Cui Tao

Yiming Li, Jianfu Li, Jianping He et al.

Though Vaccines are instrumental in global health, mitigating infectious diseases and pandemic outbreaks, they can occasionally lead to adverse events (AEs). Recently, Large Language Models (LLMs) have shown promise in effectively identifying and cataloging AEs within clinical reports. Utilizing data from the Vaccine Adverse Event Reporting System (VAERS) from 1990 to 2016, this study particularly focuses on AEs to evaluate LLMs' capability for AE extraction. A variety of prevalent LLMs, including GPT-2, GPT-3 variants, GPT-4, and Llama 2, were evaluated using Influenza vaccine as a use case. The fine-tuned GPT 3.5 model (AE-GPT) stood out with a 0.704 averaged micro F1 score for strict match and 0.816 for relaxed match. The encouraging performance of the AE-GPT underscores LLMs' potential in processing medical data, indicating a significant stride towards advanced AE detection, thus presumably generalizable to other AE extraction tasks.

Tiehang Duan, Zhenyi Wang, Gianfranco Doretto et al.

Recently, deep learning has shown to be effective for Electroencephalography (EEG) decoding tasks. Yet, its performance can be negatively influenced by two key factors: 1) the high variance and different types of corruption that are inherent in the signal, 2) the EEG datasets are usually relatively small given the acquisition cost, annotation cost and amount of effort needed. Data augmentation approaches for alleviation of this problem have been empirically studied, with augmentation operations on spatial domain, time domain or frequency domain handcrafted based on expertise of domain knowledge. In this work, we propose a principled approach to perform dynamic evolution on the data for improvement of decoding robustness. The approach is based on distributionally robust optimization and achieves robustness by optimizing on a family of evolved data distributions instead of the single training data distribution. We derived a general data evolution framework based on Wasserstein gradient flow (WGF) and provides two different forms of evolution within the framework. Intuitively, the evolution process helps the EEG decoder to learn more robust and diverse features. It is worth mentioning that the proposed approach can be readily integrated with other data augmentation approaches for further improvements. We performed extensive experiments on the proposed approach and tested its performance on different types of corrupted EEG signals. The model significantly outperforms competitive baselines on challenging decoding scenarios.

Fang Li, Yi Nian, Zenan Sun et al.

Graph representation learning (GRL) has emerged as a pivotal field that has contributed significantly to breakthroughs in various fields, including biomedicine. The objective of this survey is to review the latest advancements in GRL methods and their applications in the biomedical field. We also highlight key challenges currently faced by GRL and outline potential directions for future research.

Xinyue Hu, Zenan Sun, Yi Nian et al.

Background: Alzheimer's disease and related dementias (ADRD) ranks as the sixth leading cause of death in the US, underlining the importance of accurate ADRD risk prediction. While recent advancement in ADRD risk prediction have primarily relied on imaging analysis, yet not all patients undergo medical imaging before an ADRD diagnosis. Merging machine learning with claims data can reveal additional risk factors and uncover interconnections among diverse medical codes. Objective: Our goal is to utilize Graph Neural Networks (GNNs) with claims data for ADRD risk prediction. Addressing the lack of human-interpretable reasons behind these predictions, we introduce an innovative method to evaluate relationship importance and its influence on ADRD risk prediction, ensuring comprehensive interpretation. Methods: We employed Variationally Regularized Encoder-decoder Graph Neural Network (VGNN) for estimating ADRD likelihood. We created three scenarios to assess the model's efficiency, using Random Forest and Light Gradient Boost Machine as baselines. We further used our relation importance method to clarify the key relationships for ADRD risk prediction. Results: VGNN surpassed other baseline models by 10% in the area under the receiver operating characteristic. The integration of the GNN model and relation importance interpretation could potentially play an essential role in providing valuable insight into factors that may contribute to or delay ADRD progression. Conclusions: Employing a GNN approach with claims data enhances ADRD risk prediction and provides insights into the impact of interconnected medical code relationships. This methodology not only enables ADRD risk modeling but also shows potential for other image analysis predictions using claims data.

Xiaodi Li, Shaika Chowdhury, Chung Il Wi et al.

