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Incorporating nonparametric methods for estimating causal excursion effects in mobile health with zero-inflated count outcomes

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arXiv 2023年

作者： Liu, Xueqing Qian, Tianchen Bell, Lauren Chakraborty, Bibhas Centre for Quantitative Medicine Duke-NUS Medical School Singapore Department of Statistics University of California Irvine IrvineCA United States Medical Research Council Biostatistics Unit University of Cambridge Cambridge United Kingdom Department of Medical Statistics The London School of Hygiene and Tropical Medicine London United Kingdom Department of Statistics and Data Science National University of Singapore Singapore Department of Biostatistics and Bioinformatics Duke University DurhamNC United States

In mobile health, tailoring interventions for real-time delivery is of paramount importance. Microrandomized trials have emerged as the "gold-standard" methodology for developing such interventions. Analyzing data from these trials provides insights into the efficacy of interventions and the potential moderation by specific covariates. The "causal excursion effect", a novel class of causal estimand, addresses these inquiries. Yet, existing research mainly focuses on continuous or binary data, leaving count data largely unexplored. The current work is motivated by the Drink Less micro-randomized trial from the UK, which focuses on a zero-inflated proximal outcome, i.e., the number of screen views in the subsequent hour following the intervention decision point. To be specific, we revisit the concept of causal excursion effect, specifically for zero-inflated count outcomes, and introduce novel estimation approaches that incorporate nonparametric techniques. Bidirectional asymptotics are established for the proposed estimators. Simulation studies are conducted to evaluate the performance of the proposed methods. As an illustration, we also implement these methods to the Drink Less trial data. © 2023, CC BY.

关键词： Binary alloys

The level set kalman filter for state estimation of continuous-discrete systems

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arXiv 2021年

作者： Wang, Ningyuan Forger, Daniel B. Department of Mathematics University of Michigan Ann ArborMI48109 United States Department of Mathematics Department of Computational Medicine and Bioinformatics Michigan Institute for Data Science University of Michigan Ann ArborMI48109 United States

We propose a new extension of Kalman filtering for continuous-discrete systems with nonlinear state-space models that we name as the level set Kalman filter (LSKF). The LSKF assumes the probability distribution can be approximated as a Gaussian and updates the Gaussian distribution through a time-update step and a measurement-update step. The LSKF improves the time-update step compared to existing methods, such as the continuous-discrete cubature Kalman filter (CDCKF), by reformulating the underlying Fokker-Planck equation as an ordinary differential equation for the Gaussian, thereby avoiding the need for the explicit expression of the higher derivatives. Together with a carefully picked measurement-update method, numerical experiments show that the LSKF has a consistent performance improvement over the CD-CKF for a range of parameters. Meanwhile, the LSKF simplifies implementation, as no user-defined timestep subdivisions between measurements are required, and the spatial derivatives of the drift function are not explicitly needed. Copyright © 2021, The Authors. All rights reserved.

关键词： Kalman filters

Digitizing Farmers' Land data Collection Systems in Indonesia with the Use of Tani Millenial Apps

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Digitizing Farmers' Land Data Collection Systems in Indonesi...

International Conference on Cybernetics and Intelligent System (ICORIS)

作者： Mohammad Prasanto Bimantio Dian Pratama Putra Teddy Suparyanto Amallia Ferhat Nanda Satya Nugraha Alam Ahmad Hidayat Bens Pardamean Department of Food and Agricultural Technology Institute of Agriculture STIPER Yogyakarta Indonesia Department of Agrotechnology Institute of Agriculture STIPER Yogyakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Department of Agricultural Socio-Economics Institute of Agriculture STIPER Yogyakarta Indonesia Department of Forestry Institute of Agriculture STIPER Yogyakarta Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (纸本)9781665453967

In this era of digital world information, farmers face challenges about information management of huge data and the complexity of processes in precision farming. The data collection carried out so far can cause several difficulties, especially if the data is needed by the government or academics to support decision-making. Agricultural data collection applications only cover 12% of the market share of Android-based agriculture-based applications. In this study, Tani Milenial application is present as an alternative to support agricultural data collection activities in Indonesia. This application encourages farmers to be active and contribute independently to their role as subjects of agricultural development and is accustomed to digitally recording their agricultural activities. In this developed application system, the community, especially farmers and farmer groups, will find it easier to get information about agricultural potential data around where they carry out agricultural activities and can access this information online. Tani Milenial works as a guide to help farmers and transform agriculture but still have some gaps which should be checked and removed. The data collected can be used by various parties for research and decision-making. The app can be further improved to develop new features related to education, market information, and goods.

