Biomedical Computing

Separating algorithms from their computation schedule has become a de facto solution to tackle the challenges of developing high performance code on modern heterogeneous architectures. Common approaches include Domain-specific languages (DSLs) which provide familiar APIs to domain experts, code generation frameworks that automate the generation of fast and portable code, and runtime systems that manage threads for concurrency and parallelism. In this paper, we present the Halide code generation framework for Phylanx distributed array processing platform. This extension enables compile-time optimization of Phylanx primitives for target architectures. To accomplish this, (1) we implemented new Phylanx primitives using Halide, and (2) partially exported Halide's thread pool API to carry out parallelism on HPX (Phylanx's runtime) threads. (3) showcased HPX performance analysis tools made available to Halide applications. The evaluation of the work has been done in two steps. First, we compare the performance of Halide applications running on its native runtime with that of the new HPX backend to verify there is no cost associated with using HPX threads. Next, we compare performances of a number of original implementations of Phylanx primitives against the new ones in Halide to verify performance and portability benefits of Halide in the context of Phylanx.

Computational models of integrin-based adhesion complexes have revealed important insights into the mechanisms by which cells establish connections with their external environment. However, how changes in conformation and function of individual adhesion proteins regulate the dynamics of whole adhesion complexes remains largely elusive. This is because of the large separation in time and length scales between the dynamics of individual adhesion proteins (nanoseconds and nanometers) and the emergent dynamics of the whole adhesion complex (seconds and micrometers), and the limitations of molecular simulation approaches in extracting accurate free energies, conformational transitions, reaction mechanisms, and kinetic rates, that can inform mechanisms at the larger scales. In this review, we discuss models of integrin-based adhesion complexes and highlight their main findings regarding: (i) the conformational transitions of integrins at the molecular and macromolecular scales and (ii) the molecular clutch mechanism at the mesoscale. Lastly, we present unanswered questions in the field of modeling adhesions and propose new ideas for future exciting modeling opportunities.

Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS) to identify such interactions. Analysis of 33 enzymes from human carbohydrate metabolism identified 830 protein-metabolite interactions, including known regulators, substrates, and products as well as previously unreported interactions. We functionally validated a subset of interactions, including the isoform-specific inhibition of lactate dehydrogenase by long-chain acyl–coenzyme A. Cell treatment with fatty acids caused a loss of pyruvate-lactate interconversion dependent on lactate dehydrogenase isoform expression. These protein-metabolite interactions may contribute to the dynamic, tissue-specific metabolic flexibility that enables growth and survival in an ever-changing nutrient environment. Understanding how metabolic state influences cellular processes requires systematic analysis of low-affinity interactions of metabolites with proteins. Hicks et al. describe a method called MIDAS (mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically), which allowed them to probe such interactions for 33 enzymes of human carbohydrate metabolism and more than 400 metabolites. The authors detected many known and many new interactions, including regulation of lactate dehydrogenase by ATP and long-chain acyl coenzyme A, which may help to explain known physiological relations between fat and carbohydrate metabolism in different tissues. —LBR A mass spectrometry and dialysis method detects metabolite-protein interactions that help to control physiology.

Background

The role of fiber orientation on a global chamber level in sustaining atrial fibrillation (AF) is unknown. The goal of this study was to correlate the fiber direction derived from Diffusion Tensor Imaging (DTI) with AF inducibility.

Electrocardiographic imaging (ECGI) is a clinical and research tool for noninvasive diagnosis of cardiac electrical dysfunction. The position of the heart within the torso is both an input and common source of error in ECGI. Many studies have sought to improve cardiac localization accuracy, however, few have examined quantitatively the effects of uncertainty in the position of the heart within the torso. Recently developed uncertainty quantification (UQ) tools enable the robust application of UQ to ECGI reconstructions. In this study, we developed an ECGI formulation, which for the first time, directly incorporated uncertainty in the heart position. The result is an ECGI solution that is robust to variation in heart position. Using data from two Langendorff experimental preparations, each with 120 heartbeats distributed across three activation sequences, we found that as heart position uncertainty increased above ±10 mm, the solution quality of the ECGI degraded. However, even at large heart position uncertainty (±40 mm) our novel UQ-ECGI formulation produced reasonable solutions (root mean squared error < 1 mV, spatial correlation >0.6, temporal correlation >0.75).

Past studies have examined the differences between R and S waves of unipolar atrial signals in patients with atrial fibrillation (AF) and have shown a difference in the R to S ratio (R:S) in certain regions of the atria compared to a healthy population. This work indicates a potential use of R:S as a marker for AF. In this study, we further examine these claims and investigate temporal changes in R:S over AF development in animals.

