Shreyas Fadnavis

Shreyas Fadnavis, Amit Dhurandhar, Raquel Norel et al.

Chronic pain is a pervasive disorder which is often very disabling and is associated with comorbidities such as depression and anxiety. Neuropathic Pain (NP) is a common sub-type which is often caused due to nerve damage and has a known pathophysiology. Another common sub-type is Fibromyalgia (FM) which is described as musculoskeletal, diffuse pain that is widespread through the body. The pathophysiology of FM is poorly understood, making it very hard to diagnose. Standard medications and treatments for FM and NP differ from one another and if misdiagnosed it can cause an increase in symptom severity. To overcome this difficulty, we propose a novel framework, PainPoints, which accurately detects the sub-type of pain and generates clinical notes via summarizing the patient interviews. Specifically, PainPoints makes use of large language models to perform sentence-level classification of the text obtained from interviews of FM and NP patients with a reliable AUC of 0.83. Using a sufficiency-based interpretability approach, we explain how the fine-tuned model accurately picks up on the nuances that patients use to describe their pain. Finally, we generate summaries of these interviews via expert interventions by introducing a novel facet-based approach. PainPoints thus enables practitioners to add/drop facets and generate a custom summary based on the notion of "facet-coverage" which is also introduced in this work.

Shreyas Fadnavis, Jens Sjölund, Anders Eklund et al.

Diffusion MRI (dMRI) is the only non-invasive technique sensitive to tissue micro-architecture, which can, in turn, be used to reconstruct tissue microstructure and white matter pathways. The accuracy of such tasks is hampered by the low signal-to-noise ratio in dMRI. Today, the noise is characterized mainly by visual inspection of residual maps and estimated standard deviation. However, it is hard to estimate the impact of noise on downstream tasks based only on such qualitative assessments. To address this issue, we introduce a novel metric, Noise Uncertainty Quantification (NUQ), for quantitative image quality analysis in the absence of a ground truth reference image. NUQ uses a recent Bayesian formulation of dMRI models to estimate the uncertainty of microstructural measures. Specifically, NUQ uses the maximum mean discrepancy metric to compute a pooled quality score by comparing samples drawn from the posterior distribution of the microstructure measures. We show that NUQ allows a fine-grained analysis of noise, capturing details that are visually imperceptible. We perform qualitative and quantitative comparisons on real datasets, showing that NUQ generates consistent scores across different denoisers and acquisitions. Lastly, by using NUQ on a cohort of schizophrenics and controls, we quantify the substantial impact of denoising on group differences.

Jong Sung Park, Shreyas Fadnavis, Eleftherios Garyfallidis

Brain extraction is one of the first steps of pre-processing 3D brain MRI data and a prerequisite for any forthcoming brain imaging analyses. However, it is not a simple segmentation problem due to the complex structure of the brain and human head. Although multiple solutions have been proposed in the literature, we are still far from having truly robust methods. While previous methods have used machine learning with structural/geometric priors, with the development of Deep Learning (DL), there has been an increase in proposed Neural Network architectures. Most models focus on improving the training data and loss functions with little change in the architecture. However, the amount of accessible training data with expert-labelled ground truth vary between groups. Moreover, the labels are created not from scratch but from outputs of non-DL methods. Thus, most DL method's performance depend on the amount and quality of data one has. In this paper, we propose a novel architecture we call EVAC+ to work around this issue. We show that EVAC+ has 3 major advantages compared to other networks: (1) Multi-scale input with limited random augmentation for efficient learning, (2) a unique way of using Conditional Random Fields Recurrent Layer and (3) a loss function specifically created to enhance this architecture. We compare our model to state-of-the-art non-DL and DL methods. Results show that even with little change in the traditional architecture and limited training resources, EVAC+ achieves a high and stable Dice Coefficient and Jaccard Index along with a desirable lower surface distance. Ultimately, our model provides a robust way of accurately reducing segmentation errors in complex multi-tissue interfacing areas of brain.