Patient matching is the process of linking patients to appropriate clinical trials by accurately identifying and matching their medical records with trial eligibility criteria. We propose LLM-Match, a novel framework for patient matching leveraging fine-tuned open-source large language models. Our approach consists of four key components. First, a retrieval-augmented generation (RAG) module extracts relevant patient context from a vast pool of electronic health records (EHRs). Second, a prompt generation module constructs input prompts by integrating trial eligibility criteria (both inclusion and exclusion criteria), patient context, and system instructions. Third, a fine-tuning module with a classification head optimizes the model parameters using structured prompts and ground-truth labels. Fourth, an evaluation module assesses the fine-tuned model's performance on the testing datasets. We evaluated LLM-Match on four open datasets - n2c2, SIGIR, TREC 2021, and TREC 2022 - using open-source models, comparing it against TrialGPT, Zero-Shot, and GPT-4-based closed models. LLM-Match outperformed all baselines.

Yushan Jiang, Shuteng Niu, Dongjin Song et al.

Graft-versus-host disease (GVHD) is a rare but often fatal complication in liver transplantation, with a very high mortality rate. By harnessing multi-modal deep learning methods to integrate heterogeneous and imbalanced electronic health records (EHR), we aim to advance early prediction of GVHD, paving the way for timely intervention and improved patient outcomes. In this study, we analyzed pre-transplant electronic health records (EHR) spanning the period before surgery for 2,100 liver transplantation patients, including 42 cases of graft-versus-host disease (GVHD), from a cohort treated at Mayo Clinic between 1992 and 2025. The dataset comprised four major modalities: patient demographics, laboratory tests, diagnoses, and medications. We developed a multi-modal deep learning framework that dynamically fuses these modalities, handles irregular records with missing values, and addresses extreme class imbalance through AUC-based optimization. The developed framework outperforms all single-modal and multi-modal machine learning baselines, achieving an AUC of 0.836, an AUPRC of 0.157, a recall of 0.768, and a specificity of 0.803. It also demonstrates the effectiveness of our approach in capturing complementary information from different modalities, leading to improved performance. Our multi-modal deep learning framework substantially improves existing approaches for early GVHD prediction. By effectively addressing the challenges of heterogeneity and extreme class imbalance in real-world EHR, it achieves accurate early prediction. Our proposed multi-modal deep learning method demonstrates promising results for early prediction of a GVHD in liver transplantation, despite the challenge of extremely imbalanced EHR data.

Lijing Zhu, Qizhen Lan, Qing Tian et al.

Continual Knowledge Graph Embedding (CKGE) seeks to integrate new knowledge while preserving past information. However, existing methods struggle with efficiency and scalability due to two key limitations: (1) suboptimal knowledge preservation between snapshots caused by manually designed node/relation importance scores that ignore graph dependencies relevant to the downstream task, and (2) computationally expensive graph traversal for node/relation importance calculation, leading to slow training and high memory overhead. To address these limitations, we introduce ETT-CKGE (Efficient, Task-driven, Tokens for Continual Knowledge Graph Embedding), a novel task-guided CKGE method that leverages efficient task-driven tokens for efficient and effective knowledge transfer between snapshots. Our method introduces a set of learnable tokens that directly capture task-relevant signals, eliminating the need for explicit node scoring or traversal. These tokens serve as consistent and reusable guidance across snapshots, enabling efficient token-masked embedding alignment between snapshots. Importantly, knowledge transfer is achieved through simple matrix operations, significantly reducing training time and memory usage. Extensive experiments across six benchmark datasets demonstrate that ETT-CKGE consistently achieves superior or competitive predictive performance, while substantially improving training efficiency and scalability compared to state-of-the-art CKGE methods. The code is available at: https://github.com/lijingzhu1/ETT-CKGE/tree/main

Yiming Li, Xueqing Peng, Jianfu Li et al.

