Data Science Commons^™

Geospatial Analysis Of Agricultural Potential In The United States, Diana Febrita

Graduate Industrial Research Symposium

Traditionally, the agriculture sector is responsible for providing food and crop products. However, the role of agriculture has expanded beyond its traditional function. It is the main sector that contributes to the provision of food, income, employment, environmental protection, and local economic development. Reflecting on the roles of agriculture, understanding the potential of agriculture in the United States is crucial to discovering the prospects and challenges. This study will briefly discuss the agricultural potential in the United States based on the five assets, including natural capital, financial capital, human capital, physical capital, and social capital. To identify the states with …

Accuracy Of Nitrate Hysteresis And Flushing For Agricultural Watersheds In The Midwest, Noah Rudko, Sara K. W. Mcmillian, Jane Frankenberger, François Birgand

Graduate Industrial Research Symposium

Storm event-based metrics, such as hysteresis (HI) and flushing (FI), are used to differentiate nitrate pathways and sources, which is essential for watershed management. Estimations of these event-based metrics typically use high frequency (15-minute – hourly) measurements, but daily data are also used due to their greater availability. To date, there has been no study assessing how using lower frequency samples affect the accuracy of HI and FI, which could skew interpretation of potential nutrient pathways and sources. We used continuous measurements of nitrate collected at 9 watersheds throughout the Midwest spanning 448 storms. HI and FI were estimated from …

Characterization Of Biological Particles Using An Integrated Hyperspectral Imaging And Machine Learning, Kaeul Lim, Arezoo Ardekani

Graduate Industrial Research Symposium

Hyperspectral imaging (HSI) is a promising modality in medicine with many potential applications. This study focuses on developing a label-free lipid nanoparticle characterization method using a convolutional neural network (CNN) analysis of HSI images. The HSI data, hypercube, consists of a series of images acquired at different wavelengths for the same field of view, providing continuous spectra information for each pixel. Three distinct liposome samples were collected for analysis. Advanced image preprocessing and classification methods for HSI data were developed to differentiate liposomes based on their material compositions. Our machine learning-based classification method was able to distinguish different liposome types …

Sepsis Treatment: Reinforced Sequential Decision-Making For Saving Lives, Dipesh Tamboli, Jiayu Chen, Kiran Pranesh Jotheeswaran, Denny Yu, Vaneet Aggarwal

Graduate Industrial Research Symposium

Sepsis, a life-threatening condition triggered by the body's exaggerated response to infection, demands urgent intervention to prevent severe complications. Existing machine learning methods for managing sepsis struggle in offline scenarios, exhibiting suboptimal performance with survival rates below 50%. Our project introduces the "PosNegDM: Reinforcement Learning with Positive and Negative Demonstrations for Sequential Decision-Making" framework utilizing an innovative transformer-based model and a feedback reinforcer to replicate expert actions while considering individual patient characteristics. A mortality classifier with 96.7% accuracy guides treatment decisions towards positive outcomes. The PosNegDM framework significantly improves patient survival, saving 97.39% of patients and outperforming established machine learning …

Online Class-Incremental Learning For Real-World Food Image Classification, Siddeshwar Raghavan, Jiangpeng He, Fengqing Zhu

Graduate Industrial Research Symposium

Food image classification is essential for monitoring health and tracking dietary in image-based dietary assessment methods. However, conventional systems often rely on static datasets with fixed classes and uniform distribution. In contrast, real-world food consumption patterns, shaped by cultural, economic, and personal influences, involve dynamic and evolving data. Thus, it requires the classification system to cope with continuously evolving data. Online Class Incremental Learning (OCIL) addresses the challenge of learning continuously from a single-pass data stream while adapting to the new knowledge and reducing catastrophic forgetting. Experience Replay (ER) based OCIL methods store a small portion of previous data and …

Modelling The "Bottom-Up" Development Pattern Of Tar Spot Disease In Corn, Brenden Lane, Joaquín Guillermo Ramírez-Gil, Carlos Góngora-Canul, Mariela Sofia Fernandez Campos, Andres Cruz-Sancan, Fidel E. Jiménez-Beitia, Alex G. Acosta-Guatemal, Wily Sic, C. D. Cruz