Four canines underwent AF development protocols and endocardial sinus rhythm maps were recorded as AF progressed. Unipolar signals gathered from mapping were used to calculate R:S within the left atrium of each animal. Calculations were performed at time points: before AF initiation, 3-4 months of chronic AF, and 6 months of chronic AF. From our analysis, we observed an increase in R-dominant signals within the left atrium once AF is induced. Temporal results show that R dominance may be an indicator for chronic AF patients and may be associated with the presence of arrhythmogenic substrate. With the addition of regional information, this unipolar signal analysis could guide therapeutic strategies.

Introduction: The inverse problem of ECGI is ill-posed, so regularization must be applied to constrain the solution. Regularization is typically applied to each individual time point (instantaneous) or to the beat as a whole (global). These techniques often lead to over- or underregularization. We aimed to develop an inverse formulation that strikes a balance between these two approaches that would realize the benefits of both by implementing a sliding-window regularization. Methods: We formulated sliding-window regularization using the boundary element method with Tikhonov 0 and 2nd order regularization. We applied regularization to a varying time window of the body-surface potentials centered around each time sample. We compared reconstructed potentials from the sliding-window, instantaneous, and global regularization techniques to ground truth potentials for 10 heart beats paced from the ventricle in a large-animal model. Results: The sliding-window technique provided smoother transitions of regularization weights than instantaneous regularization while improving spatial correlation over global regularization. Discussion: Although the differences in regularization weights were nuanced, smoother transitions provided by the sliding-window regularization have the ability to eliminate discontinuities in potential seen with instantaneous regularization.

Acute myocardial ischemia is commonly diagnosed by ST-segment deviations. These deviations, however, can show a paradoxical recovery even in the face of ongoing ischemic stress. A possible mechanism for this response may be the cardio-protective effects of the autonomic nervous system (ANS) via beta-1 receptors. We assessed the role of norepinephrine (NE), a beta-1 agonist, and esmolol (ES), a beta-1 antagonist, in the recovery of ST-segment deviations during myocardial ischemia. We used an experimental model of controlled myocardial ischemia in which we simultaneously recorded electrograms intramurally and on the epicardial surface. We measured ischemia as deviations in the potentials measured at 40% of the ST-segment duration. During control intervention, 27% of epicardial electrodes showed no ischemic ST-segment deviations, whereas during the interventions with NE and ES, 100% of epicardial electrodes showed no ischemic ST-segment deviations. Intramural electrodes revealed a different behavior with 71% of electrodes showing no ischemic ST-segment deviations during control ischemia, increasing to 79% and 82% for NE infusion and ES infusion interventions, respectively. These preliminary results suggest that recovery of intramural regions of the heart is delayed by the presence of both beta-1 agonists and antagonists even as epicardial potentials show almost complete recovery.

Subject-specific geometry such as cardiac position and torso size plays an important role in electrocardiographic imaging (ECGI). Previously, we introduced a graph-based neural network (GNN) that is dependent on patient-specific geometry to improve reconstruction accuracy. However, geometric uncertainty, including changes in cardiac position and torso size, has not been addressed in network-based methods. In this study, we estimate geometrical uncertainty on GNN by applying uncertainty quantification with polynomial chaos emulators (PCE). To estimate the effect of geometric variation from common motions, we evaluated the model on samples generated by different heart torso geometries. The experiments shows that the GNN is less sensitive to heart position and torso shape and helps us direct development of similar models to account of possible variability.

Previous studies have compared recorded torso potentials with electrocardiographic forward solutions from a pericardial cage. In this study, we introduce new comparisons of the forward solutions from the sock and cage with each other and with respect to the measured potentials on the torso. The forward problem of electrocardiographic imaging is expected to achieve high levels of accuracy since it is mathematically well posed. However, unexpectedly high residual errors remain between the computed and measured torso signals in experiments. A possible source of these errors is the limited spatial coverage of the cardiac sources in most experiments; most capture potentials only from the ventricles. To resolve the relationship between spatial coverage and the accuracy of the forward simulations, we combined two methods of capturing cardiac potentials using a 240-electrode sock and a 256-electrode cage, both surrounding a heart suspended in a 192-electrode torso tank. We analyzed beats from three pacing sites and calculated the RMSE, spatial correlation, and temporal correlation. We found that the forward solutions using the sock as the cardiac source were poorer compared to those obtained from the cage. In this study, we explore the differences in forward solution accuracy using the sock and the cage and suggest some possible explanations for these differences.