In acupuncture therapy, the accurate location of acupoints is essential for its effectiveness. The advanced language understanding capabilities of large language models (LLMs) like Generative Pre-trained Transformers (GPT) present a significant opportunity for extracting relations related to acupoint locations from textual knowledge sources. This study aims to compare the performance of GPT with traditional deep learning models (Long Short-Term Memory (LSTM) and Bidirectional Encoder Representations from Transformers for Biomedical Text Mining (BioBERT)) in extracting acupoint-related location relations and assess the impact of pretraining and fine-tuning on GPT's performance. We utilized the World Health Organization Standard Acupuncture Point Locations in the Western Pacific Region (WHO Standard) as our corpus, which consists of descriptions of 361 acupoints. Five types of relations ('direction_of,' 'distance_of,' 'part_of,' 'near_acupoint,' and 'located_near') (n= 3,174) between acupoints were annotated. Five models were compared: BioBERT, LSTM, pre-trained GPT-3.5, fine-tuned GPT-3.5, as well as pre-trained GPT-4. Performance metrics included micro-average exact match precision, recall, and F1 scores. Our results demonstrate that fine-tuned GPT-3.5 consistently outperformed other models in F1 scores across all relation types. Overall, it achieved the highest micro-average F1 score of 0.92. This study underscores the effectiveness of LLMs like GPT in extracting relations related to acupoint locations, with implications for accurately modeling acupuncture knowledge and promoting standard implementation in acupuncture training and practice. The findings also contribute to advancing informatics applications in traditional and complementary medicine, showcasing the potential of LLMs in natural language processing.

Yiming Li, Fang Li, Kirk Roberts et al.

Generating discharge summaries is a crucial yet time-consuming task in clinical practice, essential for conveying pertinent patient information and facilitating continuity of care. Recent advancements in large language models (LLMs) have significantly enhanced their capability in understanding and summarizing complex medical texts. This research aims to explore how LLMs can alleviate the burden of manual summarization, streamline workflow efficiencies, and support informed decision-making in healthcare settings. Clinical notes from a cohort of 1,099 lung cancer patients were utilized, with a subset of 50 patients for testing purposes, and 102 patients used for model fine-tuning. This study evaluates the performance of multiple LLMs, including GPT-3.5, GPT-4, GPT-4o, and LLaMA 3 8b, in generating discharge summaries. Evaluation metrics included token-level analysis (BLEU, ROUGE-1, ROUGE-2, ROUGE-L) and semantic similarity scores between model-generated summaries and physician-written gold standards. LLaMA 3 8b was further tested on clinical notes of varying lengths to examine the stability of its performance. The study found notable variations in summarization capabilities among LLMs. GPT-4o and fine-tuned LLaMA 3 demonstrated superior token-level evaluation metrics, while LLaMA 3 consistently produced concise summaries across different input lengths. Semantic similarity scores indicated GPT-4o and LLaMA 3 as leading models in capturing clinical relevance. This study contributes insights into the efficacy of LLMs for generating discharge summaries, highlighting LLaMA 3's robust performance in maintaining clarity and relevance across varying clinical contexts. These findings underscore the potential of automated summarization tools to enhance documentation precision and efficiency, ultimately improving patient care and operational capability in healthcare settings.

Jianping He, Laila Rasmy, Degui Zhi et al.

Background: Recently, numerous foundation models pretrained on extensive data have demonstrated efficacy in disease prediction using Electronic Health Records (EHRs). However, there remains some unanswered questions on how to best utilize such models especially with very small fine-tuning cohorts. Methods: We utilized Med-BERT, an EHR-specific foundation model, and reformulated the disease binary prediction task into a token prediction task and a next visit mask token prediction task to align with Med-BERT's pretraining task format in order to improve the accuracy of pancreatic cancer (PaCa) prediction in both few-shot and fully supervised settings. Results: The reformulation of the task into a token prediction task, referred to as Med-BERT-Sum, demonstrates slightly superior performance in both few-shot scenarios and larger data samples. Furthermore, reformulating the prediction task as a Next Visit Mask Token Prediction task (Med-BERT-Mask) significantly outperforms the conventional Binary Classification (BC) prediction task (Med-BERT-BC) by 3% to 7% in few-shot scenarios with data sizes ranging from 10 to 500 samples. These findings highlight that aligning the downstream task with Med-BERT's pretraining objectives substantially enhances the model's predictive capabilities, thereby improving its effectiveness in predicting both rare and common diseases. Conclusion: Reformatting disease prediction tasks to align with the pretraining of foundation models enhances prediction accuracy, leading to earlier detection and timely intervention. This approach improves treatment effectiveness, survival rates, and overall patient outcomes for PaCa and potentially other cancers.

