Ragini Verma

Eamonn Kennedy, Shashank Vadlamani, Hannah M Lindsey et al.

An extensive library of symptom inventories has been developed over time to measure clinical symptoms, but this variety has led to several long standing issues. Most notably, results drawn from different settings and studies are not comparable, which limits reproducibility. Here, we present an artificial intelligence (AI) approach using semantic textual similarity (STS) to link symptoms and scores across previously incongruous symptom inventories. We tested the ability of four pre-trained STS models to screen thousands of symptom description pairs for related content - a challenging task typically requiring expert panels. Models were tasked to predict symptom severity across four different inventories for 6,607 participants drawn from 16 international data sources. The STS approach achieved 74.8% accuracy across five tasks, outperforming other models tested. This work suggests that incorporating contextual, semantic information can assist expert decision-making processes, yielding gains for both general and disease-specific clinical assessment.

Zahra Riahi Samani, Drew Parker, Hamed Akbari et al.

In malignant primary brain tumors, cancer cells infiltrate into the peritumoral brain structures which results in inevitable recurrence. Quantitative assessment of infiltrative heterogeneity in the peritumoral region, the area where biopsy or resection can be hazardous, is important for clinical decision making. Previous work on characterizing the infiltrative heterogeneity in the peritumoral region used various imaging modalities, but information of extracellular free water movement restriction has been limitedly explored. Here, we derive a unique set of Artificial Intelligence (AI)-based markers capturing the heterogeneity of tumor infiltration, by characterizing free water movement restriction in the peritumoral region using Diffusion Tensor Imaging (DTI)-based free water volume fraction maps. A novel voxel-wise deep learning-based peritumoral microenvironment index (PMI) is first extracted by leveraging the widely different water diffusivity properties of glioblastomas and brain metastases as regions with and without infiltrations in the peritumoral tissue. Descriptive characteristics of locoregional hubs of uniformly high PMI values are extracted as AI-based markers to capture distinct aspects of infiltrative heterogeneity. The proposed markers are applied to two clinical use cases on an independent population of 275 adult-type diffuse gliomas (CNS WHO grade 4), analyzing the duration of survival among Isocitrate-Dehydrogenase 1 (IDH1)-wildtypes and the differences with IDH1-mutants. Our findings provide a panel of markers as surrogates of infiltration that captures unique insight about underlying biology of peritumoral microstructural heterogeneity, establishing them as biomarkers of prognosis pertaining to survival and molecular stratification, with potential applicability in clinical decision making.

Rui Sherry Shen, Yusuf Osmanlıoğlu, Drew Parker et al.

Divergent brain connectivity is thought to underlie the behavioral and cognitive symptoms observed in many neurodevelopmental disorders. Quantifying divergence from neurotypical connectivity patterns offers a promising pathway to inform diagnosis and therapeutic interventions. While advanced neuroimaging techniques, such as diffusion MRI (dMRI), have facilitated the mapping of brain's structural connectome, the challenge lies in accurately modeling developmental trajectories within these complex networked structures to create robust neurodivergence markers. In this work, we present the Brain Representation via Individualized Deep Generative Embedding (BRIDGE) framework, which integrates normative modeling with a bio-inspired deep generative model to create a reference trajectory of connectivity transformation as part of neurotypical development. This will enable the assessment of neurodivergence by comparing individuals to the established neurotypical trajectory. BRIDGE provides a global neurodivergence score based on the difference between connectivity-based brain age and chronological age, along with region-wise neurodivergence maps that highlight localized connectivity differences. Application of BRIDGE to a large cohort of children with autism spectrum disorder demonstrates that the global neurodivergence score correlates with clinical assessments in autism, and the regional map offers insights into the heterogeneity at the individual level in neurodevelopmental disorders. Together, the neurodivergence score and map form powerful tools for quantifying developmental divergence in connectivity patterns, advancing the development of imaging markers for personalized diagnosis and intervention in various clinical contexts.

Adnan Ahmad, Drew Parker, Zahra Riahi Samani et al.

Artifacts are a common occurrence in Diffusion MRI (dMRI) scans. Identifying and removing them is essential to ensure the accuracy and viability of any post processing carried out on these scans. This makes QC (quality control) a crucial first step prior to any analysis of dMRI data. Several QC methods for artifact detection exist, however they suffer from problems like requiring manual intervention and the inability to generalize across different artifacts and datasets. In this paper, we propose an automated deep learning (DL) pipeline that utilizes a 3D-Densenet architecture to train a model on diffusion volumes for automatic artifact detection. Our method is applied on a vast dataset consisting of 9000 volumes sourced from 7 large clinical datasets. These datasets comprise scans from multiple scanners with different gradient directions, high and low b values, single shell and multi shell acquisitions. Additionally, they represent diverse subject demographics like the presence or absence of pathologies. Our QC method is found to accurately generalize across this heterogenous data by correctly detecting 92% artifacts on average across our test set. This consistent performance over diverse datasets underlines the generalizability of our method, which currently is a significant barrier hindering the widespread adoption of automated QC techniques. For these reasons, we believe that 3D-QCNet can be integrated in diffusion pipelines to effectively automate the arduous and time-intensive process of artifact detection.

Zahra Riahi Samani, Jacob Antony Alappatt, Drew Parker et al.

Quality assessment of diffusion MRI (dMRI) data is essential prior to any analysis, so that appropriate pre-processing can be used to improve data quality and ensure that the presence of MRI artifacts do not affect the results of subsequent image analysis. Manual quality assessment of the data is subjective, possibly error-prone, and infeasible, especially considering the growing number of consortium-like studies, underlining the need for automation of the process. In this paper, we have developed a deep-learning-based automated quality control (QC) tool, QC-Automator, for dMRI data, that can handle a variety of artifacts such as motion, multiband interleaving, ghosting, susceptibility, herringbone and chemical shifts. QC-Automator uses convolutional neural networks along with transfer learning to train the automated artifact detection on a labeled dataset of ~332000 slices of dMRI data, from 155 unique subjects and 5 scanners with different dMRI acquisitions, achieving a 98% accuracy in detecting artifacts. The method is fast and paves the way for efficient and effective artifact detection in large datasets. It is also demonstrated to be replicable on other datasets with different acquisition parameters.