Search Results (13)

Primary sclerosing cholangitis (PSC) is a chronic inflammatory precursor associated with an increased risk of intrahepatic cholangiocarcinoma (ICC), yet identifying malignant features within the persistent inflammatory background remains challenging. In this study, a background-deviation framework was applied to explore malignant-associated determinants during PSC-associated cholangiocarcinogenesis. Single-cell RNA sequencing data from PSC, ICC tumor tissues, and adjacent non-tumor tissues were integrated, followed by functional enrichment, CellChat analysis, Monocle 2 pseudotime reconstruction, Non-negative Matrix Factorization (NMF), STRING/Cytoscape network analysis, and diagnostic signature construction using LASSO regression and exhaustive best subset selection. Single-cell profiling suggested disease-associated cellular remodeling, including cholangiocyte expansion in ICC samples. Functional and intercellular communication analyses indicated a putative transition from an immune-dominant PSC state toward a hyper-biosynthetic ICC-associated phenotype, accompanied by a possible MIF receptor-usage shift from CXCR4 to CD44. Monocle 2 and NMF further identified candidate malignant-associated trajectories and meta-programs, with MYC/TP63-related regulatory signals emerging as potential contributors. Based on these exploratory findings, best subset selection identified a two-gene transcriptomic candidate signature comprising PMAIP1 and GADD45A, which showed promising discriminative performance in internal cross-validation and an external tumor-versus-adjacent validation cohort. These findings provide a transcriptomic basis for further validation of PSC-associated cholangiocarcinogenesis and potential ICC surveillance markers. Full article

Triple-negative breast cancer (TNBC) represents the most aggressive breast cancer subtype, with its highly heterogeneous tumor microenvironment posing substantial challenges for precision diagnosis and therapy. To address this, we aim to construct a novel prognostic framework based on tumor-immune interactions. Through integrative analysis of single-cell RNA sequencing data from 30 TNBC samples (106,132 cells), we identify key tumor expression metaprograms and uncover their interaction with an immunosuppressive dendritic-cell subset, a process associated with the NECTIN1–NECTIN4 axis. Leveraging these interactions, we developed and validated two immunological prognostic models using multi-cohort transcriptomic data, including the stress response tumor cell and pDC_CLEC4C prognostic model (SPSM) and the immune response tumor cell and pDC_CLEC4C prognostic model (IPSM). These models effectively stratified TNBC patients into distinct risk groups, with the low-risk group characterized by an immunologically active microenvironment and elevated expression of immune checkpoint genes, suggesting a potential responsiveness to immunotherapy. Furthermore, we identified several potential therapeutic agents, including imatinib and bortezomib. Collectively, our dual-model framework provides a tool for risk stratification, offers translational insights for precision treatment, and presents new directions for understanding TNBC heterogeneity and therapeutic development. Full article

The Geometric Algebra Fulcrum Library (GA-FuL) version 1.0 is introduced in this paper as a comprehensive computational library for geometric algebra (GA) and Clifford algebra (CA), in addition to other classical algebras. As a sophisticated software system, GA-FuL is useful for practical applications requiring numerical or symbolic prototyping, optimized code generation, and geometric visualization. A comprehensive overview of the GA-FuL design is provided, including its core design intentions, data-driven programming characteristics, and extensible layered design. The library is capable of representing and manipulating sparse multivectors of any dimension, scalar kind, or metric signature, including conformal and projective geometric algebras. Several practical and illustrative use cases of the library are provided to highlight its potential for mathematical, scientific, and engineering applications. The metaprogramming code optimization capabilities of GA-FuL are found to be unique among other software systems. This allows for the automated production of highly efficient code, based on powerful geometric modeling formulations provided by geometric algebra. Full article

This article introduces GTMesh, an open-source C++ library providing data structures and algorithms that facilitate the development of numerical schemes on general polytopal meshes. After discussing the features and limitations of the existing open-source alternatives, we focus on the theoretical description of geometry and the topology of conforming polytopal meshes in an arbitrary-dimensional space, using elements from graph theory. The data structure for mesh representation is explained. The main part of the article focuses on the implementation of data structures and algorithms (computation of measures, centers, normals, cell coloring) by using State-of-the-Art template metaprogramming techniques for maximum performance. The geometrical algorithms are designed to be valid regardless of the dimension of the underlying space. As an integral part of the library, a template implementation of class reflection in C++ has been created, which is sufficiently versatile and suitable for the development of numerical and data I/O algorithms working with generic data types. Finally, the use of GTMesh is demonstrated on a simple example of solving the heat equation by the finite volume method. Full article

