Globsim v.3 – Improvements to an open-source software library for utilizing atmospheric reanalyses in point-scale land surface simulation

Since the coining of the term phylodynamics, the use of phylogenies to understand infectious disease dynamics has steadily increased. As methods for phylodynamics and genomic epidemiology have proliferated and grown more computationally expensive, the epidemiological information they extract has also evolved to better complement what can be learned through traditional epidemiological data. However, for genomic epidemiology to continue to grow, and for the accumulating number of pathogen genetic sequences to fulfill their potential widespread utility, the extraction of epidemiological information from phylogenies needs to be simpler and more efficient. Summary statistics provide a straightforward way of extracting information from a phylogenetic tree, but the relationship between these statistics and epidemiological quantities needs to be better understood. In this work we address this need via simulation. Using two different benchmark scenarios, we evaluate 74 tree summary statistics and their relationship to epidemiological quantities. In addition to evaluating the epidemiological information that can be inferred from each summary statistic, we also assess the computational cost of each statistic. This helps us optimize the selection of summary statistics for specific applications. Our study offers guidelines on essential considerations for designing or choosing summary statistics. The evaluated set of summary statistics, along with additional helpful functions for phylogenetic analysis, is accessible through an open-source Python library. Our research not only illuminates the main characteristics of many tree summary statistics but also provides valuable computational tools for real-world epidemiological analyses. These contributions aim to enhance our understanding of disease spread dynamics and advance the broader utilization of genomic epidemiology in public health efforts.Author SummaryOur study focuses on the use of phylogenetic analysis to get valuable epidemiological insights. We conducted a simulation study to evaluate 74 phylogenetic summary statistics and their relationship to epidemiological quantities, shedding light on the potential of each of these statistics to quantify different characteristics of disease spread dynamics. Additionally, we assessed the computational cost of each statistic. This gives us additional information when selecting a statistic for a particular application. Our research is available through an open-source Python library. This work helps us enhance our understanding of phylogenetic tree structures and contributes to the broader application of genomic epidemiology in public health initiatives.

Land surface temperature (LST) is a key variable for monitoring and evaluating global long-term climate change. However, existing satellite-based twice-daily LST products only date back to 2000, which makes it difficult to obtain robust long-term temperature variations. In this study, we developed the first global historical twice-daily LST dataset (GT-LST), with a spatial resolution of 0.05°, using Advanced Very High Resolution Radiometer (AVHRR) Level-1b Global Area Coverage (GAC) data from 1981 to 2005. The GT-LST product was generated using four main processes: (1) GAC data reading, calibration, and pre-processing using open-source Python libraries; (2) cloud detection using the AVHRR-Phase I algorithm; (3) land surface emissivity estimation using an improved method considering annual land cover changes; and (4) LST retrieval based on a nonlinear generalized split-window algorithm. Validation with in situ measurements from Surface Radiation Budget (SURFRAD) sites showed that the overall root-mean-square errors of GT-LST varied from 2.0 K to 3.9 K, and nighttime LSTs were typically better than daytime LSTs. Inter-comparison with a common LST product (i.e., MYD11A1) revealed that the overall root-mean-square-difference (RMSD) was approximately 3.2 K, a positive bias was obtained for GT-LST, and relatively large RMSDs were obtained during the daytime, spring and summer. Furthermore, we compared our newly generated dataset with a global AVHRR daytime LST product at the selected measurements of SURFRAD sites (i.e., measurements of these two satellite datasets were valid), which revealed similar accuracies for the two datasets. However, GT-LST can additionally provide nighttime LST, which can be combined with daytime observations estimating relatively accurate monthly mean LST under all-sky conditions, with RMSE of 4.1 K. Finally, we compared GT-LST with a regional twice-daily AVHRR LST product over continental Africa in different seasons, with RMSDs ranging from 2.1 to 4.3 K. Considering these advantages, the proposed dataset provides a better data source for a range of research applications. GT-LST is freely available at https://doi.org/10.5281/zenodo.7113080 (1981–2000) (Li et al., 2022a) and https://doi.org/10.5281/zenodo.7134158 (2001–2005) (Li et al., 2022b).

