Xiaoqian Jiang

Yu-Neng Chuang, Guanchu Wang, Chia-Yuan Chang et al.

The exponential growth in scholarly publications necessitates advanced tools for efficient article retrieval, especially in interdisciplinary fields where diverse terminologies are used to describe similar research. Traditional keyword-based search engines often fall short in assisting users who may not be familiar with specific terminologies. To address this, we present a knowledge graph-based paper search engine for biomedical research to enhance the user experience in discovering relevant queries and articles. The system, dubbed DiscoverPath, employs Named Entity Recognition (NER) and part-of-speech (POS) tagging to extract terminologies and relationships from article abstracts to create a KG. To reduce information overload, DiscoverPath presents users with a focused subgraph containing the queried entity and its neighboring nodes and incorporates a query recommendation system, enabling users to iteratively refine their queries. The system is equipped with an accessible Graphical User Interface that provides an intuitive visualization of the KG, query recommendations, and detailed article information, enabling efficient article retrieval, thus fostering interdisciplinary knowledge exploration. DiscoverPath is open-sourced at https://github.com/ynchuang/DiscoverPath.

Ruixiang Tang, Xiaotian Han, Xiaoqian Jiang et al.

Recent advancements in large language models (LLMs) have led to the development of highly potent models like OpenAI's ChatGPT. These models have exhibited exceptional performance in a variety of tasks, such as question answering, essay composition, and code generation. However, their effectiveness in the healthcare sector remains uncertain. In this study, we seek to investigate the potential of ChatGPT to aid in clinical text mining by examining its ability to extract structured information from unstructured healthcare texts, with a focus on biological named entity recognition and relation extraction. However, our preliminary results indicate that employing ChatGPT directly for these tasks resulted in poor performance and raised privacy concerns associated with uploading patients' information to the ChatGPT API. To overcome these limitations, we propose a new training paradigm that involves generating a vast quantity of high-quality synthetic data with labels utilizing ChatGPT and fine-tuning a local model for the downstream task. Our method has resulted in significant improvements in the performance of downstream tasks, improving the F1-score from 23.37% to 63.99% for the named entity recognition task and from 75.86% to 83.59% for the relation extraction task. Furthermore, generating data using ChatGPT can significantly reduce the time and effort required for data collection and labeling, as well as mitigate data privacy concerns. In summary, the proposed framework presents a promising solution to enhance the applicability of LLM models to clinical text mining.

Sirui Ding, Ruixiang Tang, Daochen Zha et al.

Liver transplant is an essential therapy performed for severe liver diseases. The fact of scarce liver resources makes the organ assigning crucial. Model for End-stage Liver Disease (MELD) score is a widely adopted criterion when making organ distribution decisions. However, it ignores post-transplant outcomes and organ/donor features. These limitations motivate the emergence of machine learning (ML) models. Unfortunately, ML models could be unfair and trigger bias against certain groups of people. To tackle this problem, this work proposes a fair machine learning framework targeting graft failure prediction in liver transplant. Specifically, knowledge distillation is employed to handle dense and sparse features by combining the advantages of tree models and neural networks. A two-step debiasing method is tailored for this framework to enhance fairness. Experiments are conducted to analyze unfairness issues in existing models and demonstrate the superiority of our method in both prediction and fairness performance.

Jiayi Yuan, Ruixiang Tang, Xiaoqian Jiang et al.

The process of matching patients with suitable clinical trials is essential for advancing medical research and providing optimal care. However, current approaches face challenges such as data standardization, ethical considerations, and a lack of interoperability between Electronic Health Records (EHRs) and clinical trial criteria. In this paper, we explore the potential of large language models (LLMs) to address these challenges by leveraging their advanced natural language generation capabilities to improve compatibility between EHRs and clinical trial descriptions. We propose an innovative privacy-aware data augmentation approach for LLM-based patient-trial matching (LLM-PTM), which balances the benefits of LLMs while ensuring the security and confidentiality of sensitive patient data. Our experiments demonstrate a 7.32% average improvement in performance using the proposed LLM-PTM method, and the generalizability to new data is improved by 12.12%. Additionally, we present case studies to further illustrate the effectiveness of our approach and provide a deeper understanding of its underlying principles.

Yu-Neng Chuang, Ruixiang Tang, Xiaoqian Jiang et al.

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 prompts with large language models (LLMs) substantially boosts the efficacy of summarization tasks. However, we show that this approach also leads to increased output variance, resulting in notably divergent outputs even when prompts share similar meanings. To tackle this challenge, we introduce a model-agnostic Soft Prompt-Based Calibration (SPeC) pipeline that employs soft prompts to diminish variance while preserving the advantages of prompt-based summarization. Experimental findings on multiple clinical note tasks and LLMs indicate that our method not only bolsters performance but also effectively curbs variance for various LLMs, providing a more uniform and dependable solution for summarizing vital medical information.

Kai Zhang, John A. Lincoln, Xiaoqian Jiang et al.

Multiple Sclerosis (MS) is a chronic disease developed in human brain and spinal cord, which can cause permanent damage or deterioration of the nerves. The severity of MS disease is monitored by the Expanded Disability Status Scale (EDSS), composed of several functional sub-scores. Early and accurate classification of MS disease severity is critical for slowing down or preventing disease progression via applying early therapeutic intervention strategies. Recent advances in deep learning and the wide use of Electronic Health Records (EHR) creates opportunities to apply data-driven and predictive modeling tools for this goal. Previous studies focusing on using single-modal machine learning and deep learning algorithms were limited in terms of prediction accuracy due to the data insufficiency or model simplicity. In this paper, we proposed an idea of using patients' multimodal longitudinal and longitudinal EHR data to predict multiple sclerosis disease severity at the hospital visit. This work has two important contributions. First, we describe a pilot effort to leverage structured EHR data, neuroimaging data and clinical notes to build a multi-modal deep learning framework to predict patient's MS disease severity. The proposed pipeline demonstrates up to 25% increase in terms of the area under the Area Under the Receiver Operating Characteristic curve (AUROC) compared to models using single-modal data. Second, the study also provides insights regarding the amount useful signal embedded in each data modality with respect to MS disease prediction, which may improve data collection processes.

Yao-Shun Chuang, Xiaoqian Jiang, Chun-Teh Lee et al.

