pwc-archive/papers-with-abstracts huggingface dataset:
Glycemic Variability Before And After Hypoglycemia Across Different Timeframes In Type 1 Diabetes With And Without Automated Insulin Delivery
Authors: Ahtsham Zafar, Abiodun Solanke, Dana M. Lewis, Arsalan Shahid
Date: 2025-04-02 00:00:00

Managing Type 1 diabetes (T1D) aims to optimize glucose levels within the target range while minimizing hyperglycemia and hypoglycemia. Exercise presents additional challenges due to complex effects on glucose dynamics. Despite advancements in diabetes technology, significant gaps remain in understanding the relationship between exercise, glycemic variability (GV), and hypoglycemia in both automated insulin delivery (AID) and non-AID users. Additionally, limited research explores the temporal progression of GV before and after hypoglycemia and the impact of long-duration episodes on glucose recovery. This study analyses the Type 1 Diabetes and Exercise Initiative (T1DEXI) dataset, assessing GV, hypoglycemia, gender, and exercise interactions in AID (n=222) and non-AID (n=276) users. The study examined patterns of glycemic variability metrics like time below range (TBR) surrounding hypoglycemia events, focusing on the 48 hours before and after these events. We further assess the impact of different hypoglycemia levels (41-50 mg/dL, 51-60 mg/dL, and 61-70 mg/dL) on post-event glucose stability. GV increased before and after hypoglycemia up to 48 hours in both AID and non-AID users, with statistically significant differences. TBR elevation persisted across all groups, peaking around hypoglycemic episodes. Notably, females using AID achieved significantly improved glucose stability compared to non-AID females - a larger within-group difference than that observed in males. Individual-level AID analyses showed that long hypoglycemia episodes (>40 minutes) led to prolonged TBR elevation, suggesting slower recovery despite AID intervention. GV trends may aid in predicting hypoglycemia over extended periods. Integrating GV patterns into AID systems could enhance glucose stability and mitigate hypoglycemia cycles.
Pharmacokinetic characteristics of Jinhong tablets in normal, chronic superficial gastritis and intestinal microbial disorder rats
Authors: Tingyu Zhang, Jian Feng, Xia Gao, Xialin Chen, Hongyu Peng, Xiaoxue Fan, Xin Meng, Mingke Yin, Zhenzhong Wang, Bo Zhang, Liang Cao
Date: 2025-04-01 00:00:00

Jinhong tablet (JHT), a traditional Chinese medicine made from four herbs, effectively treats chronic superficial gastritis (CSG) by soothing the liver, relieving depression, regulating qi, and promoting blood circulation. However, its pharmacokinetics are underexplored. This study investigates JHT's pharmacokinetics in normal rats and its differences in normal, CSG, and intestinal microbial disorder rats. A quantitative method for seven active ingredients in rat plasma was established using UPLC-TQ-MS/MS. After administering various JHT doses, plasma concentrations were measured to assess pharmacokinetics in normal rats. The pharmacokinetics of four main ingredients were compared in normal, CSG, and fecal microbiota transplantation (FMT) rats. Intestinal microbial changes were evaluated by high-throughput sequencing. Spearman correlation analysis linked ingredient exposure to gut microbiota disturbances. The method showed good linearity, precision, accuracy, extraction recovery, and stability. In normal rats, all seven ingredients were rapidly absorbed. Tetrahydropalmatine, corydaline, costunolide, and rhamnosylvitexin had good exposure, while dehydrocorydaline, allocryptopine, and palmatine hydrochloride had low exposure. Tetrahydropalmatine, corydaline, and costunolide followed linear pharmacokinetics (AUC0-t, Cmax) at doses of 0.7-5.6 g/kg, while rhamnosylvitexin and dehydrocorydaline showed linearity at 0.7-2.8 g/kg. In CSG and FMT rats, pharmacokinetic differences were observed. CSG enhanced costunolide exposure and Cmax, and increased rhamnosylvitexin exposure. FMT raised corydaline exposure and rhamnosylvitexin Cmax, linked to 20 bacterial genera.
Opportunistic Screening for Pancreatic Cancer using Computed Tomography Imaging and Radiology Reports
Authors: David Le, Ramon Correa-Medero, Amara Tariq, Bhavik Patel, Motoyo Yano, Imon Banerjee
Date: 2025-03-31 00:00:00
Tasks: Deep Learning, Prognosis