Naeyma N Islam, Mathew A Coban, Jessica M Fuller et al.

Advances in genomic medicine accelerate the identi cation of mutations in disease-associated genes, but the pathogenicity of many mutations remains unknown, hindering their use in diagnostics and clinical decision-making. Predictive AI models are generated to combat this issue, but current tools display low accuracy when tested against functionally validated datasets. We show that integrating detailed conformational data extracted from molecular dynamics simulations (MDS) into advanced AI-based models increases their predictive power. We carry out an exhaustive mutational analysis of the disease gene PMM2 and subject structural models of each variant to MDS. AI models trained on this dataset outperform existing tools when predicting the known pathogenicity of mutations. Our best performing model, a neuronal networks model, also predicts the pathogenicity of several PMM2 mutations currently considered of unknown signi cance. We believe this model helps alleviate the burden of unknown variants in genomic medicine.

Song Wang, Yiliang Zhou, Ziqiang Han et al.

Data accuracy is essential for scientific research and policy development. The National Violent Death Reporting System (NVDRS) data is widely used for discovering the patterns and causes of death. Recent studies suggested the annotation inconsistencies within the NVDRS and the potential impact on erroneous suicide-cause attributions. We present an empirical Natural Language Processing (NLP) approach to detect annotation inconsistencies and adopt a cross-validation-like paradigm to identify problematic instances. We analyzed 267,804 suicide death incidents between 2003 and 2020 from the NVDRS. Our results showed that incorporating the target state's data into training the suicide-crisis classifier brought an increase of 5.4% to the F-1 score on the target state's test set and a decrease of 1.1% on other states' test set. To conclude, we demonstrated the annotation inconsistencies in NVDRS's death investigation notes, identified problematic instances, evaluated the effectiveness of correcting problematic instances, and eventually proposed an NLP improvement solution.

Dong Hyun Jeon, Lijing Zhu, Haifang Li et al.

Temporal Graph Neural Networks (TGNNs) have become indispensable for analyzing dynamic graphs in critical applications such as social networks, communication systems, and financial networks. However, the robustness of TGNNs against adversarial attacks, particularly sophisticated attacks that exploit the temporal dimension, remains a significant challenge. Existing attack methods for Spatio-Temporal Dynamic Graphs (STDGs) often rely on simplistic, easily detectable perturbations (e.g., random edge additions/deletions) and fail to strategically target the most influential nodes and edges for maximum impact. We introduce the High Impact Attack (HIA), a novel restricted black-box attack framework specifically designed to overcome these limitations and expose critical vulnerabilities in TGNNs. HIA leverages a data-driven surrogate model to identify structurally important nodes (central to network connectivity) and dynamically important nodes (critical for the graph's temporal evolution). It then employs a hybrid perturbation strategy, combining strategic edge injection (to create misleading connections) and targeted edge deletion (to disrupt essential pathways), maximizing TGNN performance degradation. Importantly, HIA minimizes the number of perturbations to enhance stealth, making it more challenging to detect. Comprehensive experiments on five real-world datasets and four representative TGNN architectures (TGN, JODIE, DySAT, and TGAT) demonstrate that HIA significantly reduces TGNN accuracy on the link prediction task, achieving up to a 35.55% decrease in Mean Reciprocal Rank (MRR) - a substantial improvement over state-of-the-art baselines. These results highlight fundamental vulnerabilities in current STDG models and underscore the urgent need for robust defenses that account for both structural and temporal dynamics.

Jianping He, Laila Rasmy, Haifang Li et al.