This study explored the usability of prompt generation on named entity recognition (NER) tasks and the performance in different settings of the prompt. The prompt generation by GPT-J models was utilized to directly test the gold standard as well as to generate the seed and further fed to the RoBERTa model with the spaCy package. In the direct test, a lower ratio of negative examples with higher numbers of examples in prompt achieved the best results with a F1 score of 0.72. The performance revealed consistency, 0.92-0.97 in the F1 score, in all settings after training with the RoBERTa model. The study highlighted the importance of seed quality rather than quantity in feeding NER models. This research reports on an efficient and accurate way to mine clinical notes for periodontal diagnoses, allowing researchers to easily and quickly build a NER model with the prompt generation approach.

Yao-Shun Chuang, Chun-Teh Lee, Ryan Brandon et al.

This study aimed to utilize text processing and natural language processing (NLP) models to mine clinical notes for the diagnosis of periodontitis and to evaluate the performance of a named entity recognition (NER) model on different regular expression (RE) methods. Two complexity levels of RE methods were used to extract and generate the training data. The SpaCy package and RoBERTa transformer models were used to build the NER model and evaluate its performance with the manual-labeled gold standards. The comparison of the RE methods with the gold standard showed that as the complexity increased in the RE algorithms, the F1 score increased from 0.3-0.4 to around 0.9. The NER models demonstrated excellent predictions, with the simple RE method showing 0.84-0.92 in the evaluation metrics, and the advanced and combined RE method demonstrating 0.95-0.99 in the evaluation. This study provided an example of the benefit of combining NER methods and NLP models in extracting target information from free-text to structured data and fulfilling the need for missing diagnoses from unstructured notes.

Yifei Ren, Jian Lou, Li Xiong et al.

Tensor factorization has received increasing interest due to its intrinsic ability to capture latent factors in multi-dimensional data with many applications such as recommender systems and Electronic Health Records (EHR) mining. PARAFAC2 and its variants have been proposed to address irregular tensors where one of the tensor modes is not aligned, e.g., different users in recommender systems or patients in EHRs may have different length of records. PARAFAC2 has been successfully applied on EHRs for extracting meaningful medical concepts (phenotypes). Despite recent advancements, current models' predictability and interpretability are not satisfactory, which limits its utility for downstream analysis. In this paper, we propose MULTIPAR: a supervised irregular tensor factorization with multi-task learning. MULTIPAR is flexible to incorporate both static (e.g. in-hospital mortality prediction) and continuous or dynamic (e.g. the need for ventilation) tasks. By supervising the tensor factorization with downstream prediction tasks and leveraging information from multiple related predictive tasks, MULTIPAR can yield not only more meaningful phenotypes but also better predictive performance for downstream tasks. We conduct extensive experiments on two real-world temporal EHR datasets to demonstrate that MULTIPAR is scalable and achieves better tensor fit with more meaningful subgroups and stronger predictive performance compared to existing state-of-the-art methods.

Tanjida Kabir, Luyao Chen, Muhammad F Walji et al.

Learning about diagnostic features and related clinical information from dental radiographs is important for dental research. However, the lack of expert-annotated data and convenient search tools poses challenges. Our primary objective is to design a search tool that uses a user's query for oral-related research. The proposed framework, Contrastive LAnguage Image REtrieval Search for dental research, Dental CLAIRES, utilizes periapical radiographs and associated clinical details such as periodontal diagnosis, demographic information to retrieve the best-matched images based on the text query. We applied a contrastive representation learning method to find images described by the user's text by maximizing the similarity score of positive pairs (true pairs) and minimizing the score of negative pairs (random pairs). Our model achieved a hit@3 ratio of 96% and a Mean Reciprocal Rank (MRR) of 0.82. We also designed a graphical user interface that allows researchers to verify the model's performance with interactions.

Qiuchen Zhang, Jing Ma, Jian Lou et al.

Deep learning models trained on large-scale data have achieved encouraging performance in many real-world tasks. Meanwhile, publishing those models trained on sensitive datasets, such as medical records, could pose serious privacy concerns. To counter these issues, one of the current state-of-the-art approaches is the Private Aggregation of Teacher Ensembles, or PATE, which achieved promising results in preserving the utility of the model while providing a strong privacy guarantee. PATE combines an ensemble of "teacher models" trained on sensitive data and transfers the knowledge to a "student" model through the noisy aggregation of teachers' votes for labeling unlabeled public data which the student model will be trained on. However, the knowledge or voted labels learned by the student are noisy due to private aggregation. Learning directly from noisy labels can significantly impact the accuracy of the student model. In this paper, we propose the PATE++ mechanism, which combines the current advanced noisy label training mechanisms with the original PATE framework to enhance its accuracy. A novel structure of Generative Adversarial Nets (GANs) is developed in order to integrate them effectively. In addition, we develop a novel noisy label detection mechanism for semi-supervised model training to further improve student model performance when training with noisy labels. We evaluate our method on Fashion-MNIST and SVHN to show the improvements on the original PATE on all measures.

Kai Zhang, Xiaoqian Jiang

In the era of big data, there is an increasing need for healthcare providers, communities, and researchers to share data and collaborate to improve health outcomes, generate valuable insights, and advance research. The Health Insurance Portability and Accountability Act of 1996 (HIPAA) is a federal law designed to protect sensitive health information by defining regulations for protected health information (PHI). However, it does not provide efficient tools for detecting or removing PHI before data sharing. One of the challenges in this area of research is the heterogeneous nature of PHI fields in data across different parties. This variability makes rule-based sensitive variable identification systems that work on one database fail on another. To address this issue, our paper explores the use of machine learning algorithms to identify sensitive variables in structured data, thus facilitating the de-identification process. We made a key observation that the distributions of metadata of PHI fields and non-PHI fields are very different. Based on this novel finding, we engineered over 30 features from the metadata of the original features and used machine learning to build classification models to automatically identify PHI fields in structured Electronic Health Record (EHR) data. We trained the model on a variety of large EHR databases from different data sources and found that our algorithm achieves 99% accuracy when detecting PHI-related fields for unseen datasets. The implications of our study are significant and can benefit industries that handle sensitive data.

Yao-Shun Chuang, Chun-Teh Lee, Oluwabunmi Tokede et al.

