Clinical application of a GPU-accelerated monte carlo dose verification for cyberknife M6 with Iris collimator.

PURPOSE: To apply an independent GPU-accelerated Monte Carlo (MC) dose verification for CyberKnife M6 with Iris collimator and evaluate the dose calculation accuracy of RayTracing (TPS-RT) algorithm and Monte Carlo (TPS-MC) algorithm in the Precision treatment planning system (TPS). METHODS: GPU-accelerated MC algorithm (ArcherQA-CK) was integrated into a commercial dose verification system, ArcherQA, to implement the patient-specific quality assurance in the CyberKnife M6 system. 30 clinical cases (10 cases in head, and 10 cases in chest, and 10 cases in abdomen) were collected in this study. For each case, three different dose calculation methods (TPS-MC, TPS-RT and ArcherQA-CK) were implemented based on the same treatment plan and compared with each other. For evaluation, the 3D global gamma analysis and dose parameters of the target volume and organs at risk (OARs) were analyzed comparatively. RESULTS: For gamma pass rates at the criterion of 2%/2 mm, the results were over 98.0% for TPS-MC vs.TPS-RT, TPS-MC vs. ArcherQA-CK and TPS-RT vs. ArcherQA-CK in head cases, 84.9% for TPS-MC vs.TPS-RT, 98.0% for TPS-MC vs. ArcherQA-CK and 83.3% for TPS-RT vs. ArcherQA-CK in chest cases, 98.2% for TPS-MC vs.TPS-RT, 99.4% for TPS-MC vs. ArcherQA-CK and 94.5% for TPS-RT vs. ArcherQA-CK in abdomen cases. For dose parameters of planning target volume (PTV) in chest cases, the deviations of TPS-RT vs. TPS-MC and ArcherQA-CK vs. TPS-MC had significant difference (P < 0.01), and the deviations of TPS-RT vs. TPS-MC and TPS-RT vs. ArcherQA-CK were similar (P > 0.05). ArcherQA-CK had less calculation time compared with TPS-MC (1.66 min vs. 65.11 min). CONCLUSIONS: Our proposed MC dose engine (ArcherQA-CK) has a high degree of consistency with the Precision TPS-MC algorithm, which can quickly identify the calculation errors of TPS-RT algorithm for some chest cases. ArcherQA-CK can provide accurate patient-specific quality assurance in clinical practice.

Pangenome graph layout by Path-Guided Stochastic Gradient Descent.

MOTIVATION: The increasing availability of complete genomes demands for models to study genomic variability within entire populations. Pangenome graphs capture the full genomic similarity and diversity between multiple genomes. In order to understand them, we need to see them. For visualization, we need a human-readable graph layout: a graph embedding in low (e.g. two) dimensional depictions. Due to a pangenome graph's potential excessive size, this is a significant challenge. RESULTS: In response, we introduce a novel graph layout algorithm: the Path-Guided Stochastic Gradient Descent (PG-SGD). PG-SGD uses the genomes, represented in the pangenome graph as paths, as an embedded positional system to sample genomic distances between pairs of nodes. This avoids the quadratic cost seen in previous versions of graph drawing by SGD. We show that our implementation efficiently computes the low-dimensional layouts of gigabase-scale pangenome graphs, unveiling their biological features. AVAILABILITY AND IMPLEMENTATION: We integrated PG-SGD in ODGI which is released as free software under the MIT open source license. Source code is available at https://github.com/pangenome/odgi.

Generalized Bézier-like model and its applications to curve and surface modeling.

The subject matter of surfaces in computer aided geometric design (CAGD) is the depiction and design of surfaces in the computer graphics arena. Due to their geometric features, modeling of Bézier curves and surfaces with their shape parameters is the most well-liked topic of research in CAGD/computer-aided manufacturing (CAM). The primary challenges in industries such as automotive, shipbuilding, and aerospace are the design of complex surfaces. In order to address this issue, the continuity constraints between surfaces are utilized to generate complex surfaces. The parametric and geometric continuities are the two metrics commonly used for establishing connections among surfaces. This paper proposes continuity constraints between two generalized Bézier-like surfaces (gBS) with different shape parameters to address the issue of modeling and designing surfaces. Initially, the generalized form of C3 and G3 of generalized Bézier-like curves (gBC) are developed. To check the validity of these constraints, some numerical examples are also analyzed with graphical representations. Furthermore, for a continuous connection among these gBS, the necessary and sufficient G1 and G2 continuity constraints are also developed. It is shown through the use of several geometric designs of gBS that the recommended basis can resolve the shape and position adjustment problems associated with Bézier surfaces more effectively than any other basis. As a result, the proposed scheme not only incorporates all of the geometric features of curve design schemes but also improves upon their faults, which are typically encountered in engineering. Mainly, by changing the values of shape parameters, we can alter the shape of the curve by our choice which is not present in the standard Bézier model. This is the main drawback of traditional Bézier model.

