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General General

Activity Recognition From Newborn Resuscitation Videos

IEEE Journal of Biomedical and Health Informatics, vol. 24, no. 11, pp. 3258-3267, Nov. 2020

Objective: Birth asphyxia is one of the leading causes of neonatal deaths. A key for survival is performing immediate and continuous quality newborn resuscitation. A dataset of recorded signals during newborn resuscitation, including videos, has been collected in Haydom, Tanzania, and the aim is to analyze the treatment and its effect on the newborn outcome. An important step is to generate timelines of relevant resuscitation activities, including ventilation, stimulation, suction, etc., during the resuscitation episodes. Methods: We propose a two-step deep neural network system, ORAA-net, utilizing low-quality video recordings of resuscitation episodes to do activity recognition during newborn resuscitation. The first step is to detect and track relevant objects using Convolutional Neural Networks (CNN) and post-processing, and the second step is to analyze the proposed activity regions from step 1 to do activity recognition using 3D CNNs. Results: The system recognized the activities newborn uncovered, stimulation, ventilation and suction with a mean precision of 77.67 %, a mean recall of 77,64 %, and a mean accuracy of 92.40 %. Moreover, the accuracy of the estimated number of Health Care Providers (HCPs) present during the resuscitation episodes was 68.32 %. Conclusion: The results indicate that the proposed CNN-based two-step ORAAnet could be used for object detection and activity recognition in noisy low-quality newborn resuscitation videos. Significance: A thorough analysis of the effect the different resuscitation activities have on the newborn outcome could potentially allow us to optimize treatment guidelines, training, debriefing, and local quality improvement in newborn resuscitation.

Øyvind Meinich-Bache, Simon Lennart Austnes, Kjersti Engan, Ivar Austvoll, Trygve Eftestøl, Helge Myklebust, Simeon Kusulla, Hussein Kidanto, Hege Ersdal

2023-03-14

General General

Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data.

In bioRxiv : the preprint server for biology

Investigators have recently introduced powerful methods for population genetic inference that rely on supervised machine learning from simulated data. Despite their performance advantages, these methods can fail when the simulated training data does not adequately resemble data from the real world. Here, we show that this "simulation mis-specification" problem can be framed as a "domain adaptation" problem, where a model learned from one data distribution is applied to a dataset drawn from a different distribution. By applying an established domain-adaptation technique based on a gradient reversal layer (GRL), originally introduced for image classification, we show that the effects of simulation mis-specification can be substantially mitigated. We focus our analysis on two state-of-the-art deep-learning population genetic methods-SIA, which infers positive selection from features of the ancestral recombination graph (ARG), and ReLERNN, which infers recombination rates from genotype matrices. In the case of SIA, the domain adaptive framework also compensates for ARG inference error. Using the d omain- ada ptive SIA (dadaSIA) model, we estimate improved selection coefficients at selected loci in the 1000 Genomes CEU population. We anticipate that domain adaptation will prove to be widely applicable in the growing use of supervised machine learning in population genetics.

Mo Ziyi, Siepel Adam

2023-Mar-01

General General

Stabl: sparse and reliable biomarker discovery in predictive modeling of high-dimensional omic data.

In Research square

High-content omic technologies coupled with sparsity-promoting regularization methods (SRM) have transformed the biomarker discovery process. However, the translation of computational results into a clinical use-case scenario remains challenging. A rate-limiting step is the rigorous selection of reliable biomarker candidates among a host of biological features included in multivariate models. We propose Stabl, a machine learning framework that unifies the biomarker discovery process with multivariate predictive modeling of clinical outcomes by selecting a sparse and reliable set of biomarkers. Evaluation of Stabl on synthetic datasets and four independent clinical studies demonstrates improved biomarker sparsity and reliability compared to commonly used SRMs at similar predictive performance. Stabl readily extends to double- and triple-omics integration tasks and identifies a sparser and more reliable set of biomarkers than those selected by state-of-the-art early- and late-fusion SRMs, thereby facilitating the biological interpretation and clinical translation of complex multi-omic predictive models. The complete package for Stabl is available online at https://github.com/gregbellan/Stabl.

Hedou Julien, Maric Ivana, Bellan Grégoire, Einhaus Jakob, Gaudilliere Dyani, Ladant Francois-Xavier, Verdonk Franck, Stelzer Ina, Feyaerts Dorien, Tsai Amy, Ganio Edward, Sabayev Maximilian, Gillard Joshua, Bonham Adam, Sato Masaki, Diop Maïgane, Angst Martin, Stevenson David, Aghaeepour Nima, Montanari Andrea, Gaudilliere Brice

2023-Feb-28

General General

Convolutional-recurrent neural networks approximate diffusion tractography from T1-weighted MRI and associated anatomical context.