Graduate Industrial Research Symposium

In 2015, the corn-infecting pathogen Phyllachora maydis (causal agent of tar spot disease) was reported for the first time in the United States. The disease has since spread across the US, causing major yield losses. In 2021 alone, 5.88 million metric tons (231.3 million bushels) of US corn yield were lost to this disease, costing an estimated US$1.25 billion. Though fungicides can protect against these agroeconomic losses, application timing can be difficult to optimize because our understanding of tar spot dynamics is still evolving. The current view is that tar spot typically develops bottom-up through a repeating infection cycle. Because …

A Machine Learning Model Of Perturb-Seq Data For Use In Space Flight Gene Expression Profile Analysis, Liam F. Johnson, James Casaletto, Lauren Sanders, Sylvain Costes

Graduate Industrial Research Symposium

The genetic perturbations caused by spaceflight on biological systems tend to have a system-wide effect which is often difficult to deconvolute it into individual signals with specific points of origin. Single cell multi-omic data can provide a profile of the perturbational effects, but does not necessarily indicate the initial point of interference within the network. The objective of this project is to take advantage of large scale and genome-wide perturbational datasets by using them to train a tuned machine learning model that is capable of predicting the effects of unseen perturbations in new data. Perturb-Seq datasets are large libraries of …

Resource Optimization For Air Mobility Under Emergency Situations, Yongxin (Jack) Liu

Math Department Colloquium Series

This project aims to improve air traffic management in emergencies. We first developed a GRU neural network to forecast weather-related airport capacity constraints using historical data, underscoring the value of real-time data analysis. We then optimized emergency evacuation air travel using Particle Swarm Optimization, demonstrating the ability to quickly aggregate evacuation flight resources cost-effectively. Finally, we provided a hybrid model combining a genetic algorithm with a neural network for evacuation planning, we show that neural network can be integrated accelerate genetic algorithms for efficient and performance assured system optimization.

Assessing Gait Metrics For Early Parkinson's Disease Prediction: A Preliminary Analysis Of Underfit Models, Daniel Salinas, Gerardo Medellin, Katherine Bolado, Tomas Gomez, Kelsey Potter-Baker, Nawaz Khan Abdul Hack, Ramu Vadukapuram

Research Symposium

Background: Parkinson's Disease (PD) is characterized by both motor and non-motor symptoms, and its diagnosis primarily relies on clinical presentation. There is a growing need for diagnostic tools to identify the early signs of PD, particularly the initial motor impairments often manifested as gait abnormalities. Here we seek to present preliminary findings to address this need. Our study focuses on using Machine Learning techniques (ML) to predict the PD clinical stage most efficiently and accurately. Specifically, we have sought to evaluate how spatiotemporal characteristics and other locomotor performance variables obtained on a walkway system can be utilized to identify the …

Deep Learning Model For Personalized Prediction Of Positive Mrsa Culture Using Time-Series Electronic Health Records, Masayuki Nigo, Laila Rasmy, Bingyu Mao, Bijun Sai Kannadath, Ziqian Xie, Degui Zhi

Faculty, Staff and Student Publications

Methicillin-resistant Staphylococcus aureus (MRSA) poses significant morbidity and mortality in hospitals. Rapid, accurate risk stratification of MRSA is crucial for optimizing antibiotic therapy. Our study introduced a deep learning model, PyTorch_EHR, which leverages electronic health record (EHR) time-series data, including wide-variety patient specific data, to predict MRSA culture positivity within two weeks. 8,164 MRSA and 22,393 non-MRSA patient events from Memorial Hermann Hospital System, Houston, Texas are used for model development. PyTorch_EHR outperforms logistic regression (LR) and light gradient boost machine (LGBM) models in accuracy (AUROC

Federated Analysis Of Wearables Data For United States Air Force Mental And Physical Readiness, Sung Yong O

