Hong Yu

Xuhai Xu, Bingsheng Yao, Yuanzhe Dong et al.

Advances in large language models (LLMs) have empowered a variety of applications. However, there is still a significant gap in research when it comes to understanding and enhancing the capabilities of LLMs in the field of mental health. In this work, we present a comprehensive evaluation of multiple LLMs on various mental health prediction tasks via online text data, including Alpaca, Alpaca-LoRA, FLAN-T5, GPT-3.5, and GPT-4. We conduct a broad range of experiments, covering zero-shot prompting, few-shot prompting, and instruction fine-tuning. The results indicate a promising yet limited performance of LLMs with zero-shot and few-shot prompt designs for mental health tasks. More importantly, our experiments show that instruction finetuning can significantly boost the performance of LLMs for all tasks simultaneously. Our best-finetuned models, Mental-Alpaca and Mental-FLAN-T5, outperform the best prompt design of GPT-3.5 (25 and 15 times bigger) by 10.9% on balanced accuracy and the best of GPT-4 (250 and 150 times bigger) by 4.8%. They further perform on par with the state-of-the-art task-specific language model. We also conduct an exploratory case study on LLMs' capability on mental health reasoning tasks, illustrating the promising capability of certain models such as GPT-4. We summarize our findings into a set of action guidelines for potential methods to enhance LLMs' capability for mental health tasks. Meanwhile, we also emphasize the important limitations before achieving deployability in real-world mental health settings, such as known racial and gender bias. We highlight the important ethical risks accompanying this line of research.

Pengshan Cai, Zonghai Yao, Fei Liu et al.

Patient portal allows discharged patients to access their personalized discharge instructions in electronic health records (EHRs). However, many patients have difficulty understanding or memorizing their discharge instructions. In this paper, we present PaniniQA, a patient-centric interactive question answering system designed to help patients understand their discharge instructions. PaniniQA first identifies important clinical content from patients' discharge instructions and then formulates patient-specific educational questions. In addition, PaniniQA is also equipped with answer verification functionality to provide timely feedback to correct patients' misunderstandings. Our comprehensive automatic and human evaluation results demonstrate our PaniniQA is capable of improving patients' mastery of their medical instructions through effective interactions

Sunjae Kwon, Zonghai Yao, Harmon S. Jordan et al.

This paper proposes a new natural language processing (NLP) application for identifying medical jargon terms potentially difficult for patients to comprehend from electronic health record (EHR) notes. We first present a novel and publicly available dataset with expert-annotated medical jargon terms from 18K+ EHR note sentences ($MedJ$). Then, we introduce a novel medical jargon extraction ($MedJEx$) model which has been shown to outperform existing state-of-the-art NLP models. First, MedJEx improved the overall performance when it was trained on an auxiliary Wikipedia hyperlink span dataset, where hyperlink spans provide additional Wikipedia articles to explain the spans (or terms), and then fine-tuned on the annotated MedJ data. Secondly, we found that a contextualized masked language model score was beneficial for detecting domain-specific unfamiliar jargon terms. Moreover, our results show that training on the auxiliary Wikipedia hyperlink span datasets improved six out of eight biomedical named entity recognition benchmark datasets. Both MedJ and MedJEx are publicly available.

Sunjae Kwon, Xun Wang, Weisong Liu et al.

Opioid related aberrant behaviors (ORABs) present novel risk factors for opioid overdose. This paper introduces a novel biomedical natural language processing benchmark dataset named ODD, for ORAB Detection Dataset. ODD is an expert-annotated dataset designed to identify ORABs from patients' EHR notes and classify them into nine categories; 1) Confirmed Aberrant Behavior, 2) Suggested Aberrant Behavior, 3) Opioids, 4) Indication, 5) Diagnosed opioid dependency, 6) Benzodiazepines, 7) Medication Changes, 8) Central Nervous System-related, and 9) Social Determinants of Health. We explored two state-of-the-art natural language processing models (fine-tuning and prompt-tuning approaches) to identify ORAB. Experimental results show that the prompt-tuning models outperformed the fine-tuning models in most categories and the gains were especially higher among uncommon categories (Suggested Aberrant Behavior, Confirmed Aberrant Behaviors, Diagnosed Opioid Dependence, and Medication Change). Although the best model achieved the highest 88.17% on macro average area under precision recall curve, uncommon classes still have a large room for performance improvement. ODD is publicly available.

Junda Wang, Zonghai Yao, Avijit Mitra et al.

This paper presents UMASS_BioNLP team participation in the MEDIQA-Chat 2023 shared task for Task-A and Task-C. We focus especially on Task-C and propose a novel LLMs cooperation system named a doctor-patient loop to generate high-quality conversation data sets. The experiment results demonstrate that our approaches yield reasonable performance as evaluated by automatic metrics such as ROUGE, medical concept recall, BLEU, and Self-BLEU. Furthermore, we conducted a comparative analysis between our proposed method and ChatGPT and GPT-4. This analysis also investigates the potential of utilizing cooperation LLMs to generate high-quality datasets.