GenoFig: a user-friendly application for the visualization and comparison of genomic regions.

MOTIVATION: Understanding the molecular evolutionary history of organisms usually requires visual comparison of genomic regions from related species or strains. Although several applications already exist to achieve this task, they are either too old, too limited, or too complex for most user's needs. RESULTS: GenoFig is a graphical application for the visualization of prokaryotic genomic regions, intended to be as easy to use as possible and flexible enough to adapt to a variety of needs. GenoFig allows the personalized representation of annotations extracted from GenBank files in a consistent way across sequences, using regular expressions. It also provides several unique options to optimize the display of homologous regions between sequences, as well as other more classical features such as sequence GC percent or GC-skew representations. In summary, GenoFig is a simple, free, and highly configurable tool to explore the evolution of specific genomic regions in prokaryotes and to produce publication-ready figures. AVAILABILITY AND IMPLEMENTATION: Genofig is fully available at https://forgemia.inra.fr/public-pgba/genofig under a GPL 3.0 license.

Comprehensive framework of GPU-accelerated image reconstruction for photoacoustic computed tomography.

Significance: Photoacoustic computed tomography (PACT) is a promising non-invasive imaging technique for both life science and clinical implementations. To achieve fast imaging speed, modern PACT systems have equipped arrays that have hundreds to thousands of ultrasound transducer (UST) elements, and the element number continues to increase. However, large number of UST elements with parallel data acquisition could generate a massive data size, making it very challenging to realize fast image reconstruction. Although several research groups have developed GPU-accelerated method for PACT, there lacks an explicit and feasible step-by-step description of GPU-based algorithms for various hardware platforms. Aim: In this study, we propose a comprehensive framework for developing GPU-accelerated PACT image reconstruction (GPU-accelerated photoacoustic computed tomography), to help the research community to grasp this advanced image reconstruction method. Approach: We leverage widely accessible open-source parallel computing tools, including Python multiprocessing-based parallelism, Taichi Lang for Python, CUDA, and possible other backends. We demonstrate that our framework promotes significant performance of PACT reconstruction, enabling faster analysis and real-time applications. Besides, we also described how to realize parallel computing on various hardware configurations, including multicore CPU, single GPU, and multiple GPUs platform. Results: Notably, our framework can achieve an effective rate of ∼ 871 times when reconstructing extremely large-scale three-dimensional PACT images on a dual-GPU platform compared to a 24-core workstation CPU. In this paper, we share example codes via GitHub. Conclusions: Our approach allows for easy adoption and adaptation by the research community, fostering implementations of PACT for both life science and medicine.

GPU-accelerated parallel image reconstruction strategies for magnetic particle imaging.

Objective. Image reconstruction is a fundamental step in magnetic particle imaging (MPI). One of the main challenges is the fact that the reconstructions are computationally intensive and time-consuming, so choosing an algorithm presents a compromise between accuracy and execution time, which depends on the application. This work proposes a method that provides both fast and accurate image reconstructions.Approach. Image reconstruction algorithms were implemented to be executed in parallel ingraphics processing units(GPUs) using the CUDA framework. The calculation of the model-based MPI calibration matrix was also implemented in GPU to allow both fast and flexible reconstructions.Main results. The parallel algorithms were able to accelerate the reconstructions by up to about6,100times in comparison to the serial Kaczmarz algorithm executed in the CPU, allowing for real-time applications. Reconstructions using the OpenMPIData dataset validated the proposed algorithms and demonstrated that they are able to provide both fast and accurate reconstructions. The calculation of the calibration matrix was accelerated by up to about 37 times.Significance. The parallel algorithms proposed in this work can provide single-frame MPI reconstructions in real time, with frame rates greater than 100 frames per second. The parallel calculation of the calibration matrix can be combined with the parallel reconstruction to deliver images in less time than the serial Kaczmarz reconstruction, potentially eliminating the need of storing the calibration matrix in the main memory, and providing the flexibility of redefining scanning and reconstruction parameters during execution.