This research addresses the issue of missing structured data in dental records by extracting diagnostic information from unstructured text. The updated periodontology classification system's complexity has increased incomplete or missing structured diagnoses. To tackle this, we use advanced AI and NLP methods, leveraging GPT-4 to generate synthetic notes for fine-tuning a RoBERTa model. This significantly enhances the model's ability to understand medical and dental language. We evaluated the model using 120 randomly selected clinical notes from two datasets, demonstrating its improved diagnostic extraction accuracy. The results showed high accuracy in diagnosing periodontal status, stage, and grade, with Site 1 scoring 0.99 and Site 2 scoring 0.98. In the subtype category, Site 2 achieved perfect scores, outperforming Site 1. This method enhances extraction accuracy and broadens its use across dental contexts. The study underscores AI and NLP's transformative impact on healthcare delivery and management. Integrating AI and NLP technologies enhances documentation and simplifies administrative tasks by precisely extracting complex clinical information. This approach effectively addresses challenges in dental diagnostics. Using synthetic training data from LLMs optimizes the training process, improving accuracy and efficiency in identifying periodontal diagnoses from clinical notes. This innovative method holds promise for broader healthcare applications, potentially improving patient care quality.

Yan Hu, Qingyu Chen, Jingcheng Du et al.

Objective: This study quantifies the capabilities of GPT-3.5 and GPT-4 for clinical named entity recognition (NER) tasks and proposes task-specific prompts to improve their performance. Materials and Methods: We evaluated these models on two clinical NER tasks: (1) to extract medical problems, treatments, and tests from clinical notes in the MTSamples corpus, following the 2010 i2b2 concept extraction shared task, and (2) identifying nervous system disorder-related adverse events from safety reports in the vaccine adverse event reporting system (VAERS). To improve the GPT models' performance, we developed a clinical task-specific prompt framework that includes (1) baseline prompts with task description and format specification, (2) annotation guideline-based prompts, (3) error analysis-based instructions, and (4) annotated samples for few-shot learning. We assessed each prompt's effectiveness and compared the models to BioClinicalBERT. Results: Using baseline prompts, GPT-3.5 and GPT-4 achieved relaxed F1 scores of 0.634, 0.804 for MTSamples, and 0.301, 0.593 for VAERS. Additional prompt components consistently improved model performance. When all four components were used, GPT-3.5 and GPT-4 achieved relaxed F1 socres of 0.794, 0.861 for MTSamples and 0.676, 0.736 for VAERS, demonstrating the effectiveness of our prompt framework. Although these results trail BioClinicalBERT (F1 of 0.901 for the MTSamples dataset and 0.802 for the VAERS), it is very promising considering few training samples are needed. Conclusion: While direct application of GPT models to clinical NER tasks falls short of optimal performance, our task-specific prompt framework, incorporating medical knowledge and training samples, significantly enhances GPT models' feasibility for potential clinical applications.

Yan Hu, Xu Zuo, Yujia Zhou et al.

Backgrounds: Information extraction (IE) is critical in clinical natural language processing (NLP). While large language models (LLMs) excel on generative tasks, their performance on extractive tasks remains debated. Methods: We investigated Named Entity Recognition (NER) and Relation Extraction (RE) using 1,588 clinical notes from four sources (UT Physicians, MTSamples, MIMIC-III, and i2b2). We developed an annotated corpus covering 4 clinical entities and 16 modifiers, and compared instruction-tuned LLaMA-2 and LLaMA-3 against BERT in terms of performance, generalizability, computational resources, and throughput to BERT. Results: LLaMA models outperformed BERT across datasets. With sufficient training data, LLaMA showed modest improvements (1% on NER, 1.5-3.7% on RE); improvements were larger with limited training data. On unseen i2b2 data, LLaMA-3-70B outperformed BERT by 7% (F1) on NER and 4% on RE. However, LLaMA models required more computing resources and ran up to 28 times slower. We implemented "Kiwi," a clinical IE package featuring both models, available at https://kiwi.clinicalnlp.org/. Conclusion: This study is among the first to develop and evaluate a comprehensive clinical IE system using open-source LLMs. Results indicate that LLaMA models outperform BERT for clinical NER and RE but with higher computational costs and lower throughputs. These findings highlight that choosing between LLMs and traditional deep learning methods for clinical IE applications should remain task-specific, taking into account both performance metrics and practical considerations such as available computing resources and the intended use case scenarios.

Anindita Nath, Savannah Mwesigwa, Yulin Dai et al.

Summary: The vast generation of genetic data poses a significant challenge in efficiently uncovering valuable knowledge. Introducing GENEVIC, an AI-driven chat framework that tackles this challenge by bridging the gap between genetic data generation and biomedical knowledge discovery. Leveraging generative AI, notably ChatGPT, it serves as a biologist's 'copilot'. It automates the analysis, retrieval, and visualization of customized domain-specific genetic information, and integrates functionalities to generate protein interaction networks, enrich gene sets, and search scientific literature from PubMed, Google Scholar, and arXiv, making it a comprehensive tool for biomedical research. In its pilot phase, GENEVIC is assessed using a curated database that ranks genetic variants associated with Alzheimer's disease, schizophrenia, and cognition, based on their effect weights from the Polygenic Score Catalog, thus enabling researchers to prioritize genetic variants in complex diseases. GENEVIC's operation is user-friendly, accessible without any specialized training, secured by Azure OpenAI's HIPAA-compliant infrastructure, and evaluated for its efficacy through real-time query testing. As a prototype, GENEVIC is set to advance genetic research, enabling informed biomedical decisions. Availability and implementation: GENEVIC is publicly accessible at https://genevic-anath2024.streamlit.app. The underlying code is open-source and available via GitHub at https://github.com/anath2110/GENEVIC.git.

Yao-Shun Chuang, Atiquer Rahman Sarkar, Yu-Chun Hsu et al.

This study examines integrating EHRs and NLP with large language models (LLMs) to improve healthcare data management and patient care. It focuses on using advanced models to create secure, HIPAA-compliant synthetic patient notes for biomedical research. The study used de-identified and re-identified MIMIC III datasets with GPT-3.5, GPT-4, and Mistral 7B to generate synthetic notes. Text generation employed templates and keyword extraction for contextually relevant notes, with one-shot generation for comparison. Privacy assessment checked PHI occurrence, while text utility was tested using an ICD-9 coding task. Text quality was evaluated with ROUGE and cosine similarity metrics to measure semantic similarity with source notes. Analysis of PHI occurrence and text utility via the ICD-9 coding task showed that the keyword-based method had low risk and good performance. One-shot generation showed the highest PHI exposure and PHI co-occurrence, especially in geographic location and date categories. The Normalized One-shot method achieved the highest classification accuracy. Privacy analysis revealed a critical balance between data utility and privacy protection, influencing future data use and sharing. Re-identified data consistently outperformed de-identified data. This study demonstrates the effectiveness of keyword-based methods in generating privacy-protecting synthetic clinical notes that retain data usability, potentially transforming clinical data-sharing practices. The superior performance of re-identified over de-identified data suggests a shift towards methods that enhance utility and privacy by using dummy PHIs to perplex privacy attacks.