Objective: This paper aims to prompt large language models (LLMs) for clinical temporal relation extraction (CTRE) in both few-shot and fully supervised settings. Materials and Methods: This study utilizes four LLMs: Encoder-based GatorTron-Base (345M)/Large (8.9B); Decoder-based LLaMA3-8B/MeLLaMA-13B. We developed full (FFT) and parameter-efficient (PEFT) fine-tuning strategies and evaluated these strategies on the 2012 i2b2 CTRE task. We explored four fine-tuning strategies for GatorTron-Base: (1) Standard Fine-Tuning, (2) Hard-Prompting with Unfrozen LLMs, (3) Soft-Prompting with Frozen LLMs, and (4) Low-Rank Adaptation (LoRA) with Frozen LLMs. For GatorTron-Large, we assessed two PEFT strategies-Soft-Prompting and LoRA with Frozen LLMs-leveraging Quantization techniques. Additionally, LLaMA3-8B and MeLLaMA-13B employed two PEFT strategies: LoRA strategy with Quantization (QLoRA) applied to Frozen LLMs using instruction tuning and standard fine-tuning. Results: Under fully supervised settings, Hard-Prompting with Unfrozen GatorTron-Base achieved the highest F1 score (89.54%), surpassing the SOTA model (85.70%) by 3.74%. Additionally, two variants of QLoRA adapted to GatorTron-Large and Standard Fine-Tuning of GatorTron-Base exceeded the SOTA model by 2.36%, 1.88%, and 0.25%, respectively. Decoder-based models with frozen parameters outperformed their Encoder-based counterparts in this setting; however, the trend reversed in few-shot scenarios. Discussions and Conclusions: This study presented new methods that significantly improved CTRE performance, benefiting downstream tasks reliant on CTRE systems. The findings underscore the importance of selecting appropriate models and fine-tuning strategies based on task requirements and data availability. Future work will explore larger models and broader CTRE applications.

Yiming Li, Deepthi Viswaroopan, William He et al.

Adverse event (AE) extraction following COVID-19 vaccines from text data is crucial for monitoring and analyzing the safety profiles of immunizations. Traditional deep learning models are adept at learning intricate feature representations and dependencies in sequential data, but often require extensive labeled data. In contrast, large language models (LLMs) excel in understanding contextual information, but exhibit unstable performance on named entity recognition tasks, possibly due to their broad but unspecific training. This study aims to evaluate the effectiveness of LLMs and traditional deep learning models in AE extraction, and to assess the impact of ensembling these models on performance. In this study, we utilized reports and posts from the VAERS (n=621), Twitter (n=9,133), and Reddit (n=131) as our corpora. Our goal was to extract three types of entities: "vaccine", "shot", and "ae". We explored and fine-tuned (except GPT-4) multiple LLMs, including GPT-2, GPT-3.5, GPT-4, and Llama-2, as well as traditional deep learning models like RNN and BioBERT. To enhance performance, we created ensembles of the three models with the best performance. For evaluation, we used strict and relaxed F1 scores to evaluate the performance for each entity type, and micro-average F1 was used to assess the overall performance. The ensemble model achieved the highest performance in "vaccine", "shot", and "ae" with strict F1-scores of 0.878, 0.930, and 0.925, respectively, along with a micro-average score of 0.903. In conclusion, this study demonstrates the effectiveness and robustness of ensembling fine-tuned traditional deep learning models and LLMs, for extracting AE-related information. This study contributes to the advancement of biomedical natural language processing, providing valuable insights into improving AE extraction from text data for pharmacovigilance and public health surveillance.

Yi Nian, Xinyue Hu, Rui Zhang et al.

To date, there are no effective treatments for most neurodegenerative diseases. Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leveraged in many biomedical applications including drug repurposing. Our objective is to construct a knowledge graph from literature to study relations between Alzheimer's disease (AD) and chemicals, drugs and dietary supplements in order to identify opportunities to prevent or delay neurodegenerative progression. We collected biomedical annotations and extracted their relations using SemRep via SemMedDB. We used both a BERT-based classifier and rule-based methods during data preprocessing to exclude noise while preserving most AD-related semantic triples. The 1,672,110 filtered triples were used to train with knowledge graph completion algorithms (i.e., TransE, DistMult, and ComplEx) to predict candidates that might be helpful for AD treatment or prevention. Among three knowledge graph completion models, TransE outperformed the other two (MR = 13.45, Hits@1 = 0.306). We leveraged the time-slicing technique to further evaluate the prediction results. We found supporting evidence for most highly ranked candidates predicted by our model which indicates that our approach can inform reliable new knowledge. This paper shows that our graph mining model can predict reliable new relationships between AD and other entities (i.e., dietary supplements, chemicals, and drugs). The knowledge graph constructed can facilitate data-driven knowledge discoveries and the generation of novel hypotheses.

