently used for learning SBN parameters does not scale up to large data sets. In this paper, we introduce several computationally efficient methods for training SBNs and show that variance reduction could be the key for better performance. Furthermore, we also introduce the variance reduction technique to improve the optimization of SBN parameters for variational Bayesian phylogenetic inference (VBPI). Extensive synthetic and real data experiments demonstrate that our methods outperform previous baseline methods on the tasks of tree topology probability estimation as well as Bayesian phylogenetic inference using SBNs.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}