关键词： Decision making Education Government Transforms data collection Agriculture Recording

Predicting drug response through tumor deconvolution by cancer cell lines

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Patterns 2024年第4期5卷 100949页

作者： Hsu, Yu-Ching Chiu, Yu-Chiao Lu, Tzu-Pin Hsiao, Tzu-Hung Chen, Yidong Bioinformatics Program Taiwan International Graduate Program National Taiwan University Taipei115 Taiwan Bioinformatics Program Institute of Statistical Science Taiwan International Graduate Program Academia Sinica Taipei115 Taiwan Institute of Health Data Analytics and Statistics Department of Public Health College of Public Health National Taiwan University Taipei100 Taiwan Greehey Children's Cancer Research Institute University of Texas Health San Antonio San AntonioTX78229 United States Department of Medicine School of Medicine University of Pittsburgh PittsburghPA15261 United States UPMC Hillman Cancer Center University of Pittsburgh PittsburghPA15232 United States Department of Medical Research Taichung Veterans General Hospital Taichung40705 Taiwan Department of Population Health Sciences University of Texas Health San Antonio San AntonioTX78229 United States

Large-scale cancer drug sensitivity data have become available for a collection of cancer cell lines, but only limited drug response data from patients are available. Bridging the gap in pharmacogenomics knowledge between in vitro and in vivo datasets remains challenging. In this study, we trained a deep learning model, Scaden-CA, for deconvoluting tumor data into proportions of cancer-type-specific cell lines. Then, we developed a drug response prediction method using the deconvoluted proportions and the drug sensitivity data from cell lines. The Scaden-CA model showed excellent performance in terms of concordance correlation coefficients (>0.9 for model testing) and the correctly deconvoluted rate (>70% across most cancers) for model validation using Cancer Cell Line Encyclopedia (CCLE) bulk RNA data. We applied the model to tumors in The Cancer Genome Atlas (TCGA) dataset and examined associations between predicted cell viability and mutation status or gene expression levels to understand underlying mechanisms of potential value for drug repurposing. © 2024 The Authors

关键词： Tumors

Duck Eggs Hatching Procedure with A Low Cost User Convenient Integrated Device for Developing Countries

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Duck Eggs Hatching Procedure with A Low Cost User Convenient...

IEEE Region 10 Humanitarian Technology Conference (R10-HTC)

作者： Eftakhar Hossain Mohammad Zeyad S.M. Masum Ahmed Md Sadik Tasrif Anubhove Energy and Technology Research Division Advanced Bioinformatics Computational Biology and Data Science Laboratory Bangladesh Chattogram Bangladesh Erasmus+ Joint MSC in Smart Cities and Communities University of the Basque Country (UPV/EHU) Bilbao Spain

Poultry agriculture is a form of livestock farming that involves raising chickens, turkeys, ducks, etc, and raises them to provide eggs or meat. However, this work sheds light on the method of hatching duck eggs which maintains a suitable environment around the eggs through an automated and low cost device by controlling temperature (T) and relative humidity (RH). This paper presents a control strategy for automatic temperature and relative humidity control systems for the egg/s hatching procedure for rural areas people or unprivileged communities in the developing countries. One of the best outcomes of this work is the proper hatching procedure steps shown from the beginning to the end. Moreover, for a better understanding and outcomes, the research work has been done under a poultry farm in Charsita village, Lakshmipur, Bangladesh for 6 consecutive months of 2020. The experiment (egg/s hatching) has been conducted under an ice-box. Furthermore, a microcontroller (ATmega328p) is used to monitor the temperature and relative humidity by receiving data from the sensor DHT22 and manipulating the appropriate temperature and humidity using a logic algorithm code. Egg/s need a constant temperature and relative humidity of 35.6 °C to 37.8 °C and 60% to 80%, respectively. Nonetheless, an LCD (16*2) with a matrix keypad (4*4) has been integrated into the unit, allowing farmers to easily set, run, and monitor the appropriate temperature and relative humidity levels within the ice-box. Finally, the results of sensor testing, system device management, and performance rates are recorded to ensure the research's success.

关键词： Temperature sensors Temperature measurement Temperature distribution Costs Rural areas Humidity Developing countries

The asymmetric particle population density method for simulation of coupled noisy oscillators: A preprint

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arXiv 2021年

A wide variety of biological phenomena can be modeled by the collective activity of a population of individual units. A common strategy for simulating such a system, the population density approach, is to take the macroscopic limit and update its population density function. However, in many cases, the coupling between the units and noise gives rise to complex behaviors challenging to existing population density approach methods. To address these challenges, we develop the asymmetric particle population density (APPD) method that efficiently and accurately simulates such populations consist of coupled elements. The APPD is well-suited for a parallel implementation. We compare the performance of the method against direct Monte-Carlo simulation and verify its accuracy by applying it to the well-studied Hodgkin-Huxley model, with a range of challenging scenarios. We find that our method can accurately reproduce complex macroscopic behaviors such as inhibitory coupling-induced clustering and noise-induced firing while being faster than the direct *** Codes 65M75 © 2021, CC BY-NC-ND.