Linghui Zeng, Ruixuan Liu, Atiquer Rahman Sarkar et al.

Ensuring the privacy of sensitive training data is crucial in privacy-preserving machine learning. However, in practical scenarios, privacy protection may be required for only a subset of features. For instance, in ICU data, demographic attributes like age and gender pose higher privacy risks due to their re-identification potential, whereas raw lab results are generally less sensitive. Traditional DP-SGD enforces privacy protection on all features in one sample, leading to excessive noise injection and significant utility degradation. We propose FusionDP, a two-step framework that enhances model utility under feature-level differential privacy. First, FusionDP leverages large foundation models to impute sensitive features given non-sensitive features, treating them as external priors that provide high-quality estimates of sensitive attributes without accessing the true values during model training. Second, we introduce a modified DP-SGD algorithm that trains models on both original and imputed features while formally preserving the privacy of the original sensitive features. We evaluate FusionDP on two modalities: a sepsis prediction task on tabular data from PhysioNet and a clinical note classification task from MIMIC-III. By comparing against privacy-preserving baselines, our results show that FusionDP significantly improves model performance while maintaining rigorous feature-level privacy, demonstrating the potential of foundation model-driven imputation to enhance the privacy-utility trade-off for various modalities.

Atiquer Rahman Sarkar, Yao-Shun Chuang, Noman Mohammed et al.

For sharing privacy-sensitive data, de-identification is commonly regarded as adequate for safeguarding privacy. Synthetic data is also being considered as a privacy-preserving alternative. Recent successes with numerical and tabular data generative models and the breakthroughs in large generative language models raise the question of whether synthetically generated clinical notes could be a viable alternative to real notes for research purposes. In this work, we demonstrated that (i) de-identification of real clinical notes does not protect records against a membership inference attack, (ii) proposed a novel approach to generate synthetic clinical notes using the current state-of-the-art large language models, (iii) evaluated the performance of the synthetically generated notes in a clinical domain task, and (iv) proposed a way to mount a membership inference attack where the target model is trained with synthetic data. We observed that when synthetically generated notes closely match the performance of real data, they also exhibit similar privacy concerns to the real data. Whether other approaches to synthetically generated clinical notes could offer better trade-offs and become a better alternative to sensitive real notes warrants further investigation.

Yiwen Lu, Lu Li, Dazheng Zhang et al.

Sample size calculations for power analysis are critical for clinical research and trial design, yet their complexity and reliance on statistical expertise create barriers for many researchers. We introduce PowerGPT, an AI-powered system integrating large language models (LLMs) with statistical engines to automate test selection and sample size estimation in trial design. In a randomized trial to evaluate its effectiveness, PowerGPT significantly improved task completion rates (99.3% vs. 88.9% for test selection, 99.3% vs. 77.8% for sample size calculation) and accuracy (94.1% vs. 55.4% in sample size estimation, p < 0.001), while reducing average completion time (4.0 vs. 9.3 minutes, p < 0.001). These gains were consistent across various statistical tests and benefited both statisticians and non-statisticians as well as bridging expertise gaps. Already under deployment across multiple institutions, PowerGPT represents a scalable AI-driven approach that enhances accessibility, efficiency, and accuracy in statistical power analysis for clinical research.

Jiaxin Liu, Xiaoqian Jiang, Xiang Li et al.

Fairness has been a significant challenge in graph neural networks (GNNs) since degree biases often result in un-equal prediction performance among nodes with varying degrees. Existing GNN models focus on prediction accuracy, frequently overlooking fairness across different degree groups. To addressthis issue, we propose a novel GNN framework, namely Fairness- Aware Asymmetric Contrastive Ensemble (FairACE), which inte-grates asymmetric contrastive learning with adversarial training to improve degree fairness. FairACE captures one-hop local neighborhood information and two-hop monophily similarity to create fairer node representations and employs a degree fairness regulator to balance performance between high-degree and low-degree nodes. During model training, a novel group-balanced fairness loss is proposed to minimize classification disparities across degree groups. In addition, we also propose a novel fairness metric, the Accuracy Distribution Gap (ADG), which can quantitatively assess and ensure equitable performance across different degree-based node groups. Experimental results on both synthetic and real-world datasets demonstrate that FairACE significantly improves degree fairness metrics while maintaining competitive accuracy in comparison to the state-of-the-art GNN models.

Wenbiao Li, Anisa Halimi, Xiaoqian Jiang et al.

This paper presents a framework for privacy-preserving verification of machine learning models, focusing on models trained on sensitive data. Integrating Local Differential Privacy (LDP) with model explanations from LIME and SHAP, our framework enables robust verification without compromising individual privacy. It addresses two key tasks: binary classification, to verify if a target model was trained correctly by applying the appropriate preprocessing steps, and multi-class classification, to identify specific preprocessing errors. Evaluations on three real-world datasets-Diabetes, Adult, and Student Record-demonstrate that while the ML-based approach is particularly effective in binary tasks, the threshold-based method performs comparably in multi-class tasks. Results indicate that although verification accuracy varies across datasets and noise levels, the framework provides effective detection of preprocessing errors, strong privacy guarantees, and practical applicability for safeguarding sensitive data.

Jing Zhang, Xiaoqian Jiang, Yingjie Xie et al.

Heterogeneous graphs can well describe the complex entity relationships in the real world. For example, online shopping networks contain multiple physical types of consumers and products, as well as multiple relationship types such as purchasing and favoriting. More and more scholars pay attention to this research because heterogeneous graph representation learning shows strong application potential in real-world scenarios. However, the existing heterogeneous graph models use data augmentation techniques to enhance the use of graph structure information, which only captures the graph structure information from the spatial topology, ignoring the information displayed in the spectrum dimension of the graph structure. To address the issue that heterogeneous graph representation learning methods fail to model spectral information, this paper introduces a spectral-enhanced graph contrastive learning model (SHCL) and proposes a spectral augmentation algorithm for the first time in heterogeneous graph neural networks. The proposed model learns an adaptive topology augmentation scheme through the heterogeneous graph itself, disrupting the structural information of the heterogeneous graph in the spectrum dimension, and ultimately improving the learning effect of the model. Experimental results on multiple real-world datasets demonstrate substantial advantages of the proposed model.

