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Radiology Radiology

Role of hippocampal subfields in neurodegenerative disease progression analyzed with a multi-scale attention-based network.

In NeuroImage. Clinical

BACKGROUND AND OBJECTIVE : Both Alzheimer's disease (AD) and Parkinson's disease (PD) are progressive neurodegenerative diseases. Early identification is very important for the prevention and intervention of their progress. Hippocampus plays a crucial role in cognition, in which there are correlations between atrophy of Hippocampal subfields and cognitive impairment in neurodegenerative diseases. Exploring biomarkers in the prediction of early cognitive impairment in AD and PD is significant for understanding the progress of neurodegenerative diseases.

METHODS : A multi-scale attention-based deep learning method is proposed to perform computer-aided diagnosis for neurodegenerative disease based on Hippocampal subfields. First, the two dimensional (2D) Hippocampal Mapping Image (HMI) is constructed and used as input of three branches of the following network. Second, the multi-scale module and attention module are integrated into the 2D residual network to improve the diversity of the extracted features and capture significance of various voxels for classification. Finally, the role of Hippocampal subfields in the progression of different neurodegenerative diseases is analyzed using the proposed method.

RESULTS : Classification experiments between normal control (NC), mild cognitive impairment (MCI), AD, PD with normal cognition (PD-NC) and PD with mild cognitive impairment (PD-MCI) are carried out using the proposed method. Experimental results show that subfields subiculum, presubiculum, CA1, and molecular layer are strongly correlated with cognitive impairment in AD and MCI, subfields GC-DG and fimbria are sensitive in detecting early stage of cognitive impairment in MCI, subfields CA3, CA4, GC-DG, and CA1 show significant atrophy in PD. For exploring the role of Hippocampal subfields in PD cognitive impairment, we find that left parasubiculum, left HATA and left presubiculum could be important biomarkers for predicting conversion from PD-NC to PD-MCI.

CONCLUSION : The proposed multi-scale attention-based network can effectively discover the correlation between subfields and neurodegenerative diseases. Experimental results are consistent with previous clinical studies, which will be useful for further exploring the role of Hippocampal subfields in neurodegenerative disease progression.

Xu Hongbo, Liu Yan, Wang Ling, Zeng Xiangzhu, Xu Yingying, Wang Zeng

2023-Mar-15

Alzheimer’s disease, Deep learning, Hippocampal subfields, Mild cognitive impairment, Parkinson disease

Radiology Radiology

Hyper-convolutions via implicit kernels for medical image analysis.

In Medical image analysis

The convolutional neural network (CNN) is one of the most commonly used architectures for computer vision tasks. The key building block of a CNN is the convolutional kernel that aggregates information from the pixel neighborhood and shares weights across all pixels. A standard CNN's capacity, and thus its performance, is directly related to the number of learnable kernel weights, which is determined by the number of channels and the kernel size (support). In this paper, we present the hyper-convolution, a novel building block that implicitly encodes the convolutional kernel using spatial coordinates. Unlike a regular convolutional kernel, whose weights are independently learned, hyper-convolution kernel weights are correlated through an encoder that maps spatial coordinates to their corresponding values. Hyper-convolutions decouple kernel size from the total number of learnable parameters, enabling a more flexible architecture design. We demonstrate in our experiments that replacing regular convolutions with hyper-convolutions can improve performance with less parameters, and increase robustness against noise. We provide our code here: https://github.com/tym002/Hyper-Convolution.

Ma Tianyu, Wang Alan Q, Dalca Adrian V, Sabuncu Mert R

2023-Mar-16

Convolutional Neural Networks, Deep Learning, Hyper-networks

General General

Examination of physical activity development in early childhood: protocol for a longitudinal cohort study of mother-toddler dyads.

In BMC pediatrics ; h5-index 44.0

BACKGROUND : Physical activity (PA) development in toddlers (age 1 and 2 years) is not well understood, partly because of a lack of analytic tools for accelerometer-based data processing that can accurately evaluate PA among toddlers. This has led to a knowledge gap regarding how parenting practices around PA, mothers' PA level, mothers' parenting stress, and child developmental and behavioral problems influence PA development in early childhood.

METHODS : The Child and Mother Physical Activity Study is a longitudinal study to observe PA development in toddlerhood and examine the influence of personal and parental characteristics on PA development. The study is designed to refine and validate an accelerometer-based machine learning algorithm for toddler activity recognition (Aim 1), apply the algorithm to compare the trajectories of toddler PA levels in males and females age 1-3 years (Aim 2), and explore the association between gross motor development and PA development in toddlerhood, as well as how parenting practices around PA, mothers' PA, mothers' parenting stress, and child developmental and behavioral problems are associated with toddlerhood PA development (Exploratory Aims 3a-c).

DISCUSSION : This study will be one of the first to use longitudinal data to validate a machine learning activity recognition algorithm and apply the algorithm to quantify free-living ambulatory movement in toddlers. The study findings will help fill a significant methodological gap in toddler PA measurement and expand the body of knowledge on the factors influencing early childhood PA development.

Welch Sarah B, Honegger Kyle, O’Brien Megan, Capan Selin, Kwon Soyang

2023-Mar-20

Accelerometry, Child development, Machine learning, Parenting, Physical activity

General General

dbCNV: deleteriousness-based model to predict pathogenicity of copy number variations.