Shreyas Fadnavis, Hamza Farooq, Maryam Afzali et al.

Fitting multi-exponential models to Diffusion MRI (dMRI) data has always been challenging due to various underlying complexities. In this work, we introduce a novel and robust fitting framework for the standard two-compartment IVIM microstructural model. This framework provides a significant improvement over the existing methods and helps estimate the associated diffusion and perfusion parameters of IVIM in an automatic manner. As a part of this work we provide capabilities to switch between more advanced global optimization methods such as simplicial homology (SH) and differential evolution (DE). Our experiments show that the results obtained from this simultaneous fitting procedure disentangle the model parameters in a reduced subspace. The proposed framework extends the seminal work originated in the MIX framework, with improved procedures for multi-stage fitting. This framework has been made available as an open-source Python implementation and disseminated to the community through the DIPY project.

Damola Agbelese, Krishna Chaitanya, Pushpak Pati et al.

Reliable uncertainty quantification (UQ) is essential in medical AI. Evidential Deep Learning (EDL) offers a computationally efficient way to quantify model uncertainty alongside predictions, unlike traditional methods such as Monte Carlo (MC) Dropout and Deep Ensembles (DE). However, all these methods often rely on a single expert's annotations as ground truth for model training, overlooking the inter-rater variability in healthcare. To address this issue, we propose MEGAN, a Multi-Expert Gating Network that aggregates uncertainty estimates and predictions from multiple AI experts via EDL models trained with diverse ground truths and modeling strategies. MEGAN's gating network optimally combines predictions and uncertainties from each EDL model, enhancing overall prediction confidence and calibration. We extensively benchmark MEGAN on endoscopy videos for Ulcerative colitis (UC) disease severity estimation, assessed by visual labeling of Mayo Endoscopic Subscore (MES), where inter-rater variability is prevalent. In large-scale prospective UC clinical trial, MEGAN achieved a 3.5% improvement in F1-score and a 30.5% reduction in Expected Calibration Error (ECE) compared to existing methods. Furthermore, MEGAN facilitated uncertainty-guided sample stratification, reducing the annotation burden and potentially increasing efficiency and consistency in UC trials.

Eleftherios Garyfallidis, Shreyas Fadnavis, Jong Sung Park et al.

Clustering is a fundamental problem in machine learning where distance-based approaches have dominated the field for many decades. This set of problems is often tackled by partitioning the data into K clusters where the number of clusters is chosen apriori. While significant progress has been made on these lines over the years, it is well established that as the number of clusters or dimensions increase, current approaches dwell in local minima resulting in suboptimal solutions. In this work, we propose a new set of distance threshold methods called Theta-based Algorithms (ThetA). Via experimental comparisons and complexity analyses we show that our proposed approach outperforms existing approaches in: a) clustering accuracy and b) time complexity. Additionally, we show that for a large class of problems, learning the optimal threshold is straightforward in comparison to learning K. Moreover, we show how ThetA can infer the sparsity of datasets in higher dimensions.

Shreyas Fadnavis, Joshua Batson, Eleftherios Garyfallidis

Diffusion-weighted magnetic resonance imaging (DWI) is the only noninvasive method for quantifying microstructure and reconstructing white-matter pathways in the living human brain. Fluctuations from multiple sources create significant additive noise in DWI data which must be suppressed before subsequent microstructure analysis. We introduce a self-supervised learning method for denoising DWI data, Patch2Self, which uses the entire volume to learn a full-rank locally linear denoiser for that volume. By taking advantage of the oversampled q-space of DWI data, Patch2Self can separate structure from noise without requiring an explicit model for either. We demonstrate the effectiveness of Patch2Self via quantitative and qualitative improvements in microstructure modeling, tracking (via fiber bundle coherency) and model estimation relative to other unsupervised methods on real and simulated data.