Yaobin Ling, Xiaoqian Jiang, Yejin Kim

In the era of big data, access to abundant data is crucial for driving research forward. However, such data is often inaccessible due to privacy concerns or high costs, particularly in healthcare domain. Generating synthetic (tabular) data can address this, but existing models typically require substantial amounts of data to train effectively, contradicting our objective to solve data scarcity. To address this challenge, we propose a novel framework to generate synthetic tabular data, powered by large language models (LLMs) that emulates the architecture of a Generative Adversarial Network (GAN). By incorporating data generation process as contextual information and utilizing LLM as the optimizer, our approach significantly enhance the quality of synthetic data generation in common scenarios with small sample sizes. Our experimental results on public and private datasets demonstrate that our model outperforms several state-of-art models regarding generating higher quality synthetic data for downstream tasks while keeping privacy of the real data.

Pulakesh Upadhyaya, Kai Zhang, Can Li et al.

Causal structure learning refers to a process of identifying causal structures from observational data, and it can have multiple applications in biomedicine and health care. This paper provides a practical review and tutorial on scalable causal structure learning models with examples of real-world data to help health care audiences understand and apply them. We reviewed traditional (combinatorial and score-based methods) for causal structure discovery and machine learning-based schemes. We also highlighted recent developments in biomedicine where causal structure learning can be applied to discover structures such as gene networks, brain connectivity networks, and those in cancer epidemiology. We also compared the performance of traditional and machine learning-based algorithms for causal discovery over some benchmark data sets. Machine learning-based approaches, including deep learning, have many advantages over traditional approaches, such as scalability, including a greater number of variables, and potentially being applied in a wide range of biomedical applications, such as genetics, if sufficient data are available. Furthermore, these models are more flexible than traditional models and are poised to positively affect many applications in the future.

Wentao Li, Jiayi Tong, Md. Monowar Anjum et al.

Objectives: This paper develops two algorithms to achieve federated generalized linear mixed effect models (GLMM), and compares the developed model's outcomes with each other, as well as that from the standard R package (`lme4'). Methods: The log-likelihood function of GLMM is approximated by two numerical methods (Laplace approximation and Gaussian Hermite approximation), which supports federated decomposition of GLMM to bring computation to data. Results: Our developed method can handle GLMM to accommodate hierarchical data with multiple non-independent levels of observations in a federated setting. The experiment results demonstrate comparable (Laplace) and superior (Gaussian-Hermite) performances with simulated and real-world data. Conclusion: We developed and compared federated GLMMs with different approximations, which can support researchers in analyzing biomedical data to accommodate mixed effects and address non-independence due to hierarchical structures (i.e., institutes, region, country, etc.).

Yaobin Ling, Pulakesh Upadhyaya, Luyao Chen et al.

Developing new drugs for target diseases is a time-consuming and expensive task, drug repurposing has become a popular topic in the drug development field. As much health claim data become available, many studies have been conducted on the data. The real-world data is noisy, sparse, and has many confounding factors. In addition, many studies have shown that drugs effects are heterogeneous among the population. Lots of advanced machine learning models about estimating heterogeneous treatment effects (HTE) have emerged in recent years, and have been applied to in econometrics and machine learning communities. These studies acknowledge medicine and drug development as the main application area, but there has been limited translational research from the HTE methodology to drug development. We aim to introduce the HTE methodology to the healthcare area and provide feasibility consideration when translating the methodology with benchmark experiments on healthcare administrative claim data. Also, we want to use benchmark experiments to show how to interpret and evaluate the model when it is applied to healthcare research. By introducing the recent HTE techniques to a broad readership in biomedical informatics communities, we expect to promote the wide adoption of causal inference using machine learning. We also expect to provide the feasibility of HTE for personalized drug effectiveness.

Chun-Teh Lee, Tanjida Kabir, Jiman Nelson et al.

Abstract: Aim: The goal was to use a Deep Convolutional Neural Network to measure the radiographic alveolar bone level to aid periodontal diagnosis. Material and methods: A Deep Learning (DL) model was developed by integrating three segmentation networks (bone area, tooth, cementoenamel junction) and image analysis to measure the radiographic bone level and assign radiographic bone loss (RBL) stages. The percentage of RBL was calculated to determine the stage of RBL for each tooth. A provisional periodontal diagnosis was assigned using the 2018 periodontitis classification. RBL percentage, staging, and presumptive diagnosis were compared to the measurements and diagnoses made by the independent examiners. Results: The average Dice Similarity Coefficient (DSC) for segmentation was over 0.91. There was no significant difference in RBL percentage measurements determined by DL and examiners (p=0.65). The Area Under the Receiver Operating Characteristics Curve of RBL stage assignment for stage I, II and III was 0.89, 0.90 and 0.90, respectively. The accuracy of the case diagnosis was 0.85. Conclusion: The proposed DL model provides reliable RBL measurements and image-based periodontal diagnosis using periapical radiographic images. However, this model has to be further optimized and validated by a larger number of images to facilitate its application.

Kai Zhang, Chao Tian, Kun Zhang et al.

The PC algorithm is the state-of-the-art algorithm for causal structure discovery on observational data. It can be computationally expensive in the worst case due to the conditional independence tests are performed in an exhaustive-searching manner. This makes the algorithm computationally intractable when the task contains several hundred or thousand nodes, particularly when the true underlying causal graph is dense. We propose a critical observation that the conditional set rendering two nodes independent is non-unique, and including certain redundant nodes do not sacrifice result accuracy. Based on this finding, the innovations of our work are two-folds. First, we innovate on a reserve order linkage pruning PC algorithm which significantly increases the algorithm's efficiency. Second, we propose a parallel computing strategy for statistical independence tests by leveraging tensor computation, which brings further speedup. We also prove the proposed algorithm does not induce statistical power loss under mild graph and data dimensionality assumptions. Experimental results show that the single-threaded version of the proposed algorithm can achieve a 6-fold speedup compared to the PC algorithm on a dense 95-node graph, and the parallel version can make a 825-fold speed-up. We also provide proof that the proposed algorithm is consistent under the same set of conditions with conventional PC algorithm.