The design of integrated energy systems (IESs) is a challenging task by reason of the highly complex configurations of these systems, the wide range of equipment used, and a diverse set of mathematical models and dedicated software employed to model it. The use of digital twins allows modeling in virtual space for various IES configurations. As a result, an optimal option of IES is obtained, which is implemented in the construction or expansion of a real-world IES. The paper proposes the principles of building digital twins for solving the IES design problems. The paper presents a new methodological approach developed by the authors to design an IES with the help of its digital twin. This approach includes the following components: the architecture of the software platform to create digital twins, a set of technologies and tools to implement the platform, methods to automatically construct a digital twin based on the Model-Driven Engineering concept, an algorithm to design an IES based on its digital twin, and principles to organize a computational process using a multi-agent approach. The results of the computational experiment using the software implementation of the IES digital twin components are presented for a test energy supply scheme. Full article

We present GenoMus, a new model for artificial musical creativity based on a procedural approach, able to represent compositional techniques behind a musical score. This model aims to build a framework for automatic creativity, that is easily adaptable to other domains beyond music. The core of GenoMus is a functional grammar designed to cover a wide range of styles, integrating traditional and contemporary composing techniques. In its encoded form, both composing methods and music scores are represented as one-dimensional arrays of normalized values. On the other hand, the decoded form of GenoMus grammar is human-readable, allowing for manual editing and the implementation of user-defined processes. Musical procedures (genotypes) are functional trees, able to generate musical scores (phenotypes). Each subprocess uses the same generic functional structure, regardless of the time scale, polyphonic structure, or traditional or algorithmic process being employed. Some works produced with the algorithm have been already published. This highly homogeneous and modular approach simplifies metaprogramming and maximizes search space. Its abstract and compact representation of musical knowledge as pure numeric arrays is optimized for the application of different machine learning paradigms. Full article

The extension for high-performance STFT (Short-Time Fourier Transform) algorithm written entirely in Java language for non-parallel computations is presented in the current paper. This solution could compete with the best available and most common algorithms supplied by libraries such as FFTW or JTransform. The main idea was to move complex computations and expensive functions to the program generation phase. Thus, only core and essential operations were executed during the runtime phase. Furthermore, new approach allows to eliminate the necessity for a rearrangement operation that uses the bit-reversal permutation technique. This article presents a brief description of the STFT solution that was worked out as an extension for the original application, in order to increase its efficiency. The solution remains a Stockham algorithm adapted using metaprogramming techniques and entails an additional reduction its execution time. Performance tests and experiments were conducted using a Java Platform and JMH library, which allowed for accurate execution time measurements. Major aspects of the Java VM like warm-up effects were also taken into consideration. Solution was applied into Electrical Capacitance Tomography measurement system in order to measure the material changes during the silo discharging industrial process. Full article

We present example quantum chemistry programs written with JaqalPaq, a python meta-programming language used to code in Jaqal (Just Another Quantum Assembly Language). These JaqalPaq algorithms are intended to be run on the Quantum Scientific Computing Open User Testbed (QSCOUT) platform at Sandia National Laboratories. Our exemplars use the variational quantum eigensolver (VQE) quantum algorithm to compute the ground state energies of the ${\mathrm{H}}_2$, ${\mathrm{HeH}}^{+}$, and $\mathrm{LiH}$ molecules. Since the exemplars focus on how to program in JaqalPaq, the calculations of the second-quantized Hamiltonians are performed with the PySCF python package, and the mappings of the fermions to qubits are obtained from the OpenFermion python package. Using the emulator functionality of JaqalPaq, we emulate how these exemplars would be executed on an error-free QSCOUT platform and compare the emulated computation of the bond-dissociation curves for these molecules with their exact forms within the relevant basis. Full article

