Multiple Subroutines Research Articles

Deep-SDM: A Unified Computational Framework for Sequential Data Modeling Using Deep Learning Models

Deep-SDM is a unified layer framework built on TensorFlow/Keras and written in Python 3.12. The framework aligns with the modular engineering principles for the design and development strategy. Transparency, reproducibility, and recombinability are the framework’s primary design criteria. The platform can extract valuable insights from numerical and text data and utilize them to predict future values by implementing long short-term memory (LSTM), gated recurrent unit (GRU), and convolution neural network (CNN). Its end-to-end machine learning pipeline involves a sequence of tasks, including data exploration, input preparation, model construction, hyperparameter tuning, performance evaluations, visualization of results, and statistical analysis. The complete process is systematic and carefully organized, from data import to model selection, encapsulating it into a unified whole. The multiple subroutines work together to provide a user-friendly and conducive pipeline that is easy to use. We utilized the Deep-SDM framework to predict the Nepal Stock Exchange (NEPSE) index to validate its reproducibility and robustness and observed impressive results.

Induction of multiple subroutines of regulated necrosis in murine macrophages by natural BH3-mimetic gossypol.

Macrophages are critical sentinel cells armed with multiple regulated necrosis pathways, including pyroptosis, apoptosis followed by secondary necrosis, and necroptosis, and are poised to undergo distinct form(s) of necrosis for tackling dangers of pathogenic infection or toxic exposure. The natural BH3-mimetic gossypol is a toxic phytochemical that can induce apoptosis and/or pyroptotic-like cell death, but what exact forms of regulated necrosis are induced remains largely unknown. Here we demonstrated that gossypol induces pyroptotic-like cell death in both unprimed and lipopolysaccharide-primed mouse bone marrow-derived macrophages (BMDMs), as evidenced by membrane swelling and ballooning accompanied by propidium iodide incorporation and lactic acid dehydrogenase release. Notably, gossypol simultaneously induces the activation of both pyroptotic and apoptotic (followed by secondary necrosis) pathways but only weakly activates the necroptosis pathway. Unexpectedly, gossypol-induced necrosis is independent of nucleotide-binding oligomerization domain-like receptor family pyrin domain containing 3 (NLRP3) inflammasome, as neither inhibitor for the NLRP3 pathway nor NLRP3 deficiency protects the macrophages from the necrosis. Furthermore, necrotic inhibitors or even pan-caspase inhibitor alone does not or only partly inhibit such necrosis. Instead, a combination of inhibitors composed of pan-caspase inhibitor IDN-6556, RIPK3 inhibitor GSK'872 and NADPH oxidase inhibitor GKT137831 not only markedly inhibits the necrosis, with all apoptotic and pyroptotic pathways being blocked, but also attenuates gossypol-induced peritonitis in mice. Lastly, the activation of the NLRP3 pathway and apoptotic caspase-3 appears to be independent of each other. Collectively, gossypol simultaneously induces the activation of multiple subroutines of regulated necrosis in macrophages depending on both apoptotic and inflammatory caspases.

A Method to Custom-build Equations of Drug Concentration as a Function of Real Time in the One-Compartment Open Model and Their Application in Multiple Intravenous Bolus and Multiple Oral Doses

A method to custom-build expressions of drug concentration as a function of total time in a one-compartment pharmacokinetic model for multiple-dose schedules is developed and successfully applied in four dosing schedules that combined administration of multiple IV bolus and oral maintenance and loading doses. The method consists of writing the terms of the mathematical sequence from the analytical solutions to drug concentration using total time, instead of time within dosing interval, extracting the pattern of the respective sequences, and finally, determining the partial sums of the series that relate to drug concentration to dose number and real-time, for each particular administration route and dosing schedule. Multiple subroutines written in Fortran language demonstrated the potential of these equations to investigate the effect of dose size on peak plasma drug concentration and peak time after multiple oral administrations and for calculating and refining experimentally determined time-dependent pharmacokinetic parameters such as non steady-state average concentration values and Area Under the Curve (AUC). It is shown that the only truly independent of dose size peak time is that of the first oral dose (). A mathematical expression was derived that relates the time to reach non steady-state peak times after multiple oral doses to the absorption and elimination rate constants for the first time. For repetitive oral dose administration, the will always be the longest peak time, while the shortest time to reach maximum plasma drug concentration will be at steady-state conditions.

Faster Algorithms for All-Pairs Small Stretch Distances in Weighted Graphs

Let G=(V,E) be a weighted undirected graph, with non-negative edge weights. We consider the problem of efficiently computing approximate distances between all pairs of vertices in G. While many efficient algorithms are known for this problem in unweighted graphs, not many results are known for this problem in weighted graphs. Zwick (J. Assoc. Comput. Mach. 49:289–317, 2002) showed that for any fixed e>0, stretch 1+e distances (a path in G between u,v∈V is said to be of stretch t if its length is at most t times the distance between u and v in G) between all pairs of vertices in a weighted directed graph on n vertices can be computed in $\tilde{O}(n^{\omega})$ time, where ω 0 in G can be computed in expected time O(n 9/4). This algorithm uses a fast rectangular matrix multiplication subroutine. We also present a combinatorial algorithm (that is, it does not use fast matrix multiplication) with expected running time O(n 9/4) for computing all-pairs stretch 5/2 distances in G. This combinatorial algorithm will serve as a key step in our all-pairs stretch 2+e distances algorithm.

