Challenges for machine learning in clinical translation of big data imaging studies

The power of many brains: Catalyzing neuropsychiatric discovery through open neuroimaging data and large-scale collaboration

Recent advances in open neuroimaging data are enhancing our comprehension of neuropsychiatric disorders. By pooling images from various cohorts, statistical power has increased, enabling the detection of subtle abnormalities and robust associations, and fostering new research methods. Global collaborations in imaging have furthered our knowledge of the neurobiological foundations of brain disorders and aided in imaging-based prediction for more targeted treatment. Large-scale magnetic resonance imaging initiatives are driving innovation in analytics and supporting generalizable psychiatric studies. We also emphasize the significant role of big data in understanding neural mechanisms and in the early identification and precise treatment of neuropsychiatric disorders. However, challenges such as data harmonization across different sites, privacy protection, and effective data sharing must be addressed. With proper governance and open science practices, we conclude with a projection of how large-scale imaging resources and collaborations could revolutionize diagnosis, treatment selection, and outcome prediction, contributing to optimal brain health.

MMGPL: Multimodal Medical Data Analysis with Graph Prompt Learning

Prompt learning has demonstrated impressive efficacy in the fine-tuning of multimodal large models to a wide range of downstream tasks. Nonetheless, applying existing prompt learning methods for the diagnosis of neurological disorder still suffers from two issues: (i) existing methods typically treat all patches equally, despite the fact that only a small number of patches in neuroimaging are relevant to the disease, and (ii) they ignore the structural information inherent in the brain connection network which is crucial for understanding and diagnosing neurological disorders. To tackle these issues, we introduce a novel prompt learning model by learning graph prompts during the fine-tuning process of multimodal models for diagnosing neurological disorders. Specifically, we first leverage GPT-4 to obtain relevant disease concepts and compute semantic similarity between these concepts and all patches. Secondly, we reduce the weight of irrelevant patches according to the semantic similarity between each patch and disease-related concepts. Moreover, we construct a graph among tokens based on these concepts and employ a graph convolutional network layer to extract the structural information of the graph, which is used to prompt the pre-trained multimodal models for diagnosing neurological disorders. Extensive experiments demonstrate that our method achieves superior performance for neurological disorder diagnosis compared with state-of-the-art methods and validated by clinicians.

An automated method for tendon image segmentation on ultrasound using grey-level co-occurrence matrix features and hidden Gaussian Markov random fields

BACKGROUND

Despite knowledge of qualitative changes that occur on ultrasound in tendinopathy, there is currently no objective and reliable means to quantify the severity or prognosis of tendinopathy on ultrasound.

OBJECTIVE

The primary objective of this study is to produce a quantitative and automated means of inferring potential structural changes in tendinopathy by developing and implementing an algorithm which performs a texture based segmentation of tendon ultrasound (US) images.

METHOD

A model-based segmentation approach is used which combines Gaussian mixture models, Markov random field theory and grey-level co-occurrence (GLCM) features. The algorithm is trained and tested on 49 longitudinal B-mode ultrasound images of the Achilles tendons which are labelled as tendinopathic (24) or healthy (25). Hyperparameters are tuned, using a training set of 25 images, to optimise a decision tree based classification of the images from texture class proportions. We segment and classify the remaining test images using the decision tree.

RESULTS

Our approach successfully detects a difference in the texture profiles of tendinopathic and healthy tendons, with 22/24 of the test images accurately classified based on a simple texture proportion cut-off threshold. Results for the tendinopathic images are also collated to gain insight into the topology of structural changes that occur with tendinopathy. It is evident that distinct textures, which are predominantly present in tendinopathic tendons, appear most commonly near the transverse boundary of the tendon, though there was a large variability among diseased tendons.

CONCLUSION

The GLCM based segmentation of tendons under ultrasound resulted in distinct segmentations between healthy and tendinopathic tendons and provides a potential tool to objectively quantify damage in tendinopathy.