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer, with most cases diagnosed at stage IV and a five-year overall survival rate below 5%. Early detection and prognosis modeling are crucial for improving patient outcomes and guiding early intervention strategies. In this study, we developed and evaluated a deep learning fusion model that integrates radiology reports and CT imaging to predict PDAC risk. The model achieved a concordance index (C-index) of 0.6750 (95% CI: 0.6429, 0.7121) and 0.6435 (95% CI: 0.6055, 0.6789) on the internal and external dataset, respectively, for 5-year survival risk estimation. Kaplan-Meier analysis demonstrated significant separation (p<0.0001) between the low and high risk groups predicted by the fusion model. These findings highlight the potential of deep learning-based survival models in leveraging clinical and imaging data for pancreatic cancer.
Assessing Validity of ICD-10 Administrative Data in Coding Comorbidities
Authors: Jie Pan, Seungwon Lee, Cheligeer Cheligeer, Bing Li, Guosong Wu, Catherine A Eastwood, Yuan Xu, Hude Quan
Date: 2025-03-31 00:00:00
Tasks: Mortality Prediction

Objectives: Administrative data is commonly used to inform chronic disease prevalence and support health informatics research. This study assessed the validity of coding comorbidity in the International Classification of Diseases, 10th Revision (ICD-10) administrative data. Methods: We analyzed three chart review cohorts (4,008 patients in 2003, 3,045 in 2015, and 9,024 in 2022) in Alberta, Canada. Nurse reviewers assessed the presence of 17 clinical conditions using a consistent protocol. The reviews were linked with administrative data using unique identifiers. We compared the accuracy in coding comorbidity by ICD-10, using chart review data as the reference standard. Results: Our findings showed that the mean difference in prevalence between chart reviews and ICD-10 for these 17 conditions was 2.1% in 2003, 7.6% in 2015, and 6.3% in 2022. Some conditions were relatively stable, such as diabetes (1.9%, 2.1%, and 1.1%) and metastatic cancer (0.3%, 1.1%, and 0.4%). For these 17 conditions, the sensitivity ranged from 39.6-85.1% in 2003, 1.3-85.2% in 2015, and 3.0-89.7% in 2022. The C-statistics for predicting in-hospital mortality using comorbidities by ICD-10 were 0.84 in 2003, 0.81 in 2015, and 0.78 in 2022. Discussion: The under-coding could be primarily due to the increase of hospital patient volumes and the limited time allocated to coders. There is a potential to develop artificial intelligence methods based on electronic health records to support coding practices and improve coding quality. Conclusion: Comorbidities were increasingly under-coded over 20 years. The validity of ICD-10 decreased but remained relatively stable for certain conditions mandated for coding. The under-coding exerted minimal impact on in-hospital mortality prediction.
A DNA-Centric Mechanism for Protein Targeting in 6mA Methylation
Authors: Li Yang, Dongbo Wang
Date: 2025-03-31 00:00:00

How DNA-binding proteins locate specific genomic targets remains a central challenge in molecular biology. Traditional protein-centric approaches, which rely on wet-lab experiments and visualization techniques, often lack genome-wide resolution and fail to capture physiological dynamics in living cells. Here, we introduce a DNA-centric strategy that leverages in vivo N6-methyladenine (6mA) data to decode the logic of protein-DNA recognition. By integrating linguistically inspired modeling with machine learning, we reveal two distinct search modes: a protein-driven diffusion mechanism and a DNA sequence-driven mechanism, wherein specific motifs function as protein traps. We further reconstruct high-resolution interaction landscapes at the level of individual sequences and trace the evolutionary trajectories of recognition motifs across species. This framework addresses fundamental limitations of protein-centered approaches and positions DNA itself as an intrinsic reporter of protein-binding behavior.
EAP4EMSIG -- Enhancing Event-Driven Microscopy for Microfluidic Single-Cell Analysis
Authors: Nils Friederich, Angelo Jovin Yamachui Sitcheu, Annika Nassal, Erenus Yildiz, Matthias Pesch, Maximilian Beichter, Lukas Scholtes, Bahar Akbaba, Thomas Lautenschlager, Oliver Neumann, Dietrich Kohlheyer, Hanno Scharr, Johannes Seiffarth, Katharina Nöh, Ralf Mikut
Date: 2025-03-30 00:00:00
Tasks: Deep Learning, Segmentation

