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Iterative Random Forest (iRF) is an improvement upon the classic Random Forest, using weighted iterations to distill the forests. Ranger is a C++ implementation of random forest or recursive partitioning, particularly suited for high dimensional data. Ranger-Based iRF uses Ranger as a base Random Forest codebase upon which iterative and scalability aspects have been added.
SLiDE (Scalable Linked Dynamic Equilibrium) replicates the blueNOTE (National Open source Tools for general Equilibrium analysis) datastream from the Wisconsin National Data Consortium. From there, it produces a recursive dynamic computable general equilibrium model of the US states and eventually the global/national economies. The datastream operations have been set up to allow for scalability of both regions and sectors represented. The model has the capability to flexibly define functional forms similar to other general equilibrium model construction software.
Hydra Autoconfig is an algorithm and software program to automatically configure a resilient network of independent ASICs that are capable of being connected as a Hydra network. The Hydra network itself is described in an invention disclosure titled: "Ad-Hoc Networks of Readout ASICs for Reliable Detector Instrumentation" (2020-091). The Hydra Autoconfig software works by first configuring a Hydra node. Then it recursively builds a Hydra network by attempting to link to each available upstream node in succession, keeping links that are verified. It then repeats on each newly generated node until no possible links remain. Once it is so configured, a reliable Hydra network of ASICs remains that can be reconfigured later to respond to damage or malfunction of one or more of the constituent ASICs.
Compiler optimizations can alter the numerical results of scientific computing applications. When numerical results differ significantly between compilers, optimization levels, and floating-point hardware, these numerical inconsistencies can impact programming productivity. Ciel is a framework that helps programmers identify locations in the source code that are affected by compiler optimizations in CPU and GPU code. Ciel uses a floating-point precision enhancement strategy, guided by a recursive bisection search algorithm with increasing search granularity, to identify the program expressions that induce numerical inconsistencies due to compiler optimizations.
The software utilizes frequency, amplitude, and phase features from sensor signals (either raw or processed) that are extracted using recursive frequency analysis, enabling (1) understanding of reactor operations under different operating conditions, (2) identifying of quiescent frequency ranges for sensor development, (3) system controls (4) predictive analytics, (5) structural health monitoring, and (6) loose part monitoring.
SAND2023-05510O GNATFinder is a software tool for extracting graphical neural activity threads (GNATs) from spiking neural networks. GNATFinder efficiently extracts GNATs from spiking neural network data. A GNAT is a graph that represents the causal relationships between individual spikes in a spiking network using a combination of the network connectivity structure and the timing of individual spikes. The software allows for identifying similar, repeating threads that often reappear in a dataset. Using quadtree data structures to recursively subdivide the time interval over which spikes were produced by the spiking network, GNATFinder allows for efficient pairwise comparisons of spike times to determine the degree of causal relatedness among all pairs of spikes in a dataset. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
pyzag is a library for efficiently training generic models defined with a recursive nonlinear function. We developed it primarily to provide an efficient means to train NEML2 models it can be used to train other, more general types of models.
The code implements the Isolation Forest (IFML) algorithm within the digital twin (DT) of the AGN-201 nuclear reactor. The DT captures real-time operational data including control rod positions, reactor power, and temperature. The IFML model isolates anomalies by detecting patterns that deviate from expected operational behavior. The algorithm recursively partitions the data and assigns anomaly scores based on the isolation of rare and different events. By tuning parameters specific to the reactor’s operational data, the IFML identifies deviations such as unauthorized material insertions or reactor reactivity shifts. The system streams data using LabView and integrates with the DeepLynx data warehouse for anomaly processing.
Reducing hallucination of Large Language Models (LLMs) is imperative for use in the sciences, where reliability and reproducibility are crucial. However, LLMs inherently lack long-term memory, making it a nontrivial, ad hoc, and inevitably biased task to fine-tune them on domain-specific literature and data. LLaMP is a multimodal retrieval-augmented generation (RAG) framework of hierarchical reasoning and acting (ReAct) agents that can dynamically and recursively interact with Materials Project to ground large language models on high-fidelity materials informatics.
This is a modification to 'cp' and 'mv' commands to make them multi-threaded. Simple benchmarks showed that multi-threading could reduce the time to copy a large Linux source directory by over 2x. The 'cp' and 'mv' utilities are part of the existing Coreutils (https://www.gnu.org/software/coreutils/) software package that get installed on all Linux distros. Changes: * Add '-j|--parallel ' flags to 'cp' and 'mv'. This allows the utilities to recursively copy regular files in directories in parallel. This does NOT parallelize multiple single file copies to a destination (like 'cp file2 file2 file3 dst/'). Along with this, add in new 'CP_NUM_THREADS' and 'MV_NUM_THREADS' environment variables to set the number of threads. This can be useful when you want to enable parallelism by default in /etc/profile. The maximum number of threads is internally capped to the number of CPUs. * Add a '-j' flag to 'sort' to complement its existing '--parallel' flag. This is only done for consistency with 'cp' and 'mv'. * Add test cases for the new flags. Also, run each 'cp' and 'mv' test both in single-threaded and multithreaded modes for extra coverage.