To Authenticity, and Beyond! Building Safe and Fair Generative AI Upon the Three Pillars of Provenance.

Provenance facts, such as who made an image and how, can provide valuable context for users to make trust decisions about visual content. Against a backdrop of inexorable progress in generative AI for computer graphics, over two billion people will vote in public elections this year. Emerging standards and provenance enhancing tools promise to play an important role in fighting fake news and the spread of misinformation. In this article, we contrast three provenance enhancing technologies-metadata, fingerprinting, and watermarking-and discuss how we can build upon the complementary strengths of these three pillars to provide robust trust signals to support stories told by real and generative images. Beyond authenticity, we describe how provenance can also underpin new models for value creation in the age of generative AI. In doing so, we address other risks arising with generative AI such as ensuring training consent, and the proper attribution of credit to creatives who contribute their work to train generative models. We show that provenance may be combined with distributed ledger technology to develop novel solutions for recognizing and rewarding creative endeavor in the age of generative AI.

AlphaKnot 2.0: a web server for the visualization of proteins' knotting and a database of knotted AlphaFold-predicted models.

The availability of 3D protein models is rapidly increasing with the development of structure prediction algorithms. With the expanding availability of data, new ways of analysis, especially topological analysis, of those predictions are becoming necessary. Here, we present the updated version of the AlphaKnot service that provides a straightforward way of analyzing structure topology. It was designed specifically to determine knot types of the predicted structure models, however, it can be used for all structures, including the ones solved experimentally. AlphaKnot 2.0 provides the user's ability to obtain the knowledge necessary to assess the topological correctness of the model. Both probabilistic and deterministic knot detection methods are available, together with various visualizations (including a trajectory of simplification steps to highlight the topological complexities). Moreover, the web server provides a list of proteins similar to the queried model within AlphaKnot's database and returns their knot types for direct comparison. We pre-calculated the topology of high-quality models from the AlphaFold Database (4th version) and there are now more than 680.000 knotted models available in the AlphaKnot database. AlphaKnot 2.0 is available at https://alphaknot.cent.uw.edu.pl/.

Clarifying Causal Effects of Interest and Underlying Assumptions in Randomized and Nonrandomized Clinical Trials in Oncology Using Directed Acyclic Graphs and Single-World Intervention Graphs.

Recent clinical trials in oncology have used increasingly complex methodologies, such as causal inference methods for intercurrent events, external control, and covariate adjustment, posing challenges in clarifying the estimand and underlying assumptions. This article proposes expressing causal structures using graphical tools-directed acyclic graphs (DAGs) and single-world intervention graphs (SWIGs)-in the planning phase of a clinical trial. It presents five rules for selecting a sufficient set of adjustment variables on the basis of a diagram representing the clinical trial, along with three case studies of randomized and single-arm trials and a brief tutorial on DAG and SWIG. Through the case studies, DAGs appear effective in clarifying assumptions for identifying causal effects, although SWIGs should complement DAGs due to their limitations in the presence of intercurrent events in oncology research.

Numerical and graphical simulation of the non-linear fractional dynamical system of bone mineralization.

The objective of the present study was to improve our understanding of the complex biological process of bone mineralization by performing mathematical modeling with the Caputo-Fabrizio fractional operator. To obtain a better understanding of Komarova's bone mineralization process, we have thoroughly examined the boundedness, existence, and uniqueness of solutions and stability analysis within this framework. To determine how model parameters affect the behavior of the system, sensitivity analysis was carried out. Furthermore, the fractional Adams-Bashforth method has been used to carry out numerical and graphical simulations. Our work is significant owing to its comparison of fractional- and integer-order models, which provides novel insight into the effectiveness of fractional operators in representing the complex dynamics of bone mineralization.