Md Monowar Anjum, Noman Mohammed, Xiaoqian Jiang

In this work, we propose a novel problem formulation for de-identification of unstructured clinical text. We formulate the de-identification problem as a sequence to sequence learning problem instead of a token classification problem. Our approach is inspired by the recent state-of -the-art performance of sequence to sequence learning models for named entity recognition. Early experimentation of our proposed approach achieved 98.91% recall rate on i2b2 dataset. This performance is comparable to current state-of-the-art models for unstructured clinical text de-identification.

Greg M. Silverman, Raymond L. Finzel, Michael V. Heinz et al.

Our objective in this study is to investigate the behavior of Boolean operators on combining annotation output from multiple Natural Language Processing (NLP) systems across multiple corpora and to assess how filtering by aggregation of Unified Medical Language System (UMLS) Metathesaurus concepts affects system performance for Named Entity Recognition (NER) of UMLS concepts. We used three corpora annotated for UMLS concepts: 2010 i2b2 VA challenge set (31,161 annotations), Multi-source Integrated Platform for Answering Clinical Questions (MiPACQ) corpus (17,457 annotations including UMLS concept unique identifiers), and Fairview Health Services corpus (44,530 annotations). Our results showed that for UMLS concept matching, Boolean ensembling of the MiPACQ corpus trended towards higher performance over individual systems. Use of an approximate grid-search can help optimize the precision-recall tradeoff and can provide a set of heuristics for choosing an optimal set of ensembles.

Yan Ding, Xiaoqian Jiang, Yejin Kim

Evaluating the blood-brain barrier (BBB) permeability of drug molecules is a critical step in brain drug development. Traditional methods for the evaluation require complicated in vitro or in vivo testing. Alternatively, in silico predictions based on machine learning have proved to be a cost-efficient way to complement the in vitro and in vivo methods. However, the performance of the established models has been limited by their incapability of dealing with the interactions between drugs and proteins, which play an important role in the mechanism behind the BBB penetrating behaviors. To address this limitation, we employed the relational graph convolutional network (RGCN) to handle the drug-protein interactions as well as the properties of each individual drug. The RGCN model achieved an overall accuracy of 0.872, an AUROC of 0.919 and an AUPRC of 0.838 for the testing dataset with the drug-protein interactions and the Mordred descriptors as the input. Introducing drug-drug similarity to connect structurally similar drugs in the data graph further improved the testing results, giving an overall accuracy of 0.876, an AUROC of 0.926 and an AUPRC of 0.865. In particular, the RGCN model was found to greatly outperform the LightGBM base model when evaluated with the drugs whose BBB penetration was dependent on drug-protein interactions. Our model is expected to provide high-confidence predictions of BBB permeability for drug prioritization in the experimental screening of BBB-penetrating drugs.

Miran Kim, Xiaoqian Jiang, Kristin Lauter et al.

Advanced computer vision technology can provide near real-time home monitoring to support "aging in place" by detecting falls and symptoms related to seizures and stroke. Affordable webcams, together with cloud computing services (to run machine learning algorithms), can potentially bring significant social benefits. However, it has not been deployed in practice because of privacy concerns. In this paper, we propose a strategy that uses homomorphic encryption to resolve this dilemma, which guarantees information confidentiality while retaining action detection. Our protocol for secure inference can distinguish falls from activities of daily living with 86.21% sensitivity and 99.14% specificity, with an average inference latency of 1.2 seconds and 2.4 seconds on real-world test datasets using small and large neural nets, respectively. We show that our method enables a 613x speedup over the latency-optimized LoLa and achieves an average of 3.1x throughput increase in secure inference compared to the throughput-optimized nGraph-HE2.

Hannah Lei, Weiqi Lu, Alan Ji et al.

Many COVID-19 patients developed prolonged symptoms after the infection, including fatigue, delirium, and headache. The long-term health impact of these conditions is still not clear. It is necessary to develop a way to follow up with these patients for monitoring their health status to support timely intervention and treatment. In the lack of sufficient human resources to follow up with patients, we propose a novel smart chatbot solution backed with machine learning to collect information (i.e., generating digital diary) in a personalized manner. In this article, we describe the design framework and components of our prototype.

Kai Zhang, Siddharth Karanth, Bela Patel et al.

We propose a robust in-time predictor for in-hospital COVID-19 patient's probability of requiring mechanical ventilation. A challenge in the risk prediction for COVID-19 patients lies in the great variability and irregular sampling of patient's vitals and labs observed in the clinical setting. Existing methods have strong limitations in handling time-dependent features' complex dynamics, either oversimplifying temporal data with summary statistics that lose information or over-engineering features that lead to less robust outcomes. We propose a novel in-time risk trajectory predictive model to handle the irregular sampling rate in the data, which follows the dynamics of risk of performing mechanical ventilation for individual patients. The model incorporates the Multi-task Gaussian Process using observed values to learn the posterior joint multi-variant conditional probability and infer the missing values on a unified time grid. The temporal imputed data is fed into a multi-objective self-attention network for the prediction task. A novel positional encoding layer is proposed and added to the network for producing in-time predictions. The positional layer outputs a risk score at each user-defined time point during the entire hospital stay of an inpatient. We frame the prediction task into a multi-objective learning framework, and the risk scores at all time points are optimized altogether, which adds robustness and consistency to the risk score trajectory prediction. Our experimental evaluation on a large database with nationwide in-hospital patients with COVID-19 also demonstrates that it improved the state-of-the-art performance in terms of AUC (Area Under the receiver operating characteristic Curve) and AUPRC (Area Under the Precision-Recall Curve) performance metrics, especially at early times after hospital admission.

Anisa Halimi, Leonard Dervishi, Erman Ayday et al.

Providing provenance in scientific workflows is essential for reproducibility and auditability purposes. Workflow systems model and record provenance describing the steps performed to obtain the final results of a computation. In this work, we propose a framework that verifies the correctness of the statistical test results that are conducted by a researcher while protecting individuals' privacy in the researcher's dataset. The researcher publishes the workflow of the conducted study, its output, and associated metadata. They keep the research dataset private while providing, as part of the metadata, a partial noisy dataset (that achieves local differential privacy). To check the correctness of the workflow output, a verifier makes use of the workflow, its metadata, and results of another statistical study (using publicly available datasets) to distinguish between correct statistics and incorrect ones. We use case the proposed framework in the genome-wide association studies (GWAS), in which the goal is to identify highly associated point mutations (variants) with a given phenotype. For evaluation, we use real genomic data and show that the correctness of the workflow output can be verified with high accuracy even when the aggregate statistics of a small number of variants are provided. We also quantify the privacy leakage due to the provided workflow and its associated metadata in the GWAS use-case and show that the additional privacy risk due to the provided metadata does not increase the existing privacy risk due to sharing of the research results. Thus, our results show that the workflow output (i.e., research results) can be verified with high confidence in a privacy-preserving way. We believe that this work will be a valuable step towards providing provenance in a privacy-preserving way while providing guarantees to the users about the correctness of the results.