Theses and Dissertations

This thesis investigates the use of machine learning and deep learning models within a federated learning framework to predict physical and mental readiness in military personnel, using wearable technology data. The collaboration with the 711th Human Performance Wing’s STRONG Lab highlights the importance of readiness as emphasized by the National Defense and Security Strategies. The study evaluates various predictive models, incorporating federated learning to ensure data privacy and security in healthcare systems. By analyzing a comprehensive dataset, the research aims to contribute to military readiness enhancement through technological advancements, supporting health and wellness initiatives to bolster the effectiveness of military …

Spec: A Soft Prompt-Based Calibration On Performance Variability Of Large Language Model In Clinical Notes Summarization, Yu-Neng Chuang, Ruixiang Tang, Xiaoqian Jiang, Xia Hu

Faculty, Staff and Student Publications

Electronic health records (EHRs) store an extensive array of patient information, encompassing medical histories, diagnoses, treatments, and test outcomes. These records are crucial for enabling healthcare providers to make well-informed decisions regarding patient care. Summarizing clinical notes further assists healthcare professionals in pinpointing potential health risks and making better-informed decisions. This process contributes to reducing errors and enhancing patient outcomes by ensuring providers have access to the most pertinent and current patient data. Recent research has shown that incorporating instruction prompts with large language models (LLMs) substantially boosts the efficacy of summarization tasks. However, we show that this approach also …

A Staged Framework For Llm-Powered Information Extraction In Government Contracts, Jung H. Yae

Theses and Dissertations

The manual extraction of meaningful insights and conversion of content into structured forms to enhance document processing require substantial resources and are susceptible to errors. Despite numerous applications of various Natural Language Processing (NLP) models to streamline the manual process, challenges persist due to domain-specific data constraints and the deficiency of annotated data. This study attempts to address these challenges by leveraging a Large Language Model (LLM) to analyze government contracts. Through rigorous evaluation, we demonstrate the LLM’s effectiveness in information extraction and mitigating hallucinations, achieving a 87.86% accuracy in metadata extraction.

On Intrinsic Dimensionality Of Data Sets And Neural Networks, Ori Chachmo

Theses and Dissertations

The concept of Intrinsic Dimensionality (ID) is of special interest in the field of Neural Networks (NNs) since it promotes both (a) a deeper understanding of the underlying mechanisms, and (b) embraces parsimonious modeling (that is, building the right-sized model for the task) with associated benefits to processing speed and storage requirements. This thesis explores the concept of ID via two separate, but related, questions. First, we study the potential of NN ID prediction by exploiting easily obtained quantities measured on the data. We then explore NN ID as an independent concept by comparing the results of different methods for …

Automated Image Registration For Titanium Aircraft Components Via Resolution-Robust Parallel Neural Networks, Paige T. Luebbering

Theses and Dissertations

Titanium alloys are vital to the structural integrity of military and commercial aircraft, comprising numerous critical components. These components are composed of microtexture regions (MTRs) that, at a specific size and orientation, can lead to aircraft failure. Existing MTR testing methods, such as Electron Backscatter Diffraction, often fall short in effectively detecting these MTRs without causing damage to the component. Addressing this gap, this thesis develops a Parallel Convolutional Neural Network (CNN) model tailored for multi-resolution image registration of Polarized Light Microscopy (PLM) images to enhance MTR identification in a non-invasive manner. The findings reveal a significant enhancement in the …

Multiple Control Of Azoquinoline Based Molecular Photoswitches, Youming Lv, Hebo Ye, Lei You

Faculty, Staff and Student Publications

Multi-addressable molecular switches with high sophistication are creating intensive interest, but are challenging to control. Herein, we incorporated ring-chain dynamic covalent sites into azoquinoline scaffolds for the construction of multi-responsive and multi-state switching systems. The manipulation of ring-chain equilibrium by acid/base and dynamic covalent reactions with primary/secondary amines allowed the regulation of

Evaluating Sojump.Com As A Tool For Online Behavioral Research In China, Alessandro Del Ponte, Lianjun Li, Lina Ang, Noah Lim, Wei Jie Seow