In bioRxiv : the preprint server for biology

Diffusion MRI (dMRI) streamline tractography is the gold-standard for in vivo estimation of white matter (WM) pathways in the brain. However, the high angular resolution dMRI acquisitions capable of fitting the microstructural models needed for tractography are often time-consuming and not routinely collected clinically, restricting the scope of tractography analyses. To address this limitation, we build on recent advances in deep learning which have demonstrated that streamline propagation can be learned from dMRI directly without traditional model fitting. Specifically, we propose learning the streamline propagator from T1w MRI to facilitate arbitrary tractography analyses when dMRI is unavailable. To do so, we present a novel convolutional-recurrent neural network (CoRNN) trained in a teacher-student framework that leverages T1w MRI, associated anatomical context, and streamline memory from data acquired for the Human Connectome Project. We characterize our approach under two common tractography paradigms, WM bundle analysis and structural connectomics, and find approximately a 5-15% difference between measures computed from streamlines generated with our approach and those generated using traditional dMRI tractography. When placed in the literature, these results suggest that the accuracy of WM measures computed from T1w MRI with our method is on the level of scan-rescan dMRI variability and raise an important question: is tractography truly a microstructural phenomenon, or has dMRI merely facilitated its discovery and implementation?

Cai Leon Y, Lee Ho Hin, Newlin Nancy R, Kerley Cailey I, Kanakaraj Praitayini, Yang Qi, Johnson Graham W, Moyer Daniel, Schilling Kurt G, Rheault Francois, Landman Bennett A

2023-Mar-08

General General

Reproducible and Clinically Translatable Deep Neural Networks for Cancer Screening.

In Research square

Cervical cancer is a leading cause of cancer mortality, with approximately 90% of the 250,000 deaths per year occurring in low- and middle-income countries (LMIC). Secondary prevention with cervical screening involves detecting and treating precursor lesions; however, scaling screening efforts in LMIC has been hampered by infrastructure and cost constraints. Recent work has supported the development of an artificial intelligence (AI) pipeline on digital images of the cervix to achieve an accurate and reliable diagnosis of treatable precancerous lesions. In particular, WHO guidelines emphasize visual triage of women testing positive for human papillomavirus (HPV) as the primary screen, and AI could assist in this triage task. Published AI reports have exhibited overfitting, lack of portability, and unrealistic, near-perfect performance estimates. To surmount recognized issues, we implemented a comprehensive deep-learning model selection and optimization study on a large, collated, multi-institutional dataset of 9,462 women (17,013 images). We evaluated relative portability, repeatability, and classification performance. The top performing model, when combined with HPV type, achieved an area under the Receiver Operating Characteristics (ROC) curve (AUC) of 0.89 within our study population of interest, and a limited total extreme misclassification rate of 3.4%, on held-aside test sets. Our work is among the first efforts at designing a robust, repeatable, accurate and clinically translatable deep-learning model for cervical screening.

Ahmed Syed Rakin, Befano Brian, Lemay Andreanne, Egemen Didem, Rodriguez Ana Cecilia, Angara Sandeep, Desai Kanan, Jeronimo Jose, Antani Sameer, Campos Nicole, Inturrisi Federica, Perkins Rebecca, Kreimer Aimee, Wentzensen Nicolas, Herrero Rolando, Del Pino Marta, Quint Wim, de Sanjose Silvia, Schiffman Mark, Kalpathy-Cramer Jayashree

2023-Mar-03

General General

EADD-YOLO: An efficient and accurate disease detector for apple leaf using improved lightweight YOLOv5.

In Frontiers in plant science

INTRODUCTION : Current detection methods for apple leaf diseases still suffer some challenges, such as the high number of parameters, low detection speed and poor detection performance for small dense spots, which limit the practical applications in agriculture. Therefore, an efficient and accurate model for apple leaf disease detection based on YOLOv5 is proposed and named EADD-YOLO.

METHODS : In the EADD-YOLO, the lightweight shufflenet inverted residual module is utilized to reconstruct the backbone network, and an efficient feature learning module designed through depthwise convolution is proposed and introduced to the neck network. The aim is to reduce the number of parameters and floating point of operations (FLOPs) during feature extraction and feature fusion, thus increasing the operational efficiency of the network with less impact on detection performance. In addition, the coordinate attention module is embedded into the critical locations of the network to select the critical spot information and suppress useless information, which is to enhance the detection accuracy of diseases with various sizes from different scenes. Furthermore, the SIoU loss replaces CIoU loss as the bounding box regression loss function to improve the accuracy of prediction box localization.

RESULTS : The experimental results indicate that the proposed method can achieve the detection performance of 95.5% on the mean average precision and a speed of 625 frames per second (FPS) on the apple leaf disease dataset (ALDD). Compared to the latest research method on the ALDD, the detection accuracy and speed of the proposed method were improved by 12.3% and 596 FPS, respectively. In addition, the parameter quantity and FLOPs of the proposed method were much less than other relevant popular algorithms.

DISCUSSION : In summary, the proposed method not only has a satisfactory detection effect, but also has fewer parameters and high calculation efficiency compared with the existing approaches. Therefore, the proposed method provides a high-performance solution for the early diagnosis of apple leaf disease and can be applied in agricultural robots. The code repository is open-sourced at https://github.com/AWANWY/EADD-YOLO.

Zhu Shisong, Ma Wanli, Wang Jianlong, Yang Meijuan, Wang Yongmao, Wang Chunyang

2023

SIoU loss, apple leaf, coordinate attention, depthwise convolution, disease detection