Accurate prediction of drug combination risk levels based on relational graph convolutional network and multi-head attention.

BACKGROUND: Accurately identifying the risk level of drug combinations is of great significance in investigating the mechanisms of combination medication and adverse reactions. Most existing methods can only predict whether there is an interaction between two drugs, but cannot directly determine their accurate risk level. METHODS: In this study, we propose a multi-class drug combination risk prediction model named AERGCN-DDI, utilizing a relational graph convolutional network with a multi-head attention mechanism. Drug-drug interaction events with varying risk levels are modeled as a heterogeneous information graph. Attribute features of drug nodes and links are learned based on compound chemical structure information. Finally, the AERGCN-DDI model is proposed to predict drug combination risk level based on heterogenous graph neural network and multi-head attention modules. RESULTS: To evaluate the effectiveness of the proposed method, five-fold cross-validation and ablation study were conducted. Furthermore, we compared its predictive performance with baseline models and other state-of-the-art methods on two benchmark datasets. Empirical studies demonstrated the superior performances of AERGCN-DDI. CONCLUSIONS: AERGCN-DDI emerges as a valuable tool for predicting the risk levels of drug combinations, thereby aiding in clinical medication decision-making, mitigating severe drug side effects, and enhancing patient clinical prognosis.

PROTAX-GPU: a scalable probabilistic taxonomic classification system for DNA barcodes.

DNA-based identification is vital for classifying biological specimens, yet methods to quantify the uncertainty of sequence-based taxonomic assignments are scarce. Challenges arise from noisy reference databases, including mislabelled entries and missing taxa. PROTAX addresses these issues with a probabilistic approach to taxonomic classification, advancing on methods that rely solely on sequence similarity. It provides calibrated probabilistic assignments to a partially populated taxonomic hierarchy, accounting for taxa that lack references and incorrect taxonomic annotation. While effective on smaller scales, global application of PROTAX necessitates substantially larger reference libraries, a goal previously hindered by computational barriers. We introduce PROTAX-GPU, a scalable algorithm capable of leveraging the global Barcode of Life Data System (>14 million specimens) as a reference database. Using graphics processing units (GPU) to accelerate similarity and nearest-neighbour operations and the JAX library for Python integration, we achieve over a 1000 × speedup compared with the central processing unit (CPU)-based implementation without compromising PROTAX's key benefits. PROTAX-GPU marks a significant stride towards real-time DNA barcoding, enabling quicker and more efficient species identification in environmental assessments. This capability opens up new avenues for real-time monitoring and analysis of biodiversity, advancing our ability to understand and respond to ecological dynamics. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

Maboss for HPC environments: implementations of the continuous time Boolean model simulator for large CPU clusters and GPU accelerators.

BACKGROUND: Computational models in systems biology are becoming more important with the advancement of experimental techniques to query the mechanistic details responsible for leading to phenotypes of interest. In particular, Boolean models are well fit to describe the complexity of signaling networks while being simple enough to scale to a very large number of components. With the advance of Boolean model inference techniques, the field is transforming from an artisanal way of building models of moderate size to a more automatized one, leading to very large models. In this context, adapting the simulation software for such increases in complexity is crucial. RESULTS: We present two new developments in the continuous time Boolean simulators: MaBoSS.MPI, a parallel implementation of MaBoSS which can exploit the computational power of very large CPU clusters, and MaBoSS.GPU, which can use GPU accelerators to perform these simulations. CONCLUSION: These implementations enable simulation and exploration of the behavior of very large models, thus becoming a valuable analysis tool for the systems biology community.

Sparse Spiking Neural-Like Membrane Systems on Graphics Processing Units.

The parallel simulation of Spiking Neural P systems is mainly based on a matrix representation, where the graph inherent to the neural model is encoded in an adjacency matrix. The simulation algorithm is based on a matrix-vector multiplication, which is an operation efficiently implemented on parallel devices. However, when the graph of a Spiking Neural P system is not fully connected, the adjacency matrix is sparse and hence, lots of computing resources are wasted in both time and memory domains. For this reason, two compression methods for the matrix representation were proposed in a previous work, but they were not implemented nor parallelized on a simulator. In this paper, they are implemented and parallelized on GPUs as part of a new Spiking Neural P system with delays simulator. Extensive experiments are conducted on high-end GPUs (RTX2080 and A100 80GB), and it is concluded that they outperform other solutions based on state-of-the-art GPU libraries when simulating Spiking Neural P systems.