Political Science Faculty Articles and Research

SoJump.com (wjx.cn; in short: SoJump) is a survey company that allows researchers to build and deploy inexpensive online surveys in China. Here we evaluate SoJump’s data quality and similarity to the national benchmark. In the first study, we compare SoJump’s performance in China to MTurk’s performance against national benchmarks in the United States and India. In the second study, we compare three Chinese platforms in two-wave panel studies. We conducted the panels on SoJump, Credamo (SoJump’s major competitor), and Cint (national benchmark). We included attention and comprehension checks, economic games, cognitive tasks, and a framing experiment. We find that SoJump’s …

Anomaly Detection On Small Wind Turbine Blades Using Deep Learning Algorithms, Bridger Altice, Edwin Nazario, Mason Davis, Mohammad Shekaramiz, Todd K. Moon, Mohammad A. S. Masoum

Electrical and Computer Engineering Faculty Publications

Wind turbine blade maintenance is expensive, dangerous, time-consuming, and prone to misdiagnosis. A potential solution to aid preventative maintenance is using deep learning and drones for inspection and early fault detection. In this research, five base deep learning architectures are investigated for anomaly detection on wind turbine blades, including Xception, Resnet-50, AlexNet, and VGG-19, along with a custom convolutional neural network. For further analysis, transfer learning approaches were also proposed and developed, utilizing these architectures as the feature extraction layers. In order to investigate model performance, a new dataset containing 6000 RGB images was created, making use of indoor and …

The Pathogenicity Of Vancomycin-Resistant Enterococcus Faecalis To Colon Cancer Cells, Li Zhang, Mingxia Deng, Jing Liu, Jiajie Zhang, Fangyu Wang, Wei Yu

Faculty, Staff and Student Publications

BACKGROUND: The aim of this study was to investigate the pathogenicity of vancomycin-resistant Enterococcus faecalis (VREs) to human colon cells in vitro.

METHODS: Three E. faecalis isolates (2 VREs and E. faecalis ATCC 29212) were cocultured with NCM460, HT-29 and HCT116 cells. Changes in cell morphology and bacterial adhesion were assessed at different time points. Interleukin-8 (IL-8) and vascular endothelial growth factor A (VEGFA) expression were measured via RT-qPCR and enzyme-linked immunosorbent assay (ELISA), respectively. Cell migration and human umbilical vein endothelial cells (HUVECs) tube formation assays were used for angiogenesis studies. The activity of PI3K/AKT/mTOR signaling pathway was measured …

Hillside Agricultural Machinery And Agricultural Intelligence Driven By New Technologies, Hong Qiao, Yanfeng Lyu, Enhao Zheng

Bulletin of Chinese Academy of Sciences (Chinese Version)

Hilly and mountainous areas play a crucial role in China’s agricultural production. However, the low level of comprehensive mechanization for crop cultivation, planting, and harvesting in these regions severely hampers the modernization of agriculture. The complex terrain and diverse cropping patterns in hilly areas necessitate the development of specialized agricultural machinery and robots tailored to these unique landscapes. To advance this process, the Chinese government has introduced a series of policies in recent years to support the research and development of agricultural machinery for hilly regions, providing strong backing for the advancement of agricultural technology in these areas. Against this …

The Fuxi Farm: Practice Exploration And Reflection On Integrated Innovation Of Smart Agriculture Technology, Yucheng Zhang, Xiaobo Zhang, Shuqin Gao, Congcong Zheng, Jingyao Zhang, Ya Wen, Lujun Li, Zhuo Wang, Tie Li, Honglong Zhao

Bulletin of Chinese Academy of Sciences (Chinese Version)

Smart agriculture plays a pivotal role in enhancing food security by optimizing resource use and improving crop yields through the application of AI technologies. The establishment of smart farms is critical to rapidly integrating AI into agricultural production, offering platforms for both the deployment and testing of AI solutions and equipment. This paper examines the development of smart farms, with a focus on practices from developed countries, and assesses the current status of smart farming in China. We then focus on exploring the content, pathways, and practices for constructing a smart agricultural production system in China through the establishment of …