Yi Deng, Xiaoqian Jiang, Qi Long

Distributed health data networks that use information from multiple sources have drawn substantial interest in recent years. However, missing data are prevalent in such networks and present significant analytical challenges. The current state-of-the-art methods for handling missing data require pooling data into a central repository before analysis, which may not be possible in a distributed health data network. In this paper, we propose a privacy-preserving distributed analysis framework for handling missing data when data are vertically partitioned. In this framework, each institution with a particular data source utilizes the local private data to calculate necessary intermediate aggregated statistics, which are then shared to build a global model for handling missing data. To evaluate our proposed methods, we conduct simulation studies that clearly demonstrate that the proposed privacy-preserving methods perform as well as the methods using the pooled data and outperform several naïve methods. We further illustrate the proposed methods through the analysis of a real dataset. The proposed framework for handling vertically partitioned incomplete data is substantially more privacy-preserving than methods that require pooling of the data, since no individual-level data are shared, which can lower hurdles for collaboration across multiple institutions and build stronger public trust.

Yuqi Si, Jingcheng Du, Zhao Li et al.

Patient representation learning refers to learning a dense mathematical representation of a patient that encodes meaningful information from Electronic Health Records (EHRs). This is generally performed using advanced deep learning methods. This study presents a systematic review of this field and provides both qualitative and quantitative analyses from a methodological perspective. We identified studies developing patient representations from EHRs with deep learning methods from MEDLINE, EMBASE, Scopus, the Association for Computing Machinery (ACM) Digital Library, and Institute of Electrical and Electronics Engineers (IEEE) Xplore Digital Library. After screening 363 articles, 49 papers were included for a comprehensive data collection. We noticed a typical workflow starting with feeding raw data, applying deep learning models, and ending with clinical outcome predictions as evaluations of the learned representations. Specifically, learning representations from structured EHR data was dominant (37 out of 49 studies). Recurrent Neural Networks were widely applied as the deep learning architecture (LSTM: 13 studies, GRU: 11 studies). Disease prediction was the most common application and evaluation (31 studies). Benchmark datasets were mostly unavailable (28 studies) due to privacy concerns of EHR data, and code availability was assured in 20 studies. We show the importance and feasibility of learning comprehensive representations of patient EHR data through a systematic review. Advances in patient representation learning techniques will be essential for powering patient-level EHR analyses. Future work will still be devoted to leveraging the richness and potential of available EHR data. Knowledge distillation and advanced learning techniques will be exploited to assist the capability of learning patient representation further.

Kanglin Hsieh, Yinyin Wang, Luyao Chen et al.

Amid the pandemic of 2019 novel coronavirus disease (COVID-19) infected by SARS-CoV-2, a vast amount of drug research for prevention and treatment has been quickly conducted, but these efforts have been unsuccessful thus far. Our objective is to prioritize repurposable drugs using a drug repurposing pipeline that systematically integrates multiple SARS-CoV-2 and drug interactions, deep graph neural networks, and in-vitro/population-based validations. We first collected all the available drugs (n= 3,635) involved in COVID-19 patient treatment through CTDbase. We built a SARS-CoV-2 knowledge graph based on the interactions among virus baits, host genes, pathways, drugs, and phenotypes. A deep graph neural network approach was used to derive the candidate representation based on the biological interactions. We prioritized the candidate drugs using clinical trial history, and then validated them with their genetic profiles, in vitro experimental efficacy, and electronic health records. We highlight the top 22 drugs including Azithromycin, Atorvastatin, Aspirin, Acetaminophen, and Albuterol. We further pinpointed drug combinations that may synergistically target COVID-19. In summary, we demonstrated that the integration of extensive interactions, deep neural networks, and rigorous validation can facilitate the rapid identification of candidate drugs for COVID-19 treatment. This is a post-peer-review, pre-copyedit version of an article published in Scientific Reports The final authenticated version is available online at: https://www.nature.com/articles/s41598-021-02353-5

Yeongjae Gil, Xiaoqian Jiang, Miran Kim et al.

Data integration and sharing maximally enhance the potential for novel and meaningful discoveries. However, it is a non-trivial task as integrating data from multiple sources can put sensitive information of study participants at risk. To address the privacy concern, we present a distributed Bayesian learning approach via Preconditioned Stochastic Gradient Langevin Dynamics with RMSprop, which combines differential privacy and homomorphic encryption in a harmonious manner while protecting private information. We applied the proposed secure and privacy-preserving distributed Bayesian learning approach to logistic regression and survival analysis on distributed data, and demonstrated its feasibility in terms of prediction accuracy and time complexity, compared to the centralized approach.

Rui Zhang, Luca Giancardo, Danilo A. Pena et al.

In this paper, we studied the association between the change of structural brain volumes to the potential development of Alzheimer's disease (AD). Using a simple abstraction technique, we converted regional cortical and subcortical volume differences over two time points for each study subject into a graph. We then obtained substructures of interest using a graph decomposition algorithm in order to extract pivotal nodes via multi-view feature selection. Intensive experiments using robust classification frameworks were conducted to evaluate the performance of using the brain substructures obtained under different thresholds. The results indicated that compact substructures acquired by examining the differences between patient groups were sufficient to discriminate between AD and healthy controls with an area under the receiver operating curve of 0.72.

Xiaoqian Jiang, Samden Lhatoo, Guo-Qiang Zhang et al.

Existing studies consider Alzheimer's disease (AD) a comorbidity of epilepsy, but also recognize epilepsy to occur more frequently in patients with AD than those without. The goal of this paper is to understand the relationship between epilepsy and AD by studying causal relations among subgroups of epilepsy patients. We develop an approach combining representation learning with tensor factorization to provide an in-depth analysis of the risk factors among epilepsy patients for AD. An epilepsy-AD cohort of ~600,000 patients were extracted from Cerner Health Facts data (50M patients). Our experimental results not only suggested a causal relationship between epilepsy and later onset of AD ( p = 1.92e-51), but also identified five epilepsy subgroups with distinct phenotypic patterns leading to AD. While such findings are preliminary, the proposed method combining representation learning with tensor factorization seems to be an effective approach for risk factor analysis.