Abstract. Land surface temperature (LST) is a key variable for monitoring and evaluating global long-term climate change. However, existing satellite-based twice-daily LST products only date back to 2000, which makes it difficult to obtain robust long-term temperature variations. In this study, we developed the first global historical twice-daily LST dataset (GT-LST), with a spatial resolution of 0.05∘, using Advanced Very High Resolution Radiometer (AVHRR) Level-1b Global Area Coverage (GAC) data from 1981 to 2021. The GT-LST product was generated using four main processes: (1) GAC data reading, calibration, and preprocessing using open-source Python libraries; (2) cloud detection using the AVHRR-Phase I algorithm; (3) land surface emissivity estimation using an improved method considering annual land cover changes; (4) LST retrieval based on a nonlinear generalized split-window algorithm. Validation with in situ measurements from Surface Radiation Budget (SURFRAD) sites and Baseline Surface Radiation Network sites showed that the overall root-mean-square errors (RMSEs) of GT-LST varied from 1.6 to 4.0 K, and nighttime LSTs were typically better than daytime LSTs. Intercomparison with the Moderate Resolution Imaging Spectroradiometer LST products (MYD11A1 and MYD21A1) revealed that the overall root-mean-square difference (RMSD) was approximately 3.0 K. Compared with MYD11A1 LST, GT-LST was overestimated, and relatively large RMSDs were obtained during the daytime, spring, and summer, whereas the significantly smaller positive bias was obtained between GT-LST and MYD21A1 LST. Furthermore, we compared our newly generated dataset with a global AVHRR daytime LST product at the selected measurements of SURFRAD sites (i.e., measurements of these two satellite datasets were valid), which revealed similar accuracies for the two datasets. However, GT-LST can additionally provide nighttime LST, which can be combined with daytime observations estimating relatively accurate monthly mean LST, with an RMSE of 2.7 K. Finally, we compared GT-LST with a regional twice-daily AVHRR LST product over continental Africa in different seasons, with RMSDs ranging from 2.1 to 4.3 K. Considering these advantages, the proposed dataset provides a better data source for a range of research applications. GT-LST is freely available at https://doi.org/10.5281/zenodo.7113080 (1981–2000) (Li et al., 2022a), https://doi.org/10.5281/zenodo.7134158 (2001–2005) (Li et al., 2022b), and https://doi.org/10.5281/zenodo.7813607 (2006–2021) (J. H. Li et al., 2023).

IMDLIB: An open-source library for retrieval, processing and spatiotemporal exploratory assessments of gridded meteorological observation datasets over India

An optimization methodology has been developed for the aluminum alloy wheel casting process. The methodology is focused on improving the timing of cooling processes in a die to achieve improved casting quality. This methodology utilizes (1) a casting process model, which was developed within the commercial finite element package, ABAQUS™—ABAQUS is a trademark of Dassault Systems; (2) a Python-based results extraction procedure; and (3) a numerical optimization module from the open-source Python library, Scipy. To achieve optimal casting quality, a set of constraints have been defined to ensure directional solidification, and an objective function, based on the solidification cooling rates, has been defined to either maximize, or target a specific, cooling rate. The methodology has been applied to a series of casting and die geometries with different cooling system configurations, including a 2-D axisymmetric wheel and die assembly generated from a full-scale prototype wheel. The results show that, with properly defined constraint and objective functions, solidification conditions can be improved and optimal cooling conditions can be achieved leading to process productivity and product quality improvements.

Current interpretability methods for Large Language Models (LLMs) operate on a fundamental yet flawed assumption: that subword tokens represent independent semantic units.We prove that this assumption creates a fidelity bottleneck in Morphologically Rich Languages (MRLs), where semantic meaning is densely encoded in sub-token morphemes.We term this phenomenon the Tokenization-Morphology Misalignment (TMM).To resolve TMM, we introduce MAFEX (Morpheme-Aligned Faithful Explanations), a theoretically grounded framework that redefines feature attribution as a linear projection from the computational (token) basis to the linguistic (morpheme) basis.We evaluate our method on a diverse suite of Turkish LLMs, including BERTurk, BERTurk-Sentiment, Cosmos-BERT, and Kumru-2B.On our embedded benchmark (N = 20), MAFEX achieves an average F1@1 of 91.25% compared to 13.75% for standard token-level baselines (IG, SHAP, DeepLIFT), representing a +77.5% absolute improvement, establishing it as the new standard for faithful multilingual interpretability.* The MAFEX framework and evaluation suite is available as a comprehensive, open-source Python library at https: //github.com/anilyagiz/mafex(pip install mafex) to facilitate reproducible multilingual XAI research.