Exploring q-Bernstein-Bézier surfaces in Minkowski space: Analysis, modeling, and applications.

In this paper, we examine q-Bernstein-Bézier surfaces in Minkowski space-[Formula: see text] with q as the shape parameter. These surfaces, a generalization of Bézier surfaces, have applications in mathematics, computer-aided geometric design, and computer graphics for the surface formation and modeling. We analyze the timelike and spacelike cases of q-Bernstein-Bézier surfaces using known boundary control points. The mean curvature and Gaussian curvature of these q-Bernstein-Bézier surfaces are computed by finding the respective fundamental coefficients. We also investigate the shape operator dependency for timelike and spacelike q-Bernstein-Bézier surfaces in Minkowski space-[Formula: see text], and provide biquadratic and bicubic q-Bernstein-Bézier surfaces as illustrative examples for different values of the shape controlling parameter q.

Subjective perception of visual field defects using random noise-moving images in patients with glaucoma: A comparison of computer graphics and analog noises.

PURPOSE: Random noise-moving images (noises) can make glaucoma patients with no subjective symptoms aware of visual field abnormalities. To explore this concept, we developed a noise using computer graphics (CG) and investigated the difference in the subjective perception of visual field abnormalities between CG and conventional analog noises. METHODS: We enrolled individuals with glaucoma (205 eyes), preperimetric glaucoma (PPG; 19 eyes), and normal eyes (35 eyes). For a CG noise, a series of still images was made by randomly selecting five monochromatic tones on 2-mm square dots, and these images were drawn at 60 frames per second (fps) to create a noise-moving image. The participants were asked to describe their perceived shadows on a paper. The results were categorized as follows based on the pattern deviation probability map of the Humphrey field analyzer (HFA): "agreement," "partial agreement," "disagreement," and "no response." The glaucoma stage was classified into four stages, from M1 to M4, based on the HFA's mean deviation. RESULT: The detection rates (agreement and partial agreement) were 80.5% and 65.4% for the CG and analog noises, respectively, with CG noise showing a significantly higher detection rate in all glaucoma eyes (P < 0.001). The detection rates tended to increase as the glaucoma stage progressed, and in Stage M3, these were 93.9% and 78.8% for the CG and analog noises, respectively. The PPG eyes did not exhibit subjective abnormalities for both noises. The specificity values were 97.1% and 100% for the CG and analog noises, respectively. CONCLUSION: The CG noise is more effective than the analog noise in evaluating the subjective perception of visual field abnormalities in patients with glaucoma.

Learning dynamic graph representations through timespan view contrasts.

The rich information underlying graphs has inspired further investigation of unsupervised graph representation. Existing studies mainly depend on node features and topological properties within static graphs to create self-supervised signals, neglecting the temporal components carried by real-world graph data, such as timestamps of edges. To overcome this limitation, this paper explores how to model temporal evolution on dynamic graphs elegantly. Specifically, we introduce a new inductive bias, namely temporal translation invariance, which illustrates the tendency of the identical node to keep similar labels across different timespans. Based on this assumption, we develop a dynamic graph representation framework CLDG that encourages the node to maintain locally consistent temporal translation invariance through contrastive learning on different timespans. Except for standard CLDG which only considers explicit topological links, our further proposed CLDG＋＋additionally employs graph diffusion to uncover global contextual correlations between nodes, and designs a multi-scale contrastive learning objective composed of local-local, local-global, and global-global contrasts to enhance representation capabilities. Interestingly, by measuring the consistency between different timespans to shape anomaly indicators, CLDG and CLDG＋＋are seamlessly integrated with the task of spotting anomalies on dynamic graphs, which has broad applications in many high-impact domains, such as finance, cybersecurity, and healthcare. Experiments demonstrate that CLDG and CLDG＋＋both exhibit desirable performance in downstream tasks including node classification and dynamic graph anomaly detection. Moreover, CLDG significantly reduces time and space complexity by implicitly exploiting temporal cues instead of complicated sequence models. The code and data are available at https://github.com/yimingxu24/CLDG.