Tuning algorithmic parameters to optimize the performance of large, complicated computational codes is an important problem involving finding the optima and identifying regimes defined by non-smooth boundaries in black-box functions. Within the Bayesian optimization framework, the Gaussian process surrogate model produces smooth mean functions, but functions in the tuning problem are often non-smooth, which is exacerbated by the fact that we usually have limited sequential samples from the black-box function. Here, motivated by these issues encountered in tuning, we propose a novel Gaussian process model called a clustered Gaussian process (cGP), where the components are dynamically updated by clustering. In our studies, the performance of cGP can be better than stationary GPs in nearly 90% of the experiments and better than non-stationary GPs in nearly 70% of the repeated experiments while requiring less computational cost. cGP provides a novel approach for dynamic GP, computes more efficiently than recursive partitioning, and discovers non-smoothness regimes. We provide extensive experiments including high-performance computing (HPC) and industrial simulation functions to show the effectiveness of our methods.
BACKGROUND:Ontologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners and quality control checks, extracting dependencies and application-specific subsets, generating standard reports, and generating release files in multiple formats. Similar to more general software development, automation is the key to executing and managing these tasks effectively and to releasing more robust products in standard forms. For ontologies using the Web Ontology Language (OWL), the OWL API Java library is the foundation for a range of software tools, including the Protégé ontology editor. In the Open Biological and Biomedical Ontologies (OBO) community, we recognized the need to package a wide range of low-level OWL API functionality into a library of common higher-level operations and to make those operations available as a command-line tool. RESULTS:ROBOT (a recursive acronym for "ROBOT is an OBO Tool") is an open source library and command-line tool for automating ontology development tasks. The library can be called from any programming language that runs on the Java Virtual Machine (JVM). Most usage is through the command-line tool, which runs on macOS, Linux, and Windows. ROBOT provides ontology processing commands for a variety of tasks, including commands for converting formats, running a reasoner, creating import modules, running reports, and various other tasks. These commands can be combined into larger workflows using a separate task execution system such as GNU Make, and workflows can be automatically executed within continuous integration systems. CONCLUSIONS:ROBOT supports automation of a wide range of ontology development tasks, focusing on OBO conventions. It packages common high-level ontology development functionality into a convenient library, and makes it easy to configure, combine, and execute individual tasks in comprehensive, automated workflows. This helps ontology developers to efficiently create, maintain, and release high-quality ontologies, so that they can spend more time focusing on development tasks. It also helps guarantee that released ontologies are free of certain types of logical errors and conform to standard quality control checks, increasing the overall robustness and efficiency of the ontology development lifecycle.
Background: Development of distant metastases (DM) is associated with markedly decreased survival in parathyroid carcinoma (PC). We sought to identify factors associated with development of DM and to quantify the effect that development of DM had on overall survival (OS). Methods: Patients with surgically resected local/regional PC treated or surveilled at a tertiary-referral cancer hospital from 1980 to 2017 were included. We assessed the association between biochemical and clinicopathologic factors (preoperative parathyroid hormone (PTH) levels, sex, race, age, preoperative serum calcium levels, serum calcium levels at 6 months postop, tumor size, and extent of resection) with the development of DM. We also assessed the effect of development of DM on OS. Results: Seventy-five patients with PC were assessed; 17 (22.7%) developed DM at a median follow-up of 77 months. The cumulative incidence of DM in the cohort was 20, 30, and 38% at 5, 10, and 20 years respectively. Tumor size > 3.2 cm based on recursive partitioning analysis was the only significant predictor for development of DM (hazard ratio (HR) = 3.51; 95% confidence interval [CI] 1.04–11.91; p = 0.04). Median OS for the entire cohort was 17 years compared with 40 months for the cohort who developed DM. The HR for death after distant metastasis was 9.6 (95% CI 4.2–22.3; p < 0.0001). Conclusions: Development of distant metastasis during surveillance is associated with decreased OS, including late recurrences. Primary tumor size should be considered in future interval surveillance and development of treatment algorithms.
Introduction: Despite the crucially prognostic value of lymph node metastasis (LNM) in patients with medullary thyroid cancer (MTC), only the LNM compartment alone was reflected in the 8th edition of the American Joint Committee on Cancer (AJCC) system. Objective: This study aimed to incorporate the metastatic lymph node number and metastatic lymph node ratio to generate a more accurate and appropriate N staging system for patients with MTC based on recursive partitioning analysis. Design, Setting, and Patients: Two cohorts were included in the analysis, including 1374 MTC patients from the Surveillance, Epidemiology, and End Results database as the derivation cohort, and 164 patients from Fudan University Shanghai Cancer Center as the validation cohort. The predictive performance of the alternative proposed N staging system was compared with that of the 8th AJCC system by using the Harrell concordance index (C-index) and the area under the receiver operating characteristic curve (AUC). Results: In the derivation cohort, the C-index and the AUC at 10 years were 0.778 and 0.789, respectively, for the novel N staging system, and 0.749 and 0.741, respectively, for the 8th AJCC N staging system. Similar trends were also observed in the validation cohort. The proposed N staging system had a better prognostic performance. Conclusion: With some improvements, the novel N staging system for MTC suggested from this research may be assessed for potential adoption in the next edition of the AJCC N staging system.