Accelerate Innovation Of Forage Intelligent Breeding Technology: Reflection And Suggestions, Haichun Jing, Weijuan Hu, Jingbo Jin, Jingyu Zhang, Yao Zhou, Yue Gong, Gang Yao, Lei Wang, Kang Chong

Bulletin of Chinese Academy of Sciences (Chinese Version)

The world is facing unprecedented changes today, with continuous population growth intensifying the pressure on food demand. The shift towards diversified dietary structures has increased the demand for feed grains, while climate change further threatens China’s food security by affecting agricultural productivity and carbon sequestration economy. At present, China has entered a new era of food supply and feed. As the food supply for animals, forage is the core component of feed, and its industrial development has profound strategic significance for ensuring national food security. This study analyzes the current situation of China’s forage seed industry, summarizes the cutting-edge achievements …

Rapid Soil Detection Technology Aids In Assessing Soil Nutrients In China, Wei Wu, Xiaoyong Liao, Xiaopeng Li, Yuntao Wu, Huixian Lu, Yucheng Zhang, Jiabao Zhang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Soil quality is the core issue for ensuring China’s food security, and soil health is the top priority of soil quality. Comprehensive, rapid and accurate acquisition of soil background data is the prerequisite for achieving homogeneous soil management and formulating balanced fertilization strategies, which will play a key role in improving non-point source pollution caused by unreasonable fertilization and achieving balanced grain yield increase. This study reviews rapid soil testing methods both domestically and internationally. Based on previous research, it proposes a technical approach to rapidly detect soil nutrient concentrations by calculating the gamma quanta released during the decay of …

Artificial Intelligence Innovation For Smart Plant Factory To Diversify Its Big Food Production Functions, Huaqin Gong, Haichun Jing, Xin Tan, Xianhui Wang, Yucheng Zhang, Rongcheng Lin, Mingyu Yang, Shuang Lin, Hualing Xie, Yanping Yang, Shitang Ye, Peng Li, Tingyun Kuang

Bulletin of Chinese Academy of Sciences (Chinese Version)

China’s food security is facing more and more severe and complex challenges, such as tight balance between food demand and supply, the upgrading of consumption structure, and resource constraints. The plant factory is an advanced scenario in agricultural production, a diversified food production system that gets rid of the constraints of “ask for food from the mother nature” and respond to disasters and wars, and is oriented to space. Nevertheless, the high cost greatly limits the application and development of plant factories. The rapid development of artificial intelligence will bring new opportunities for the innovative development and expansion of plant …

Data And Intelligent Driven Space Science Experimental Research: New Exploration Under Ai4s Paradigm, Shengyang Li, Kang Liu, Yunfei Liu, Chufan Lai

Bulletin of Chinese Academy of Sciences (Chinese Version)

As artificial intelligence (AI) technology continues to advance, it is revolutionizing various scientific fields, giving rise to a new research paradigm known as AI for Science (AI4S). This study highlights the unique multidisciplinary advantages of AI in space science experiments conducted under microgravity conditions. It provides a comprehensive analysis of AI-driven approaches to multimodal space science experiment data pattern mining, domain knowledge extraction, interdisciplinary knowledge integration, and cognitive intelligence. The study reveals AI’s substantial potential to enhance intelligent scientific research, cognition, and discovery within the realm of space science experiments. The findings suggest that data-driven space science research, as a …

Cancergpt For Few Shot Drug Pair Synergy Prediction Using Large Pretrained Language Models, Tianhao Li, Sandesh Shetty, Advaith Kamath, Ajay Jaiswal, Xiaoqian Jiang, Ying Ding, Yejin Kim

Faculty, Staff and Student Publications

Large language models (LLMs) have been shown to have significant potential in few-shot learning across various fields, even with minimal training data. However, their ability to generalize to unseen tasks in more complex fields, such as biology and medicine has yet to be fully evaluated. LLMs can offer a promising alternative approach for biological inference, particularly in cases where structured data and sample size are limited, by extracting prior knowledge from text corpora. Here we report our proposed few-shot learning approach, which uses LLMs to predict the synergy of drug pairs in rare tissues that lack structured data and features. …