Microfluidic Live-Cell Imaging yields data on microbial cell factories. However, continuous acquisition is challenging as high-throughput experiments often lack realtime insights, delaying responses to stochastic events. We introduce three components in the Experiment Automation Pipeline for Event-Driven Microscopy to Smart Microfluidic Single-Cell Analysis: a fast, accurate Deep Learning autofocusing method predicting the focus offset, an evaluation of real-time segmentation methods and a realtime data analysis dashboard. Our autofocusing achieves a Mean Absolute Error of 0.0226\textmu m with inference times below 50~ms. Among eleven Deep Learning segmentation methods, Cellpose~3 reached a Panoptic Quality of 93.58\%, while a distance-based method is fastest (121~ms, Panoptic Quality 93.02\%). All six Deep Learning Foundation Models were unsuitable for real-time segmentation.
Improving Diseases Predictions Utilizing External Bio-Banks
Authors: Hido Pinto, Eran Segal
Date: 2025-03-30 00:00:00
Tasks: Survival Analysis

Machine learning has been successfully used in critical domains, such as medicine. However, extracting meaningful insights from biomedical data is often constrained by the lack of their available disease labels. In this research, we demonstrate how machine learning can be leveraged to enhance explainability and uncover biologically meaningful associations, even when predictive improvements in disease modeling are limited. We train LightGBM models from scratch on our dataset (10K) to impute metabolomics features and apply them to the UK Biobank (UKBB) for downstream analysis. The imputed metabolomics features are then used in survival analysis to assess their impact on disease-related risk factors. As a result, our approach successfully identified biologically relevant connections that were not previously known to the predictive models. Additionally, we applied a genome-wide association study (GWAS) on key metabolomics features, revealing a link between vascular dementia and smoking. Although being a well-established epidemiological relationship, this link was not embedded in the model's training data, which validated the method's ability to extract meaningful signals. Furthermore, by integrating survival models as inputs in the 10K data, we uncovered associations between metabolic substances and obesity, demonstrating the ability to infer disease risk for future patients without requiring direct outcome labels. These findings highlight the potential of leveraging external bio-banks to extract valuable biomedical insights, even in data-limited scenarios. Our results demonstrate that machine learning models trained on smaller datasets can still be used to uncover real biological associations when carefully integrated with survival analysis and genetic studies.
Deep Learning-Based Hypoglycemia Classification Across Multiple Prediction Horizons
Authors: Beyza Cinar, Jennifer Daniel Onwuchekwa, Maria Maleshkova
Date: 2025-03-25 00:00:00
Tasks: Deep Learning

Type 1 diabetes (T1D) management can be significantly enhanced through the use of predictive machine learning (ML) algorithms, which can mitigate the risk of adverse events like hypoglycemia. Hypoglycemia, characterized by blood glucose levels below 70 mg/dL, is a life-threatening condition typically caused by excessive insulin administration, missed meals, or physical activity. Its asymptomatic nature impedes timely intervention, making ML models crucial for early detection. This study integrates short- (up to 2h) and long-term (up to 24h) prediction horizons (PHs) within a single classification model to enhance decision support. The predicted times are 5-15 min, 15-30 min, 30 min-1h, 1-2h, 2-4h, 4-8h, 8-12h, and 12-24h before hypoglycemia. In addition, a simplified model classifying up to 4h before hypoglycemia is compared. We trained ResNet and LSTM models on glucose levels, insulin doses, and acceleration data. The results demonstrate the superiority of the LSTM models when classifying nine classes. In particular, subject-specific models yielded better performance but achieved high recall only for classes 0, 1, and 2 with 98%, 72%, and 50%, respectively. A population-based six-class model improved the results with at least 60% of events detected. In contrast, longer PHs remain challenging with the current approach and may be considered with different models.
Clustering Analysis of Long-term Cardiovascular Complications in COVID-19 Patients
Authors: Seyed Ali Sadegh-Zadeh, Alireza Soleimani Mamalo, Mahsa Behnemoon, Masoud Ojarudi, Naser Gharebaghi, Mohammad Reza Pashaei
Date: 2025-03-23 00:00:00
Tasks: Clustering, Heart Rate Variability