Cloud2FEM: A finite element mesh generator based on point clouds of existing/historical structures

We present ichor, an open-source Python library that simplifies data management in computational chemistry and streamlines machine learning force field development. Ichor implements many easily extensible file management tools, in addition to a lazy file reading system, allowing efficient management of hundreds of thousands of computational chemistry files. Data from calculations can be readily stored into databases for easy sharing and post-processing. Raw data can be directly processed by ichor to create machine learning-ready datasets. In addition to powerful data-related capabilities, ichor provides interfaces to popular workload management software employed by High Performance Computing clusters, making for effortless submission of thousands of separate calculations with only a single line of Python code. Furthermore, a simple-to-use command line interface has been implemented through a series of menu systems to further increase accessibility and efficiency of common important ichor tasks. Finally, ichor implements general tools for visualization and analysis of datasets and tools for measuring machine-learning model quality both on test set data and in simulations. With the current functionalities, ichor can serve as an end-to-end data procurement, data management, and analysis solution for machine-learning force-field development.

MOCAT-pySSEM: An open-source Python library and user interface for orbital debris and source sink environmental modeling

BackgroundClinical natural language processing (cNLP) systems are of crucial importance due to their increasing capability in extracting clinically important information from free text contained in electronic health records (EHRs). The conversion of a nonstructured representation of a patient’s clinical history into a structured format enables medical doctors to generate clinical knowledge at a level that was not possible before. Finally, the interpretation of the insights gained provided by cNLP systems has a great potential in driving decisions about clinical practice. However, carrying out robust evaluations of those cNLP systems is a complex task that is hindered by a lack of standard guidance on how to systematically approach them.ObjectiveOur objective was to offer natural language processing (NLP) experts a methodology for the evaluation of cNLP systems to assist them in carrying out this task. By following the proposed phases, the robustness and representativeness of the performance metrics of their own cNLP systems can be assured.MethodsThe proposed evaluation methodology comprised five phases: (1) the definition of the target population, (2) the statistical document collection, (3) the design of the annotation guidelines and annotation project, (4) the external annotations, and (5) the cNLP system performance evaluation. We presented the application of all phases to evaluate the performance of a cNLP system called “EHRead Technology” (developed by Savana, an international medical company), applied in a study on patients with asthma. As part of the evaluation methodology, we introduced the Sample Size Calculator for Evaluations (SLiCE), a software tool that calculates the number of documents needed to achieve a statistically useful and resourceful gold standard.ResultsThe application of the proposed evaluation methodology on a real use-case study of patients with asthma revealed the benefit of the different phases for cNLP system evaluations. By using SLiCE to adjust the number of documents needed, a meaningful and resourceful gold standard was created. In the presented use-case, using as little as 519 EHRs, it was possible to evaluate the performance of the cNLP system and obtain performance metrics for the primary variable within the expected CIs.ConclusionsWe showed that our evaluation methodology can offer guidance to NLP experts on how to approach the evaluation of their cNLP systems. By following the five phases, NLP experts can assure the robustness of their evaluation and avoid unnecessary investment of human and financial resources. Besides the theoretical guidance, we offer SLiCE as an easy-to-use, open-source Python library.

Proteins act through physical interactions with other molecules to maintain organismal health. Protein-protein interaction (PPI) networks have proved to be a powerful framework for obtaining insight into protein functions, cellular organization, response to signals, and disease states. In multicellular organisms, protein content varies between tissues, influencing tissue morphology and function. Weighted PPI networks, reflecting the likelihood of interactions in specific tissues, offer insights into tissue-specific processes and disease mechanisms. We hypothesized that detecting anomalous nodes in these networks could reveal proteins with key tissue-specific functions. Here, we introduce Weighted Graph Anomalous Node Detection (WGAND), a novel machine-learning algorithm to identify anomalous nodes in weighted graphs. WGAND estimates expected edge weights and uses deviations to generate anomaly detection features, which are then used to score network nodes. We applied WGAND to weighted PPI networks of 17 human tissues. High-ranking anomalous nodes were enriched for proteins associated with tissue-specific diseases and tissue-specific biological processes, such as neuron signaling in the brain and spermatogenesis in the testis. WGAND outperformed other methods in terms of area under the ROC curve and precision at K, highlighting its effectiveness in uncovering biologically meaningful anomalies. Our findings demonstrate WGAND's potential as a powerful tool for detecting anomalous proteins with significant biological roles. By identifying proteins involved in critical tissue-specific processes and diseases, WGAND offers valuable insights for discovering novel biomarkers and therapeutic targets. Its versatile algorithm is suitable for any weighted graph and is broadly applicable across various fields. The WGAND algorithm is available as an open-source Python library at https://github.com/data4goodlab/wgand.