In science and engineering using edge-embedded software, it is necessary to demonstrate the validity of results; therefore, the software responsible for operating an edge system is required to guarantee its own validity. The aim of this study is to guarantee the validity of the sampled-time filter and time domain as fundamental elements of autonomous edge software. This requires the update law of a sampled-time filter to be invoked once per every control cycle, which we guaranteed by using the proposed domain specific language implemented by a metaprogramming design pattern in modern C++ (C++11 and later). The time-domain elements were extracted from the software, after which they were able to be injected into the extracted software independent from the execution environment of the software. The proposed approach was shown to be superior to conventional approaches that only rely on the attention of programmers to detect design defects. This shows that it is possible to guarantee the validity of edge software by using only a general embedded programming language such as modern C++ without auxiliary verification and validation toolchains. Full article

There is sufficient information in the far-field of a radiating dipole antenna to rediscover the Maxwell Equations and the wave equations of light, including the speed of light $c.$ We created TheoSea, a Julia program that does this in a few seconds, and the key insight is that the compactness of theories drives the search. The program is a computational embodiment of the scientific method: observation, consideration of candidate theories, and validation. Full article

Despite the importance of sparse matrices in numerous fields of science, software implementations remain difficult to use for non-expert users, generally requiring the understanding of the underlying details of the chosen sparse matrix storage format. In addition, to achieve good performance, several formats may need to be used in one program, requiring explicit selection and conversion between the formats. This can be both tedious and error-prone, especially for non-expert users. Motivated by these issues, we present a user-friendly and open-source sparse matrix class for the C++ language, with a high-level application programming interface deliberately similar to the widely-used MATLAB language. This facilitates prototyping directly in C++ and aids the conversion of research code into production environments. The class internally uses two main approaches to achieve efficient execution: (i) a hybrid storage framework, which automatically and seamlessly switches between three underlying storage formats (compressed sparse column, red-black tree, coordinate list) depending on which format is best suited and/or available for specific operations, and (ii) a template-based meta-programming framework to automatically detect and optimise the execution of common expression patterns. Empirical evaluations on large sparse matrices with various densities of non-zero elements demonstrate the advantages of the hybrid storage framework and the expression optimisation mechanism. Full article

A Python non-uniform fast Fourier transform (PyNUFFT) package has been developed to accelerate multidimensional non-Cartesian image reconstruction on heterogeneous platforms. Since scientific computing with Python encompasses a mature and integrated environment, the time efficiency of the NUFFT algorithm has been a major obstacle to real-time non-Cartesian image reconstruction with Python. The current PyNUFFT software enables multi-dimensional NUFFT accelerated on a heterogeneous platform, which yields an efficient solution to many non-Cartesian imaging problems. The PyNUFFT also provides several solvers, including the conjugate gradient method, ℓ1 total variation regularized ordinary least square (L1TV-OLS), and ℓ1 total variation regularized least absolute deviation (L1TV-LAD). Metaprogramming libraries have been employed to accelerate PyNUFFT. The PyNUFFT package has been tested on multi-core central processing units (CPUs) and graphic processing units (GPUs), with acceleration factors of 6.3–9.5× on a 32-thread CPU platform and 5.4–13× on a GPU. Full article

This paper introduces the sensor-networked IoT model as a prototype to support the design of Body Area Network (BAN) applications for healthcare. Using the model, we analyze the synergistic effect of the functional requirements (data collection from the human body and transferring it to the top level) and non-functional requirements (trade-offs between energy-security-environmental factors, treated as Quality-of-Service (QoS)). We use feature models to represent the requirements at the earliest stage for the analysis and describe a model-driven methodology to design the possible BAN applications. Firstly, we specify the requirements as the problem domain (PD) variability model for the BAN applications. Next, we introduce the generative technology (meta-programming as the solution domain (SD)) and the mapping procedure to map the PD feature-based variability model onto the SD feature model. Finally, we create an executable meta-specification that represents the BAN functionality to describe the variability of the problem domain though transformations. The meta-specification (along with the meta-language processor) is a software generator for multiple BAN-oriented applications. We validate the methodology with experiments and a case study to generate a family of programs for the BAN sensor controllers. This enables to obtain the adequate measure of QoS efficiently through the interactive adjustment of the meta-parameter values and re-generation process for the concrete BAN application. Full article