Semantic units: organizing knowledge graphs into semantically meaningful units of representation.

BACKGROUND: In today's landscape of data management, the importance of knowledge graphs and ontologies is escalating as critical mechanisms aligned with the FAIR Guiding Principles-ensuring data and metadata are Findable, Accessible, Interoperable, and Reusable. We discuss three challenges that may hinder the effective exploitation of the full potential of FAIR knowledge graphs. RESULTS: We introduce "semantic units" as a conceptual solution, although currently exemplified only in a limited prototype. Semantic units structure a knowledge graph into identifiable and semantically meaningful subgraphs by adding another layer of triples on top of the conventional data layer. Semantic units and their subgraphs are represented by their own resource that instantiates a corresponding semantic unit class. We distinguish statement and compound units as basic categories of semantic units. A statement unit is the smallest, independent proposition that is semantically meaningful for a human reader. Depending on the relation of its underlying proposition, it consists of one or more triples. Organizing a knowledge graph into statement units results in a partition of the graph, with each triple belonging to exactly one statement unit. A compound unit, on the other hand, is a semantically meaningful collection of statement and compound units that form larger subgraphs. Some semantic units organize the graph into different levels of representational granularity, others orthogonally into different types of granularity trees or different frames of reference, structuring and organizing the knowledge graph into partially overlapping, partially enclosed subgraphs, each of which can be referenced by its own resource. CONCLUSIONS: Semantic units, applicable in RDF/OWL and labeled property graphs, offer support for making statements about statements and facilitate graph-alignment, subgraph-matching, knowledge graph profiling, and for management of access restrictions to sensitive data. Additionally, we argue that organizing the graph into semantic units promotes the differentiation of ontological and discursive information, and that it also supports the differentiation of multiple frames of reference within the graph.

Wagner diagram for modeling O2pathway-calculation and graphical display by the Helsinki O2Pathway Tool.

Objective.Maximal O2uptake (V˙O2max) reflects the individual's maximal rate of O2transport and utilization through the integrated whole-body pathway composed of the lungs, heart, blood, circulation, and metabolically active tissues. As such,V˙O2maxis strongly associated with physical capacity as well as overall health and thus acts as one predictor of physical performance and as a vital sign in determination of status and progress of numerous clinical conditions. Quantifying the contribution of single parts of the multistep O2pathway toV˙O2maxprovides mechanistic insights into exercise (in)tolerance and into therapy-, training-, or disuse-induced adaptations at individual or group levels. We developed a desktop application (Helsinki O2Pathway Tool-HO2PT) to model numerical and graphical display of the O2pathway based on the 'Wagner diagram' originally formulated by Peter D. Wagner and his colleagues.Approach.The HO2PT was developed and programmed in Python to integrate the Fick principle and Fick's law of diffusion into a computational system to import, calculate, graphically display, and export variables of the Wagner diagram.Main results.The HO2PT models O2pathway both numerically and graphically according to the Wagner diagram and pertains to conditions under which the mitochondrial oxidative capacity of metabolically active tissues exceeds the capacity of the O2transport system to deliver O2to the mitochondria. The tool is based on the Python open source code and libraries and freely and publicly available online for Windows, macOS, and Linux operating systems.Significance.The HO2PT offers a novel functional and demonstrative platform for those interested in examiningV˙O2maxand its determinants by using the Wagner diagram. It will improve access to and usability of Wagner's and his colleagues' integrated physiological model and thereby benefit users across the wide spectrum of contexts such as scientific research, education, exercise testing, sports coaching, and clinical medicine.

Drawing human pedigree charts with DrawPed.

Creating pedigree charts is a recurring task in biomedical research, but there are few online tools for drawing complex human pedigrees available and even fewer are free. With DrawPed we aim to close this gap. DrawPed automatically draws pedigree charts from standard PED format pedigree files. Users can also create pedigrees from scratch and interactively edit existing pedigrees. The application can display conditions not captured in a PED file such as deceased persons or suspected consanguinity of parents. Pedigree charts are displayed as SVGs, which are scalable and hence publication-ready. Pedigrees can be exported as PED files for storage, exchange, or use in other applications. DrawPed is open source and freely available at https://www.genecascade.org/DrawPed/.