The platelet integrin α_IIbβ₃ undergoes long range conformational transitions associated with its functional conversion from inactive (low affinity) to active (high affinity) states during hemostasis. Although new conformations intermediate between the well-characterized bent and extended states have been identified, their molecular dynamic properties and functions in the assembly of adhesions remain largely unexplored. In this study, we evaluated the properties of intermediate conformations of integrin α_IIbβ₃ and characterized their effects on the assembly of adhesions by combining all-atom simulations, principal component analysis, and mesoscale modeling. Our results show that in the low affinity, bent conformation, the integrin ectodomain tends to pivot around the legs; in intermediate conformations the upper headpiece becomes partially extended, away from the lower legs. In the fully open, active state, α_IIbβ₃ is flexible and the motions between upper headpiece and lower legs are accompanied by fluctuations of the transmembrane helices. At the mesoscale, bent integrins form only unstable adhesions, but intermediate or open conformations stabilize the adhesions. These studies reveal a mechanism by which small variations in ligand binding affinity and enhancement of the ligand-bound lifetime in the presence of actin retrograde flow stabilize α_IIbβ₃ integrin adhesions.

Background:

Computational biomedical simulations frequently contain parameters that model physical features, material coefficients, and physiological effects, whose values are typically assumed known a priori. Understanding the effect of variability in those assumed values is currently a topic of great interest. A general-purpose software tool that quantifies how variation in these parameters affects model outputs is not broadly available in biomedicine. For this reason, we developed the ‘UncertainSCI’ uncertainty quantification software suite to facilitate analysis of uncertainty due to parametric variability.

Computational fluid dynamics (CFD) is known for producing high-dimensional spatiotemporal data. Recent advances in machine learning (ML) have introduced a myriad of techniques for extracting physical information from CFD. Identifying an optimal set of coordinates for representing the data in a low-dimensional embedding is a crucial first step toward data-driven reduced-order modeling and other ML tasks. This is usually done via principal component analysis (PCA), which gives an optimal linear approximation. However, fluid flows are often complex and have nonlinear structures, which cannot be discovered or efficiently represented by PCA. Several unsupervised ML algorithms have been developed in other branches of science for nonlinear dimensionality reduction (NDR), but have not been extensively used for fluid flows. Here, four manifold learning and two deep learning (autoencoder)-based NDR methods are investigated and compared to PCA. These are tested on two canonical fluid flow problems (laminar and turbulent) and two biomedical flows in brain aneurysms. The data reconstruction capabilities of these methods are compared, and the challenges are discussed. The temporal vs spatial arrangement of data and its influence on NDR mode extraction is investigated. Finally, the modes are qualitatively compared. The results suggest that using NDR methods would be beneficial for building more efficient reduced-order models of fluid flows. All NDR techniques resulted in smaller reconstruction errors for spatial reduction. Temporal reduction was a harder task; nevertheless, it resulted in physically interpretable modes. Our work is one of the first comprehensive comparisons of various NDR methods in unsteady flows.

Deep neural networks have shown promise in image reconstruction tasks, although often on the premise of large amounts of training data. In this paper, we present a new approach to exploit the geometry and physics underlying electrocardiographic imaging (ECGI) to learn efficiently with a relatively small dataset. We first introduce a non-Euclidean encoding-decoding network that allows us to describe the unknown and measurement variables over their respective geometrical domains. We then explicitly model the geometry-dependent physics in between the two domains via a bipartite graph over their graphical embeddings. We applied the resulting network to reconstruct electrical activity on the heart surface from body-surface potentials. In a series of generalization tasks with increasing difficulty, we demonstrated the improved ability of the network to generalize across geometrical changes underlying the data using less than 10% of training data and fewer variations of training geometry in comparison to its Euclidean alternatives. In both simulation and real-data experiments, we further demonstrated its ability to be quickly fine-tuned to new geometry using a modest amount of data.

Prior knowledge about the imaging physics provides a mechanistic forward operator that plays an important role in image reconstruction, although myriad sources of possible errors in the operator could negatively impact the reconstruction solutions. In this work, we propose to embed the traditional mechanistic forward operator inside a neural function, and focus on modeling and correcting its unknown errors in an interpretable manner. This is achieved by a conditional generative model that transforms a given mechanistic operator with unknown errors, arising from a latent space of self-organizing clusters of potential sources of error generation. Once learned, the generative model can be used in place of a fixed forward operator in any traditional optimization-based reconstruction process where, together with the inverse solution, the error in prior mechanistic forward operator can be minimized and the potential source of error uncovered. We apply the presented method to the reconstruction of heart electrical potential from body surface potential. In controlled simulation experiments and in-vivo real data experiments, we demonstrate that the presented method allowed reduction of errors in the physics-based forward operator and thereby delivered inverse reconstruction of heart-surface potential with increased accuracy.