Self-supervised segmentation and characterization of fiber bundles in anatomic tracing data

Anatomic tracing is the gold standard tool for delineating brain connections and for validating more recently developed imaging approaches such as diffusion MRI tractography. A key step in the analysis of data from tracer experiments is the careful, manual charting of fiber trajectories on histological sections. This is a very time-consuming process, which limits the amount of annotated tracer data that are available for validation studies. Thus, there is a need to accelerate this process by developing a method for computer-assisted segmentation. Such a method must be robust to the common artifacts in tracer data, including variations in the intensity of stained axons and background, as well as spatial distortions introduced by sectioning and mounting the tissue. The method should also achieve satisfactory performance using limited manually charted data for training. Here we propose the first deeplearning method, with a self-supervised loss function, for segmentation of fiber bundles on histological sections from macaque brains that have received tracer injections. We address the limited availability of manual labels with a semi-supervised training technique that takes advantage of unlabeled data to improve performance. We also introduce anatomic and across-section continuity constraints to improve accuracy. We show that our method can be trained on manually charted sections from a single case and segment unseen sections from different cases, with a true positive rate of ~0.80. We further demonstrate the utility of our method by quantifying the density of fiber bundles as they travel through different white-matter pathways. We show that fiber bundles originating in the same injection site have different levels of density when they travel through different pathways, a finding that can have implications for microstructure-informed tractography methods. The code for our method is available at https://github.com/v-sundaresan/fiberbundle_seg_tracing.

Functional connectomics in depression: insights into therapies

Depression is a common mental disorder characterized by heterogeneous cognitive and behavioral symptoms. The emerging research paradigm of functional connectomics has provided a quantitative theoretical framework and analytic tools for parsing variations in the organization and function of brain networks in depression. In this review, we first discuss recent progress in depression-associated functional connectome variations. We then discuss treatment-specific brain network outcomes in depression and propose a hypothetical model highlighting the advantages and uniqueness of each treatment in relation to the modulation of specific brain network connectivity and symptoms of depression. Finally, we look to the future promise of combining multiple treatment types in clinical practice, using multisite datasets and multimodal neuroimaging approaches, and identifying biological depression subtypes.

The evolution of Big Data in neuroscience and neurology

Neurological diseases are on the rise worldwide, leading to increased healthcare costs and diminished quality of life in patients. In recent years, Big Data has started to transform the fields of Neuroscience and Neurology. Scientists and clinicians are collaborating in global alliances, combining diverse datasets on a massive scale, and solving complex computational problems that demand the utilization of increasingly powerful computational resources. This Big Data revolution is opening new avenues for developing innovative treatments for neurological diseases. Our paper surveys Big Data's impact on neurological patient care, as exemplified through work done in a comprehensive selection of areas, including Connectomics, Alzheimer's Disease, Stroke, Depression, Parkinson's Disease, Pain, and Addiction (e.g., Opioid Use Disorder). We present an overview of research and the methodologies utilizing Big Data in each area, as well as their current limitations and technical challenges. Despite the potential benefits, the full potential of Big Data in these fields currently remains unrealized. We close with recommendations for future research aimed at optimizing the use of Big Data in Neuroscience and Neurology for improved patient outcomes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40537-023-00751-2.

The foundation and architecture of precision medicine in neurology and psychiatry

Neurological and psychiatric diseases have high degrees of genetic and pathophysiological heterogeneity, irrespective of clinical manifestations. Traditional medical paradigms have focused on late-stage syndromic aspects of these diseases, with little consideration of the underlying biology. Advances in disease modeling and methodological design have paved the way for the development of precision medicine (PM), an established concept in oncology with growing attention from other medical specialties. We propose a PM architecture for central nervous system diseases built on four converging pillars: multimodal biomarkers, systems medicine, digital health technologies, and data science. We discuss Alzheimer's disease (AD), an area of significant unmet medical need, as a case-in-point for the proposed framework. AD can be seen as one of the most advanced PM-oriented disease models and as a compelling catalyzer towards PM-oriented neuroscience drug development and advanced healthcare practice.