In BMC genomics ; h5-index 78.0

BACKGROUND : Copy number variation (CNV) is a type of structural variation, which is a gain or loss event with abnormal changes in copy number. Methods to predict the pathogenicity of CNVs are required to realize the relationship between these variants and clinical phenotypes. ClassifyCNV, X-CNV, StrVCTVRE, etc. have been trained to predict the pathogenicity of CNVs, but few studies have been reported based on the deleterious significance of features.

RESULTS : From single nucleotide polymorphism (SNP), gene and region dimensions, we collected 79 informative features that quantitatively describe the characteristics of CNV, such as CNV length, the number of protein genes, the number of three prime untranslated region. Then, according to the deleterious significance, we formulated quantitative methods for features, which fall into two categories: the first is variable type, including maximum, minimum and mean; the second is attribute type, which is measured by numerical sum. We used Gradient Boosted Trees (GBT) algorithm to construct dbCNV, which can be used to predict pathogenicity for five-tier classification and binary classification of CNVs. We demonstrated that the distribution of most feature values was consistent with the deleterious significance. The five-tier classification model accuracy for 0.85 and 0.79 in loss and gain CNVs, which proved that it has high discrimination power in predicting the pathogenicity of five-tier classification CNVs. The binary model achieved area under curve (AUC) values of 0.96 and 0.81 in the validation set, respectively, in gain and loss CNVs.

CONCLUSION : The performance of the dbCNV suggest that functional deleteriousness-based model of CNV is a promising approach to support the classification prediction and to further understand the pathogenic mechanism.

Lv Kangqi, Chen Dayang, Xiong Dan, Tang Huamei, Ou Tong, Kan Lijuan, Zhang Xiuming

2023-Mar-20

Copy number variation, Machine learning, Pathogenicity, XGBoost

General General

Robust classification using average correlations as features (ACF).

In BMC bioinformatics

MOTIVATION : In single-cell transcriptomics and other omics technologies, large fractions of missing values commonly occur. Researchers often either consider only those features that were measured for each instance of their dataset, thereby accepting severe loss of information, or use imputation which can lead to erroneous results. Pairwise metrics allow for imputation-free classification with minimal loss of data.

RESULTS : Using pairwise correlations as metric, state-of-the-art approaches to classification would include the K-nearest-neighbor- (KNN) and distribution-based-classification-classifier. Our novel method, termed average correlations as features (ACF), significantly outperforms those approaches by training tunable machine learning models on inter-class and intra-class correlations. Our approach is characterized in simulation studies and its classification performance is demonstrated on real-world datasets from single-cell RNA sequencing and bottom-up proteomics. Furthermore, we demonstrate that variants of our method offer superior flexibility and performance over KNN classifiers and can be used in conjunction with other machine learning methods. In summary, ACF is a flexible method that enables missing value tolerant classification with minimal loss of data.

Schumann Yannis, Neumann Julia E, Neumann Philipp

2023-Mar-20

Classification, Correlation, Machine learning, Missing values, scRNA-seq

General General

Using artificial intelligence to support rapid, mixed-methods analysis: Developing an automated qualitative assistant (AQUA).

In Annals of family medicine

Context: Qualitative research - crucial for understanding human behavior - remains underutilized, in part due to the time and cost of annotating qualitative data (coding). Artificial intelligence (AI) has been suggested as a means to reduce those burdens. Older AI techniques (Latent Semantic Indexing / Latent Dirichlet Allocation (LSI/LDA)) have fallen short, in part because qualitative data is rife with idiom, non-standard expressions, and jargon. Objective: To develop an AI platform using updated techniques to augment qualitative data coding. Study Design and Analysis: We previously completed traditional qualitative analysis of a large dataset, with 11 qualitative categories and 72 subcategories (categories), and a final Cohen's kappa ≥ 0.65 as a measure of human inter-coder reliability (ICR) after coding. We built our Automated Qualitative Assistant (AQUA) using a semi-classical approach, replacing LSI/LDA with a graph-theoretic topic extraction and clustering method. AQUA was given the previously-identified qualitative categories and tasked with coding free-text data into those categories. Item coding was scored using cosine-similarity. Population Studied: Pennsylvanian adults. Instrument: Free-text responses to five open ended questions related to the COVID-19 pandemic (e.g. "What worries you most about the COVID-19 pandemic?"). Outcome Measures: AQUA's coding was compared to human coding using Cohen's kappa. This was done on all categories in aggregate, and also on category clusters to identify category groups amenable to AQUA support. AQUA's time to complete coding was compared to the time taken by the human coding team. Dataset: Five unlimited free-text survey answers from 538 responders. Results: AQUA's kappa for all categories was low (kappa~0.45), reflecting the challenge of automated analysis of diverse language. However, for several 3-category combinations (with less linguistic diversity), AQUA performed comparably to human coders, with an ICR kappa range of 0.62 to 0.72 based on test-train split. AQUA's analysis (including human interpretation) took approximately 5 hours, compared to approximately 30 person hours for traditional coding. Conclusions: AQUA enables qualitative researchers to identify categories amenable to automated coding, and to rapidly conduct that coding on the entirety of very large datasets. This saves time and money, and avoids limitations inherent in limiting qualitative analysis to limited samples of a given dataset.

Lennon Robert, Calo William, Miller Erin, Zgierska Aleksandra, Van Scoy Lauren, Fraleigh Robert

2022-Apr-01