Mortality Outcomes In A Large Population With And Without Covert Cerebrovascular Disease, Úna Clancy, Eric J Puttock, Wansu Chen, William Whiteley, Ellen M Vickery, Lester Y Leung, Patrick H Luetmer, David F Kallmes, Sunyang Fu, Chengyi Zheng, Hongfang Liu, David M Kent

Faculty, Staff and Student Publications

Covert cerebrovascular disease (CCD) is frequently reported on neuroimaging and associates with increased dementia and stroke risk. We aimed to determine how incidentally-discovered CCD during clinical neuroimaging in a large population associates with mortality. We screened CT and MRI reports of adults aged ≥50 in the Kaiser Permanente Southern California health system who underwent neuroimaging for a non-stroke clinical indication from 2009-2019. Natural language processing identified incidental covert brain infarcts (CBI) and/or white matter hyperintensities (WMH), grading WMH as mild/moderate/severe. Models adjusted for age, sex, ethnicity, multimorbidity, vascular risks, depression, exercise, and imaging modality. Of n=241,028, the mean age was …

Strategies To Combine 3d Vasculature And Brain Cta With Deep Neural Networks: Application To Lvo, Uma M Lal-Trehan Estrada, Arnau Oliver, Sunil A Sheth, Xavier Lladó, Luca Giancardo

Faculty, Staff and Student Publications

Automated tools to detect large vessel occlusion (LVO) in acute ischemic stroke patients using brain computed tomography angiography (CTA) have been shown to reduce the time for treatment, leading to better clinical outcomes. There is a lot of information in a single CTA and deep learning models do not have an obvious way of being conditioned on areas most relevant for LVO detection, i.e., the vasculature structure. In this work, we compare and contrast strategies to make convolutional neural networks focus on the vasculature without discarding context information of the brain parenchyma and propose an attention-inspired strategy to encourage this. …

Generalizable Pipeline For Constructing Hiv Risk Prediction Models Across Electronic Health Record Systems, Sarah B May, Thomas P Giordano, Assaf Gottlieb

Faculty, Staff and Student Publications

OBJECTIVE: The HIV epidemic remains a significant public health issue in the United States. HIV risk prediction models could be beneficial for reducing HIV transmission by helping clinicians identify patients at high risk for infection and refer them for testing. This would facilitate initiation on treatment for those unaware of their status and pre-exposure prophylaxis for those uninfected but at high risk. Existing HIV risk prediction algorithms rely on manual construction of features and are limited in their application across diverse electronic health record systems. Furthermore, the accuracy of these models in predicting HIV in females has thus far been …

The Il6/Jak/Stat3 Signaling Axis Is A Therapeutic Vulnerability In Smarcb1-Deficient Bladder Cancer, Chandra Sekhar Amara, Karthik Reddy Kami Reddy, Yang Yuntao, Yuen San Chan, Danthasinghe Waduge Badrajee Piyarathna, Lacey Elizabeth Dobrolecki, David J H Shih, Zhongcheng Shi, Jun Xu, Shixia Huang, Matthew J Ellis, Andrea B Apolo, Leomar Y Ballester, Jianjun Gao, Donna E Hansel, Yair Lotan, H Courtney Hodges, Seth P Lerner, Chad J Creighton, Arun Sreekumar, W Jim Zheng, Pavlos Msaouel, Shyam M Kavuri, Nagireddy Putluri

Faculty, Staff and Student Publications

SMARCB1 loss has long been observed in many solid tumors. However, there is a need to elucidate targetable pathways driving growth and metastasis in SMARCB1-deficient tumors. Here, we demonstrate that SMARCB1 deficiency, defined as genomic SMARCB1 copy number loss associated with reduced mRNA, drives disease progression in patients with bladder cancer by engaging STAT3. SMARCB1 loss increases the chromatin accessibility of the STAT3 locus in vitro. Orthotopically implanted SMARCB1 knockout (KO) cell lines exhibit increased tumor growth and metastasis. SMARCB1-deficient tumors show an increased IL6/JAK/STAT3 signaling axis in in vivo models and patients. Furthermore, a pSTAT3 selective inhibitor, TTI-101, reduces …