Efficient computation of the genomic relationship matrix and other matrices used in single‐step evaluation

Genomic evaluations can be calculated using a unified procedure that combines phenotypic, pedigree and genomic information. Implementation of such a procedure requires the inverse of the relationship matrix based on pedigree and genomic relationships. The objective of this study was to investigate efficient computing options to create relationship matrices based on genomic markers and pedigree information as well as their inverses. SNP maker information was simulated for a panel of 40 K SNPs, with the number of genotyped animals up to 30 000. Matrix multiplication in the computation of the genomic relationship was by a simple 'do' loop, by two optimized versions of the loop, and by a specific matrix multiplication subroutine. Inversion was by a generalized inverse algorithm and by a LAPACK subroutine. With the most efficient choices and parallel processing, creation of matrices for 30 000 animals would take a few hours. Matrices required to implement a unified approach can be computed efficiently. Optimizations can be either by modifications of existing code or by the use of efficient automatic optimizations provided by open source or third-party libraries.

Wedderburn Rank Reduction and Krylov Subspace Method for Tensor Approximation. Part 1: Tucker Case

New algorithms are proposed for the Tucker approximation of a 3-tensor, that access it using only the tensor-by-vector-by-vector multiplication subroutine. In the matrix case, Krylov methods are methods of choice to approximate the dominant column and row subspaces of a sparse or structured matrix given through the matrix-by-vector multiplication subroutine. Using the Wedderburn rank reduction formula, we propose an algorithm of matrix approximation that computes Krylov subspaces and allows generalization to the tensor case. Several variants of proposed tensor algorithms differ by pivoting strategies, overall cost and quality of approximation. By convincing numerical experiments we show that the proposed methods are faster and more accurate than the minimal Krylov recursion, proposed recently by Elden and Savas.

Algorithm-based fault tolerance applied to high performance computing

We present a new approach to fault tolerance for High Performance Computing system. Our approach is based on a careful adaptation of the Algorithm-Based Fault Tolerance technique [K. Huang, J. Abraham, Algorithm-based fault tolerance for matrix operations, IEEE Transactions on Computers (Spec. Issue Reliable & Fault-Tolerant Comp.) 33 (1984) 518–528] to the need of parallel distributed computation. We obtain a strongly scalable mechanism for fault tolerance. We can also detect and correct errors (bit-flip) on the fly of a computation. To assess the viability of our approach, we have developed a fault-tolerant matrix–matrix multiplication subroutine and we propose some models to predict its running time. Our parallel fault-tolerant matrix–matrix multiplication scores 1.4 TFLOPS on 484 processors (cluster jacquard.nersc.gov) and returns a correct result while one process failure has happened. This represents 65% of the machine peak efficiency and less than 12% overhead with respect to the fastest failure-free implementation. We predict (and have observed) that, as we increase the processor count, the overhead of the fault tolerance drops significantly.

Regulators Acting in Combinatorial Codes Also Act Independently in Single Differentiating Neurons

In the Drosophila ventral nerve cord, a small number of neurons express the LIM-homeodomain gene apterous (ap). These ap neurons can be subdivided based upon axon pathfinding and their expression of neuropeptidergic markers. ap, the zinc finger gene squeeze, the bHLH gene dimmed, and the BMP pathway are all required for proper specification of these cells. Here, using several ap neuron terminal differentiation markers, we have resolved how each of these factors contributes to ap neuron diversity. We find that these factors interact genetically and biochemically in subtype-specific combinatorial codes to determine certain defining aspects of ap neuron subtype identity. However, we also find that ap, dimmed, and squeeze additionally act independently of one another to specify certain other defining aspects of ap neuron subtype identity. Therefore, within single neurons, we show that single regulators acting in numerous molecular contexts differentially specify multiple subtype-specific traits.

Double Subroutine Self‐Assembly; Spontaneous Generation of a Nanocyclic Dodecanuclear Cu1 Inorganic Architecture

AbstractThe newly synthesised ligand 2 combines binding components known to undergo specific and distinct self‐assembly processes with Cu1 ions. It complexes Cu1 to form, in almost quantitative yield, a large inorganic architecture 1 made up from four ligand molecules and twelve metal ions. The structure of 1 was ascertained by X‐ray radiocrystallography as well as by NMR spectroscopy and electrospray mass spectrometry. It consists of a macrocycle of nanometric dimension with an external diameter of 28 Å; the central cavity has a diameter of 11 Å, which contains four PF−6 anions as well as solvent molecules. The spontaneous formation of 1 results from a self‐assembly process based on a “program” combining two assembly subroutines, each specific to one of the ligand subunits. Self‐assembly through double or, more generally, multiple subroutines can be used to generate a wide variety of highly complex inorganic supramolecular architectures by combination of two or more assembly processes.

Review of Some Methods of Programming of Literal Developments in Celestial Mechanics

view Abstract Citations (12) References (2) Co-Reads Similar Papers Volume Content Graphics Metrics Export Citation NASA/ADS Review of Some Methods of Programming of Literal Developments in Celestial Mechanics Kovalevsky, J. Abstract A comparative study of two programs written to perform algebra on trigonometric series with polynomial coefficients is given. One program is due to D. Barton and the other one to a group from the Bureau des Longitudes and Meudon Observatory. The internal arrangement of the terms of the series in the computer and the multiplication subroutine are described for both programs. Finally, some general principles that render such programs efficient are set forth. Publication: The Astronomical Journal Pub Date: April 1968 DOI: 10.1086/110618 Bibcode: 1968AJ.....73..203K full text sources ADS |