We present fmmpy, an open-source Python library that implements the Frequency Modulated Möbius (FMM) model for robust decomposition of oscillatory signals into interpretable components. Beyond addressing the computational limitations of earlier implementations, fmmpy provides a significantly more flexible and general framework for applying the FMM model in diverse real-world scenarios. The package incorporates optimized algorithms and robust parameter constraint handling, showing how its improved flexibility and efficiency make it feasible to address problems that were previously too complex or slow to solve. This makes the FMM model more accessible and adaptable for diverse applications in biomedical, engineering, and other signal processing fields. To demonstrate its practical utility, we present two representative use cases: ECG analysis and signal spectrography, showing how the enhanced algorithms enable novel insights and solutions in these domains.

Accounting for biological and practical requirements in DNA sequence design often results in challenging optimization problems. Current software solutions are problem-specific and hard to combine. DNA Chisel is an easy-to-use, easy-to-extend sequence optimization framework allowing to freely define and combine optimization specifications via Python scripts or Genbank annotations. The framework is available as a web application (https://cuba.genomefoundry.org/sculpt_a_sequence) or open-source Python library (see at https://github.com/Edinburgh-Genome-Foundry/DNAChisel for code and documentation). Supplementary data are available at Bioinformatics online.

Evaluating the influence of observed daily weather on observed fire-related effects (e.g. smoke production, carbon emissions and burn severity) often involves knowing exactly what day any given area has burned. As such, several studies have used fire progression maps – in which the perimeter of an actively burning fire is mapped at a fairly high temporal resolution – or MODIS satellite data to determine the day-of-burning, thereby allowing an evaluation of the influence of daily weather. However, fire progression maps have many caveats, the most substantial being that they are rarely mapped on a daily basis and may not be available in remote locations. Although MODIS fire detection data provide an alternative due to its global coverage and high temporal resolution, its coarse spatial resolution (1 km2) often requires that it be downscaled. An objective evaluation of how to best downscale, or interpolate, MODIS fire detection data is necessary. I evaluated 10 spatial interpolation techniques on 21 fires by comparing the day-of-burning as estimated with spatial interpolation of MODIS fire detection data to the day-of-burning that was recorded in fire progression maps. The day-of-burning maps generated with the best performing interpolation technique showed reasonably high quantitative and qualitative agreement with fire progression maps. Consequently, the methods described in this paper provide a viable option for producing day-of-burning data where fire progression maps are of poor quality or unavailable.

We introduce , an open-source Python library designed for mesh agglomeration in both two- and three-dimensions, based on employing Graph Neural Networks (GNN). serves as a comprehensive solution for training a variety of GNN models, integrating deep learning and other advanced algorithms such as METIS and k-means to facilitate mesh agglomeration and quality metric computation. The library’s introduction is outlined through its code structure and primary features. The GNN framework adopts a graph bisection methodology that capitalizes on connectivity and geometric mesh information via SAGE convolutional layers, in line with the methodology proposed in (Antonietti and Manuzzi in J Comput Phys 452:110900, 2022; Antonietti et al. in Polytopal mesh agglomeration via geometrical deep learning for three-dimensional heterogeneous domains, arXiv:2406.10587 , 2024). Additionally, the proposed library incorporates reinforcement learning to enhance the accuracy and robustness of the model initially suggested in [1, 2] for predicting coarse partitions within a multilevel framework. A detailed tutorial is provided to guide the user through the process of mesh agglomeration and the training of a GNN bisection model. We present several examples of mesh agglomeration conducted by , demonstrating the library’s applicability across various scenarios. Furthermore, the performance of the newly introduced models is contrasted with that of METIS and k-means, illustrating that the proposed GNN models are competitive regarding partition quality and computational efficiency. Finally, we exhibit the versatility of ’s interface through its integration with , an open-source library implementing discontinuous Galerkin methods on polytopal grids for the numerical discretization of multiphysics differential problems.