The Cellular-Potts model is a powerful and ubiquitous framework for developing computational models for simulating complex multicellular biological systems. Cellular-Potts models (CPMs) are often computationally expensive due to the explicit modeling of interactions among large numbers of individual model agents and diffusive fields described by partial differential equations (PDEs). In this work, we develop a convolutional neural network (CNN) surrogate model using a U-Net architecture that accounts for periodic boundary conditions. We use this model to accelerate the evaluation of a mechanistic CPM previously used to investigate in vitro vasculogenesis. The surrogate model was trained to predict 100 computational steps ahead (Monte-Carlo steps, MCS), accelerating simulation evaluations by a factor of 562 times compared to single-core CPM code execution on CPU. Over short timescales of up to 3 recursive evaluations, or 300 MCS, our model captures the emergent behaviors demonstrated by the original Cellular-Potts model such as vessel sprouting, extension and anastomosis, and contraction of vascular lacunae. This approach demonstrates the potential for deep learning to serve as a step toward efficient surrogate models for CPM simulations, enabling faster evaluation of computationally expensive CPM simulations of biological processes.
Oyster aquaculture and restoration in the Chesapeake Bay are vital, yet hatcheries frequently struggle with inconsistent larval growth and sudden mass mortality events. Unpredictable disruptions in larval production cause large economic losses, represent a perceived risk to growers, and impede industry expansion. To better understand associations between production yield and its potential predictors, we applied machine learning (random forest, and neural network) and statistical (generalized additive model) models to a comprehensive dataset of environmental, water quality, and operational parameters from a Maryland oyster hatchery, aiming to identify key yield predictors and develop a robust forecasting tool. We used recursive Boruta algorithm for variable selection, pinpointing critical predictors, and employed cross-validation to fine-tune model settings. Shapley value analysis offered crucial insights into model interpretations, highlighting week number, Normalized Difference Vegetation Index, salinity, turbidity, and fecundity as primary drivers of yield variability. For low-yield cases, salinity-related variables were particularly important. Our findings provide an early warning system for potential production downturns, empowering hatchery operators to make data-driven decisions for optimizing water conditions, feeding schedules, and broodstock management. By boosting predictability and efficiency, this research directly supports economic stability of the oyster industry and ecological health of the Chesapeake Bay.
Due to the limited capacity of GPU memory, the majority of prior work on graph applications on GPUs has been restricted to graphs of modest sizes that fit in memory. Recent hardware and software advances make it possible to address much larger host memory transparently as a part of a feature known as unified virtual memory. While accessing host memory over an interconnect is understandably slower, the problem space has not been sufficiently explored in the context of a challenging workload with low computational intensity and an irregular data access pattern such as graph traversal. We analyse the performance of breadth first search (BFS) for several large graphs in the context of unified memory and identify the key factors that contribute to slowdowns. Next, we propose a lightweight offline graph reordering algorithm, HALO (Harmonic Locality Ordering), that can be used as a pre-processing step for static graphs. HALO yields speedups of 1.5x-1.9x over baseline in subsequent traversals. Our method specifically aims to cover large directed real world graphs in addition to undirected graphs whereas prior methods only account for the latter. Additionally, we demonstrate ties between the locality ordering problem and graph compression and show that prior methods from graph compression such as recursive graph bisection can be suitably adapted to this problem.
Cumulative Spatial Impact Layers™ (CSIL) is a GIS-based tool that summarizes spatio-temporal datasets based on overlapping features and attributes. Applying a recursive quadtree method and multiple additive frameworks, the CSIL tool allows users to analyze raster and vector datasets simultaneously by calculating data, record, or attribute density. The CSIL tool was designed based on the original approach (Bauer et al. 2015) and more information on the tool overall along with applications can be found in Romeo et al. 2019). Providing an efficient summary of disparate geospatial data, CSIL bridges the gap between understanding data and analysis. Bauer, J. R., Nelson, J., Romeo, L., Eynard, J., Sim, L., Halama, J., Rose, K., & Graham, J. (2015). A spatio-temporal approach to analyze broad risks and potential impacts associated with uncontrolled hydrocarbon release events in the offshore Gulf of Mexico (NETL-TRS-2-2015 EPAct Technical Report Series). U.S. Department of Energy, National Energy Technology Laboratory: Morgantown, WV; p 60. Romeo, L., Nelson, J., Wingo, P., Bauer, J., Justman, D., & Rose, K. (2019). Cumulative spatial impact layers: A novel multivariate spatio-temporal analytical summarization tool. Transactions in GIS.