Yi Nian, Jingcheng Du, Larry Bu et al.

To date, there are no effective treatments for most neurodegenerative diseases. However, certain foods may be associated with these diseases and bring an opportunity to prevent or delay neurodegenerative progression. Our objective is to construct a knowledge graph for neurodegenerative diseases using literature mining to study their relations with diet. We collected biomedical annotations (Disease, Chemical, Gene, Species, SNP&Mutation) in the abstracts from 4,300 publications relevant to both neurodegenerative diseases and diet using PubTator, an NIH-supported tool that can extract biomedical concepts from literature. A knowledge graph was created from these annotations. Graph embeddings were then trained with the node2vec algorithm to support potential concept clustering and similar concept identification. We found several food-related species and chemicals that might come from diet and have an impact on neurodegenerative diseases.

Mohcine Madkour, Keith Butler, Eric Mercer et al.

Many clinical workflows depend on interactive computer systems for highly technical, conceptual work products, such as diagnoses, treatment plans, care coordination, and case management. We describe an automatic logic reasoner to verify objective specifications for these highly technical, but abstract, work products that are essential to care. The conceptual work products specifications serve as a fundamental output requirement, which must be clearly stated, correct and solvable. There is strategic importance for such specifications because, in turn, they enable system model checking to verify that machine functions taken with user procedures are actually able to achieve these abstract products. We chose case management of Multiple Sclerosis (MS) outpatients as our use case for its challenging complexity. As a first step, we illustrate how graphical class and state diagrams from UML can be developed and critiqued with subject matter experts to serve as specifications of the conceptual work product of case management. A key feature is that the specification must be declarative and thus independent of any process or technology. Our Work Domain Ontology with tools from Semantic Web is needed to translate UML class and state diagrams for verification of solvability with automatic reasoning. The solvable model will then be ready for subsequent use with model checking on the system of human procedures and machine functions. We used the expressive rule language SPARQL Inferencing Notation (SPIN) to develop formal representations of the UML class diagram, the state machine, and their interactions. Using SPIN, we proved the consistency of the interactions of static and dynamic concepts. We discussed how the new SPIN rule engine could be incorporated in the Object Management Group (OMG) Ontology Definition Metamodel (ODM)

Laila Rasmy, Yang Xiang, Ziqian Xie et al.

Deep learning (DL) based predictive models from electronic health records (EHR) deliver impressive performance in many clinical tasks. Large training cohorts, however, are often required to achieve high accuracy, hindering the adoption of DL-based models in scenarios with limited training data size. Recently, bidirectional encoder representations from transformers (BERT) and related models have achieved tremendous successes in the natural language processing domain. The pre-training of BERT on a very large training corpus generates contextualized embeddings that can boost the performance of models trained on smaller datasets. We propose Med-BERT, which adapts the BERT framework for pre-training contextualized embedding models on structured diagnosis data from 28,490,650 patients EHR dataset. Fine-tuning experiments are conducted on two disease-prediction tasks: (1) prediction of heart failure in patients with diabetes and (2) prediction of pancreatic cancer from two clinical databases. Med-BERT substantially improves prediction accuracy, boosting the area under receiver operating characteristics curve (AUC) by 2.02-7.12%. In particular, pre-trained Med-BERT substantially improves the performance of tasks with very small fine-tuning training sets (300-500 samples) boosting the AUC by more than 20% or equivalent to the AUC of 10 times larger training set. We believe that Med-BERT will benefit disease-prediction studies with small local training datasets, reduce data collection expenses, and accelerate the pace of artificial intelligence aided healthcare.

Muhammad Amith, Rebecca Lin, Rachel Cunningham et al.