This study investigates long-term cardiovascular complications in COVID-19 patients using advanced clustering techniques. The objective was to analyse ECG parameters, demographic data, comorbidities, and hospitalization details to identify patterns in cardiovascular health outcomes. We applied K-means clustering and identified three distinct clusters: Cluster 0 with moderate heart rate variability and ICU admissions, Cluster 1 with lower heart rate variability and ICU admissions, and Cluster 2 with higher heart rate variability and ICU admissions, indicating higher risk profiles.
Causal analysis of extreme risk in a network of industry portfolios
Authors: Claudia Klüppelberg, Mario Krali
Date: 2025-04-01 00:00:00
Tasks: parameter estimation

We present a methodology for causal risk analysis in a network. Causal dependence is formulated by a max-linear structural equation model, which expresses each node variable as a max-linear function of its parental node variables in a directed acyclic graph and some exogenous innovation. We determine directed~paths~responsible~for extreme risk propagation in the network. We give algorithms for structure learning and parameter estimation and apply them to a network of financial data.
Segmentation variability and radiomics stability for predicting Triple-Negative Breast Cancer subtype using Magnetic Resonance Imaging
Authors: Isabella Cama, Alejandro Guzmán, Cristina Campi, Michele Piana, Karim Lekadir, Sara Garbarino, Oliver Díaz
Date: 2025-04-02 00:00:00
Tasks: feature selection, Segmentation

Most papers caution against using predictive models for disease stratification based on unselected radiomic features, as these features are affected by contouring variability. Instead, they advocate for the use of the Intraclass Correlation Coefficient (ICC) as a measure of stability for feature selection. However, the direct effect of segmentation variability on the predictive models is rarely studied. This study investigates the impact of segmentation variability on feature stability and predictive performance in radiomics-based prediction of Triple-Negative Breast Cancer (TNBC) subtype using Magnetic Resonance Imaging. A total of 244 images from the Duke dataset were used, with segmentation variability introduced through modifications of manual segmentations. For each mask, explainable radiomic features were selected using the Shapley Additive exPlanations method and used to train logistic regression models. Feature stability across segmentations was assessed via ICC, Pearson's correlation, and reliability scores quantifying the relationship between feature stability and segmentation variability. Results indicate that segmentation accuracy does not significantly impact predictive performance. While incorporating peritumoral information may reduce feature reproducibility, it does not diminish feature predictive capability. Moreover, feature selection in predictive models is not inherently tied to feature stability with respect to segmentation, suggesting that an overreliance on ICC or reliability scores for feature selection might exclude valuable predictive features.
shapr: Explaining Machine Learning Models with Conditional Shapley Values in R and Python
Authors: Martin Jullum, Lars Henry Berge Olsen, Jon Lachmann, Annabelle Redelmeier
Date: 2025-04-02 00:00:00

This paper introduces the shapr R package, a versatile tool for generating Shapley value based prediction explanations for machine learning and statistical regression models. Moreover, the shaprpy Python library brings the core capabilities of shapr to the Python ecosystem. Shapley values originate from cooperative game theory in the 1950s, but have over the past few years become a widely used method for quantifying how a model's features/covariates contribute to specific prediction outcomes. The shapr package emphasizes conditional Shapley value estimates, providing a comprehensive range of approaches for accurately capturing feature dependencies -- a crucial aspect for correct model explanation, typically lacking in similar software. In addition to regular tabular data, the shapr R package includes specialized functionality for explaining time series forecasts. The package offers a minimal set of user functions with sensible default values for most use cases while providing extensive flexibility for advanced users to fine-tune computations. Additional features include parallelized computations, iterative estimation with convergence detection, and rich visualization tools. shapr also extends its functionality to compute causal and asymmetric Shapley values when causal information is available. Overall, the shapr and shaprpy packages aim to enhance the interpretability of predictive models within a powerful and user-friendly framework.
Time-to-event prediction for grouped variables using Exclusive Lasso
Authors: Dayasri Ravi, Andreas Groll
Date: 2025-04-02 00:00:00
Tasks: feature selection, regression, Survival Prediction, Time-to-Event Prediction