Clinical adoption of personalized virtual heart simulations faces challenges in model personalization and expensive computation. While an ideal solution is an efficient neural surrogate that at the same time is personalized to an individual subject, the state-of-the-art is either concerned with personalizing an expensive simulation model, or learning an efficient yet generic surrogate. This paper presents a completely new concept to achieve personalized neural surrogates in a single coherent framework of meta-learning (metaPNS). Instead of learning a single neural surrogate, we pursue the process of learning a personalized neural surrogate using a small amount of context data from a subject, in a novel formulation of few-shot generative modeling underpinned by: 1) a set-conditioned neural surrogate for cardiac simulation that, conditioned on subject-specific context data, learns to generate query simulations not included in the context set, and 2) a meta-model of amortized variational inference that learns to condition the neural surrogate via simple feed-forward embedding of context data. As test time, metaPNS delivers a personalized neural surrogate by fast feed-forward embedding of a small and flexible number of data available from an individual, achieving -- for the first time -- personalization and surrogate construction for expensive simulations in one end-to-end learning framework. Synthetic and real-data experiments demonstrated that metaPNS was able to improve personalization and predictive accuracy in comparison to conventionally-optimized cardiac simulation models, at a fraction of computation.

Electrocardiographic imaging (ECGI) presents a clinical opportunity to noninvasively understand the sources of arrhythmias for individual patients. To help increase the effectiveness of ECGI, we provide new ways to visualise associated measurement and modelling errors. In this paper, we study source localisation uncertainty in two steps: First, we perform Monte Carlo simulations of a simple inverse ECGI source localisation model with error sampling to understand the variations in ECGI solutions. Second, we present multiple visualisation techniques, including confidence maps, level-sets, and topology-based visualisations, to better understand uncertainty in source localization. Our approach offers a new way to study uncertainty in the ECGI pipeline.

For inverse problems one attempts to infer spatially variable functions from indirect measurements of a system. To practitioners of inverse problems, the concept of ``information'' is familiar when discussing key questions such as which parts of the function can be inferred accurately and which cannot. For example, it is generally understood that we can identify system parameters accurately only close to detectors, or along ray paths between sources and detectors, because we have ``the most information'' for these places.

Although referenced in many publications, the ``information'' that is invoked in such contexts is not a well understood and clearly defined quantity. Herein, we present a definition of information density that is based on the variance of coefficients as derived from a Bayesian reformulation of the inverse problem. We then discuss three areas in which this information density can be useful in practical algorithms for the solution of inverse problems, and illustrate the usefulness in one of these areas -- how to choose the discretization mesh for the function to be reconstructed -- using numerical experiments.

Computational models have made it possible to study the effect of fibrosis and scar on atrial fibrillation (AF) and plan future personalized treatments. Here, we study the effect of area available for fibrillatory waves to sustain AF. Then we use it to plan for AF ablation to improve procedural outcomes. CARPentry was used to create patient-specific models to determine the association between the size of residual contiguous areas available for AF wavefronts to propagate and sustain AF [fibrillatory area (FA)] after ablation with procedural outcomes. The FA was quantified in a novel manner accounting for gaps in ablation lines. We selected 30 persistent AF patients with known ablation outcomes. We divided the atrial surface into five areas based on ablation scar pattern and anatomical landmarks and calculated the FAs. We validated the models based on clinical outcomes and suggested future ablation lines that minimize the FAs and terminate rotor activities in simulations. We also simulated the effects of three common antiarrhythmic drugs. In the patient-specific models, the predicted arrhythmias matched the clinical outcomes in 25 of 30 patients (accuracy 83.33%). The average largest FA (FA_max) in the recurrence group was 8517 ± 1444 vs. 6772 ± 1531 mm² in the no recurrence group (p < 0.004). The final FAs after adding the suggested ablation lines in the AF recurrence group reduced the average FA_max from 8517 ± 1444 to 6168 ± 1358 mm² (p < 0.001) and stopped the sustained rotor activity. Simulations also correctly anticipated the effect of antiarrhythmic drugs in 5 out of 6 patients who used drug therapy post unsuccessful ablation (accuracy 83.33%). Sizes of FAs available for AF wavefronts to propagate are important determinants for ablation outcomes. FA size in combination with computational simulations can be used to direct ablation in persistent AF to minimize the critical mass required to sustain recurrent AF.

Purpose:

A subset of patients with metopic craniosynostosis are noted to have elevated intracranial pressure (ICP). However, it is not known if the propensity for elevated ICP is influenced by the severity of metopic cranial dysmorphology.