The human papillomavirus (HPV) vaccine is the most effective way to prevent HPV-related cancers. Integrating provider vaccine counseling is crucial to improving HPV vaccine completion rates. Automating the counseling experience through a conversational agent could help improve HPV vaccine coverage and reduce the burden of vaccine counseling for providers. In a previous study, we tested a simulated conversational agent that provided HPV vaccine counseling for parents using the Wizard of OZ protocol. In the current study, we assessed the conversational agent among young college adults (n=24), a population that may have missed the HPV vaccine during their adolescence when vaccination is recommended. We also administered surveys for system and voice usability, and for health beliefs concerning the HPV vaccine. Participants perceived the agent to have high usability that is slightly better or equivalent to other voice interactive interfaces, and there is some evidence that the agent impacted their beliefs concerning the harms, uncertainty, and risk denials for the HPV vaccine. Overall, this study demonstrates the potential for conversational agents to be an impactful tool for health promotion endeavors.

Jingcheng Du, Chongliang Luo, Qiang Wei et al.

In this study, we proposed a convolutional neural network model for gender prediction using English Twitter text as input. Ensemble of proposed model achieved an accuracy at 0.8237 on gender prediction and compared favorably with the state-of-the-art performance in a recent author profiling task. We further leveraged the trained models to predict the gender labels from an HPV vaccine related corpus and identified gender difference in public perceptions regarding HPV vaccine. The findings are largely consistent with previous survey-based studies.

Hansi Zhang, Christopher Wheldon, Adam G. Dunn et al.

Objectives To test the feasibility of using Twitter data to assess determinants of consumers' health behavior towards Human papillomavirus (HPV) vaccination informed by the Integrated Behavior Model (IBM). Methods We used three Twitter datasets spanning from 2014 to 2018. We preprocessed and geocoded the tweets, and then built a rule-based model that classified each tweet into either promotional information or consumers' discussions. We applied topic modeling to discover major themes, and subsequently explored the associations between the topics learned from consumers' discussions and the responses of HPV-related questions in the Health Information National Trends Survey (HINTS). Results We collected 2,846,495 tweets and analyzed 335,681 geocoded tweets. Through topic modeling, we identified 122 high-quality topics. The most discussed consumer topic is "cervical cancer screening"; while in promotional tweets, the most popular topic is to increase awareness of "HPV causes cancer". 87 out of the 122 topics are correlated between promotional information and consumers' discussions. Guided by IBM, we examined the alignment between our Twitter findings and the results obtained from HINTS. 35 topics can be mapped to HINTS questions by keywords, 112 topics can be mapped to IBM constructs, and 45 topics have statistically significant correlations with HINTS responses in terms of geographic distributions. Conclusion Not only mining Twitter to assess consumers' health behaviors can obtain results comparable to surveys but can yield additional insights via a theory-driven approach. Limitations exist, nevertheless, these encouraging results impel us to develop innovative ways of leveraging social media in the changing health communication landscape.

Jingcheng Du, Qingyu Chen, Yifan Peng et al.

In multi-label text classification, each textual document can be assigned with one or more labels. Due to this nature, the multi-label text classification task is often considered to be more challenging compared to the binary or multi-class text classification problems. As an important task with broad applications in biomedicine such as assigning diagnosis codes, a number of different computational methods (e.g. training and combining binary classifiers for each label) have been proposed in recent years. However, many suffered from modest accuracy and efficiency, with only limited success in practical use. We propose ML-Net, a novel deep learning framework, for multi-label classification of biomedical texts. As an end-to-end system, ML-Net combines a label prediction network with an automated label count prediction mechanism to output an optimal set of labels by leveraging both predicted confidence score of each label and the contextual information in the target document. We evaluate ML-Net on three independent, publicly-available corpora in two kinds of text genres: biomedical literature and clinical notes. For evaluation, example-based measures such as precision, recall and f-measure are used. ML-Net is compared with several competitive machine learning baseline models. Our benchmarking results show that ML-Net compares favorably to the state-of-the-art methods in multi-label classification of biomedical texts. ML-NET is also shown to be robust when evaluated on different text genres in biomedicine. Unlike traditional machine learning methods, ML-Net does not require human efforts in feature engineering and is highly efficient and scalable approach to tasks with a large set of labels (no need to build individual classifiers for each separate label). Finally, ML-NET is able to dynamically estimate the label count based on the document context in a more systematic and accurate manner.