The integration of high-dimensional genomic data and clinical data into time-to-event prediction models has gained significant attention due to the growing availability of these datasets. Traditionally, a Cox regression model is employed, concatenating various covariate types linearly. Given that much of the data may be redundant or irrelevant, feature selection through penalization is often desirable. A notable characteristic of these datasets is their organization into blocks of distinct data types, such as methylation and clinical predictors, which requires selecting a subset of covariates from each group due to high intra-group correlations. For this reason, we propose utilizing Exclusive Lasso regularization in place of standard Lasso penalization. We apply our methodology to a real-life cancer dataset, demonstrating enhanced survival prediction performance compared to the conventional Cox regression model.
Cause or Trigger? From Philosophy to Causal Modeling
Authors: Kateřina Hlaváčková-Schindler, Rainer Wöß, Vera Pecorino, Philip Schindler
Date: 2025-04-02 00:00:00
Tasks: Philosophy

Not much has been written about the role of triggers in the literature on causal reasoning, causal modeling, or philosophy. In this paper, we focus on describing triggers and causes in the metaphysical sense and on characterizations that differentiate them from each other. We carry out a philosophical analysis of these differences. From this, we formulate a definition that clearly differentiates triggers from causes and can be used for causal reasoning in natural sciences. We propose a mathematical model and the Cause-Trigger algorithm, which, based on given data to observable processes, is able to determine whether a process is a cause or a trigger of an effect. The possibility to distinguish triggers from causes directly from data makes the algorithm a useful tool in natural sciences using observational data, but also for real-world scenarios. For example, knowing the processes that trigger causes of a tropical storm could give politicians time to develop actions such as evacuation the population. Similarly, knowing the triggers of processes that cause global warming could help politicians focus on effective actions. We demonstrate our algorithm on the climatological data of two recent cyclones, Freddy and Zazu. The Cause-Trigger algorithm detects processes that trigger high wind speed in both storms during their cyclogenesis. The findings obtained agree with expert knowledge.
Data-Driven Knowledge Transfer in Batch $Q^*$ Learning
Authors: Elynn Chen, Xi Chen, Wenbo Jing
Date: 2024-04-01 00:00:00
Tasks: Decision Making, Marketing, Navigate, Q-Learning, Transfer Learning

In data-driven decision-making in marketing, healthcare, and education, it is desirable to utilize a large amount of data from existing ventures to navigate high-dimensional feature spaces and address data scarcity in new ventures. We explore knowledge transfer in dynamic decision-making by concentrating on batch stationary environments and formally defining task discrepancies through the lens of Markov decision processes (MDPs). We propose a framework of Transferred Fitted $Q$-Iteration algorithm with general function approximation, enabling the direct estimation of the optimal action-state function $Q^*$ using both target and source data. We establish the relationship between statistical performance and MDP task discrepancy under sieve approximation, shedding light on the impact of source and target sample sizes and task discrepancy on the effectiveness of knowledge transfer. We show that the final learning error of the $Q^*$ function is significantly improved from the single task rate both theoretically and empirically.
Domain Adaptation Under MNAR Missingness
Authors: Tyrel Stokes, Hyungrok Do, Saul Blecker, Rumi Chunara, Samrachana Adhikari
Date: 2025-04-01 00:00:00
Tasks: Domain Adaptation, Imputation

Current domain adaptation methods under missingness shift are restricted to Missing At Random (MAR) missingness mechanisms. However, in many real-world examples, the MAR assumption may be too restrictive. When covariates are Missing Not At Random (MNAR) in both source and target data, the common covariate shift solutions, including importance weighting, are not directly applicable. We show that under reasonable assumptions, the problem of MNAR missingness shift can be reduced to an imputation problem. This allows us to leverage recent methodological developments in both the traditional statistics and machine/deep-learning literature for MNAR imputation to develop a novel domain adaptation procedure for MNAR missingness shift. We further show that our proposed procedure can be extended to handle simultaneous MNAR missingness and covariate shifts. We apply our procedure to Electronic Health Record (EHR) data from two hospitals in south and northeast regions of the US. In this setting we expect different hospital networks and regions to serve different populations and to have different procedures, practices, and software for inputting and recording data, causing simultaneous missingness and covariate shifts.