关键词： Population distribution

K-Means Clustering Model to Discriminate Copper-Resistant Bacteria as Bioremediation Agents

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Procedia Computer science 2021年 179卷 804-812页

作者： Ika Nurlaila Wahyu Irawati Kartika Purwandari Bens Pardamean Information Systems Department BINUS Online Learning Bina Nusantara University Jakarta Indonesia 11480 Department of Biology Education Faculty of Education Pelita Harapan University Tangerang Indonesia 15811 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

Copper (Cu) has been excessively used for some valuable commodities and this creates environmental problems. The inorganic element becomes toxic when presents beyond the recommended tolerated concentration. Bacterial-based remediation is seen to be an excellent tool to overcome it as it reduces the copper contamination without yielding any other forms of contamination. There are some pivotal properties in the bacteria render them being considered as bioremediation agents against coppers contamination, namely bioaccumulation and biosorption. In the present study, we question if these bacteria could be clustered into a strong and representative proximity according to their functional properties. Mostly, bacteria are grouped based on their genetic profiles derived from the 16S rRNA sequencing. We propose that our K-Means clustering model can be employed to identify genetically-unlabelled bacteria. But first, a prominent reference should be developed and we are in this phase. We figured out the K-Means clustering model do not pull the same-genus bacteria into the same cluster. Instead, the model gathers into a proximity those isolates with similarity on a functional characteristic termed minimum inhibitory concentration (MIC), regardless their origins and their hierarchy in taxonomy.

关键词： Copper-Resistant Bacteria K-Means Minimum Inhibitory Concentration

Recording provenance of workflow runs with RO-Crate

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arXiv 2023年

作者： Leo, Simone Crusoe, Michael R. Rodríguez-Navas, Laura Sirvent, Raül Kanitz, Alexander De Geest, Paul Wittner, Rudolf Pireddu, Luca Garijo, Daniel Fernández, José M. Colonnelli, Iacopo Gallo, Matej Ohta, Tazro Suetake, Hirotaka Capella-Gutierrez, Salvador de Wit, Renske Kinoshita, Bruno P. Soiland-Reyes, Stian CA Pula Italy Vrije Universiteit Amsterdam Amsterdam Netherlands DTL Projects Netherlands Forschungszentrum Jülich Germany Barcelona Supercomputing Center Barcelona Spain Biozentrum University of Basel Basel Switzerland Swiss Institute of Bioinformatics Lausanne Switzerland VIB Data Core Gent Belgium Faculty of Informatics Masaryk University Brno Czech Republic Institute of Computer Science Masaryk University Brno Czech Republic BBMRI-ERIC Graz Austria Ontology Engineering Group Universidad Politécnica de Madrid Madrid Spain Computer Science Department Università degli Studi di Torino Torino Italy Database Center for Life Science Joint Support-Center for Data Science Research Research Organization of Information and Systems Shizuoka Japan Institute for Advanced Academic Research Chiba University Chiba Japan Sator Incorporated Tokyo Japan Department of Computer Science The University of Manchester Manchester United Kingdom Informatics Institute University of Amsterdam Amsterdam Netherlands

Recording the provenance of scientific computation results is key to the support of traceability, reproducibility and quality assessment of data products. Several data models have been explored to address this need, providing representations of workflow plans and their executions as well as means of packaging the resulting information for archiving and sharing. However, existing approaches tend to lack interoperable adoption across workflow management systems. In this work we present Workflow Run RO-Crate, an extension of RO-Crate (Research Object Crate) and *** to capture the provenance of the execution of computational workflows at different levels of granularity and bundle together all their associated objects (inputs, outputs, code, etc.). The model is supported by a diverse, open community that runs regular meetings, discussing development, maintenance and adoption aspects. Workflow Run RO-Crate is already implemented by several workflow management systems, allowing interoperable comparisons between workflow runs from heterogeneous systems. We describe the model, its alignment to standards such as W3C PROV, and its implementation in six workflow systems. Finally, we illustrate the application of Workflow Run RO-Crate in two use cases of machine learning in the digital image analysis domain. © 2023, CC BY.

关键词： Workflow management

Nesting of Touching Polygons

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arXiv 2024年

作者： Seemann, Carsten R. Stadler, Peter F. Hellmuth, Marc Swarm Intelligence and Complex Systems Group Department of Computer Science Leipzig University Augustusplatz 10 LeipzigD-04109 Germany Bioinformatics Group Department of Computer Science Interdisciplinary Center for Bioinformatics Leipzig University Härtelstraße 16-18 LeipzigD-04107 Germany Halle-Jena-Leipzig Competence Center for Scalable Data Services and Solutions Dresden-Leipzig Leipzig Research Center for Civilization Diseases Centre for Biotechnology and Biomedicine Leipzig University Härtelstraße 16-18 LeipzigD-04107 Germany Max Planck Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Institute for Theoretical Chemistry University of Vienna Währingerstraße 17 WienA-1090 Austria Facultad de Ciencias Universidad Nacional de Colombia Sede Bogotá Colombia The Santa Fe Institute 1399 Hyde Park Rd. Santa FeNM87501 United States Department of Mathematics Faculty of Science Stockholm University StockholmSE - 106 91 Sweden

Polygons are cycles embedded into the plane;their vertices are associated with x- and y-coordinates and the edges are straight lines. Here, we consider a set of polygons with pairwise non-overlapping interior that may touch along their boundaries. Ideas of the sweep line algorithm by Bajaj and Dey for non-touching polygons are adapted to accommodate polygons that share boundary points. The algorithms established here achieves a running time of O(n + N log N), where n is the total number of vertices and N MSC Codes 05C10 Copyright © 2024, The Authors. All rights reserved.

关键词： Geometry