Yejin Kim, Xiaoqian Jiang, Luyao Chen et al.

Sleep change is commonly reported in Alzheimer's disease (AD) patients and their brain wave studies show decrease in dreaming and non-dreaming stages. Although sleep disturbance is generally considered as a consequence of AD, it might also be a risk factor of AD as new biological evidence shows. Leveraging National Sleep Research Resource (NSRR), we built a unique cohort of 83 cases and 331 controls with clinical variables and EEG signals. Supervised tensor factorization method was applied for this temporal dataset to extract discriminative sleep patterns. Among the 30 patterns extracted, we identified 5 significant patterns (4 patterns for AD likely and 1 pattern for normal ones) and their visual patterns provide interesting linkage to sleep with repeated wakefulness, insomnia, epileptic seizure, and etc. This study is preliminary but findings are interesting, which is a first step to provide quantifiable evidences to measure sleep as a risk factor of AD.

Yikuan Li, Liang Yao, Chengsheng Mao et al.

Acute kidney injury (AKI) in critically ill patients is associated with significant morbidity and mortality. Development of novel methods to identify patients with AKI earlier will allow for testing of novel strategies to prevent or reduce the complications of AKI. We developed data-driven prediction models to estimate the risk of new AKI onset. We generated models from clinical notes within the first 24 hours following intensive care unit (ICU) admission extracted from Medical Information Mart for Intensive Care III (MIMIC-III). From the clinical notes, we generated clinically meaningful word and concept representations and embeddings, respectively. Five supervised learning classifiers and knowledge-guided deep learning architecture were used to construct prediction models. The best configuration yielded a competitive AUC of 0.779. Our work suggests that natural language processing of clinical notes can be applied to assist clinicians in identifying the risk of incident AKI onset in critically ill patients upon admission to the ICU.

Jian Liang, Ziqi Liu, Jiayu Zhou et al.

Multi-task learning (MTL) refers to the paradigm of learning multiple related tasks together. In contrast, in single-task learning (STL) each individual task is learned independently. MTL often leads to better trained models because they can leverage the commonalities among related tasks. However, because MTL algorithms can ``leak" information from different models across different tasks, MTL poses a potential security risk. Specifically, an adversary may participate in the MTL process through one task and thereby acquire the model information for another task. The previously proposed privacy-preserving MTL methods protect data instances rather than models, and some of them may underperform in comparison with STL methods. In this paper, we propose a privacy-preserving MTL framework to prevent information from each model leaking to other models based on a perturbation of the covariance matrix of the model matrix. We study two popular MTL approaches for instantiation, namely, learning the low-rank and group-sparse patterns of the model matrix. Our algorithms can be guaranteed not to underperform compared with STL methods. We build our methods based upon tools for differential privacy, and privacy guarantees, utility bounds are provided, and heterogeneous privacy budgets are considered. The experiments demonstrate that our algorithms outperform the baseline methods constructed by existing privacy-preserving MTL methods on the proposed model-protection problem.

Jason N. Doctor, Jaideep Vaidya, Xiaoqian Jiang et al.

Secure computation of equivalence has fundamental application in many different areas, including healthcare. We study this problem in the context of matching an individual identity to link medical records across systems. We develop an efficient solution for equivalence based on existing work that can evaluate the greater than relation. We implement the approach and demonstrate its effectiveness on data, as well as demonstrate how it meets regulatory criteria for risk.

Yejin Kim, Jimeng Sun, Hwanjo Yu et al.

Tensor factorization models offer an effective approach to convert massive electronic health records into meaningful clinical concepts (phenotypes) for data analysis. These models need a large amount of diverse samples to avoid population bias. An open challenge is how to derive phenotypes jointly across multiple hospitals, in which direct patient-level data sharing is not possible (e.g., due to institutional policies). In this paper, we developed a novel solution to enable federated tensor factorization for computational phenotyping without sharing patient-level data. We developed secure data harmonization and federated computation procedures based on alternating direction method of multipliers (ADMM). Using this method, the multiple hospitals iteratively update tensors and transfer secure summarized information to a central server, and the server aggregates the information to generate phenotypes. We demonstrated with real medical datasets that our method resembles the centralized training model (based on combined datasets) in terms of accuracy and phenotypes discovery while respecting privacy.

Md Nazmus Sadat, Md Momin Al Aziz, Noman Mohammed et al.

Recent studies demonstrate that effective healthcare can benefit from using the human genomic information. For instance, analysis of tumor genomes has revealed 140 genes whose mutations contribute to cancer. As a result, many institutions are using statistical analysis of genomic data, which are mostly based on genome-wide association studies (GWAS). GWAS analyze genome sequence variations in order to identify genetic risk factors for diseases. These studies often require pooling data from different sources together in order to unravel statistical patterns or relationships between genetic variants and diseases. In this case, the primary challenge is to fulfill one major objective: accessing multiple genomic data repositories for collaborative research in a privacy-preserving manner. Due to the sensitivity and privacy concerns regarding the genomic data, multi-jurisdictional laws and policies of cross-border genomic data sharing are enforced among different regions of the world. In this article, we present SAFETY, a hybrid framework, which can securely perform GWAS on federated genomic datasets using homomorphic encryption and recently introduced secure hardware component of Intel Software Guard Extensions (Intel SGX) to ensure high efficiency and privacy at the same time. Different experimental settings show the efficacy and applicability of such hybrid framework in secure conduction of GWAS. To the best of our knowledge, this hybrid use of homomorphic encryption along with Intel SGX is not proposed or experimented to this date. Our proposed framework, SAFETY is up to 4.82 times faster than the best existing secure computation technique.

Aditya Menon, Xiaoqian Jiang, Shankar Vembu et al.

In many real-world applications of machine learning classifiers, it is essential to predict the probability of an example belonging to a particular class. This paper proposes a simple technique for predicting probabilities based on optimizing a ranking loss, followed by isotonic regression. This semi-parametric technique offers both good ranking and regression performance, and models a richer set of probability distributions than statistical workhorses such as logistic regression. We provide experimental results that show the effectiveness of this technique on real-world applications of probability prediction.