Zhichao Yang, Shufan Wang, Bhanu Pratap Singh Rawat et al.

Automatic International Classification of Diseases (ICD) coding aims to assign multiple ICD codes to a medical note with average length of 3,000+ tokens. This task is challenging due to a high-dimensional space of multi-label assignment (tens of thousands of ICD codes) and the long-tail challenge: only a few codes (common diseases) are frequently assigned while most codes (rare diseases) are infrequently assigned. This study addresses the long-tail challenge by adapting a prompt-based fine-tuning technique with label semantics, which has been shown to be effective under few-shot setting. To further enhance the performance in medical domain, we propose a knowledge-enhanced longformer by injecting three domain-specific knowledge: hierarchy, synonym, and abbreviation with additional pretraining using contrastive learning. Experiments on MIMIC-III-full, a benchmark dataset of code assignment, show that our proposed method outperforms previous state-of-the-art method in 14.5% in marco F1 (from 10.3 to 11.8, P<0.001). To further test our model on few-shot setting, we created a new rare diseases coding dataset, MIMIC-III-rare50, on which our model improves marco F1 from 17.1 to 30.4 and micro F1 from 17.2 to 32.6 compared to previous method.

Bingsheng Yao, Yao Du, Yue Fu et al.

Advanced AI technologies are increasingly integrated into clinical domains to advance patient care. The design and development of clinical AI technologies necessitate seamless collaboration between clinical and technical experts. However, such interdisciplinary teams are often unsuccessful, with a lack of systematic analysis of collaboration barriers and coping strategies. This work examines two clinical AI collaborations in the context of speech-language pathology via semi-structured interviews with six clinical and seven technical experts. Using Activity Theory (AT) as our analytical lens, we examine persistent knowledge gaps and collaboration tensions across clinical and technical workflows, and show how clinical data can function as boundary objects while interdisciplinary collaborators may act as knowledge brokers to help address these challenges. Our findings contribute to CSCW research on interdisciplinary teams' data work by showing how shared clinical data, boundary objects, and broker roles shape coordination in early-stage clinical AI collaboration, and by providing insights into best practices for future collaboration.

Jiarui Lu, Bo-Hsiang Tseng, Joel Ruben Antony Moniz et al.

Providing voice assistants the ability to navigate multi-turn conversations is a challenging problem. Handling multi-turn interactions requires the system to understand various conversational use-cases, such as steering, intent carryover, disfluencies, entity carryover, and repair. The complexity of this problem is compounded by the fact that these use-cases mix with each other, often appearing simultaneously in natural language. This work proposes a non-autoregressive query rewriting architecture that can handle not only the five aforementioned tasks, but also complex compositions of these use-cases. We show that our proposed model has competitive single task performance compared to the baseline approach, and even outperforms a fine-tuned T5 model in use-case compositions, despite being 15 times smaller in parameters and 25 times faster in latency.

Md Shahidul Salim, Lian Fu, Arav Adikesh Ramakrishnan et al.

We present MedCOD (Medical Chain-of-Dictionary), a hybrid framework designed to improve English-to-Spanish medical translation by integrating domain-specific structured knowledge into large language models (LLMs). MedCOD integrates domain-specific knowledge from both the Unified Medical Language System (UMLS) and the LLM-as-Knowledge-Base (LLM-KB) paradigm to enhance structured prompting and fine-tuning. We constructed a parallel corpus of 2,999 English-Spanish MedlinePlus articles and a 100-sentence test set annotated with structured medical contexts. Four open-source LLMs (Phi-4, Qwen2.5-14B, Qwen2.5-7B, and LLaMA-3.1-8B) were evaluated using structured prompts that incorporated multilingual variants, medical synonyms, and UMLS-derived definitions, combined with LoRA-based fine-tuning. Experimental results demonstrate that MedCOD significantly improves translation quality across all models. For example, Phi-4 with MedCOD and fine-tuning achieved BLEU 44.23, chrF++ 28.91, and COMET 0.863, surpassing strong baseline models like GPT-4o and GPT-4o-mini. Ablation studies confirm that both MedCOD prompting and model adaptation independently contribute to performance gains, with their combination yielding the highest improvements. These findings highlight the potential of structured knowledge integration to enhance LLMs for medical translation tasks.

Qixuan Sun, Yaqi Yin, Hong Yu

Emotion-cause pair extraction (ECPE), an emerging task in sentiment analysis, aims at extracting pairs of emotions and their corresponding causes in documents. This is a more challenging problem than emotion cause extraction (ECE), since it requires no emotion signals which are demonstrated as an important role in the ECE task. Existing work follows a two-stage pipeline which identifies emotions and causes at the first step and pairs them at the second step. However, error propagation across steps and pair combining without contextual information limits the effectiveness. Therefore, we propose a Dual-Questioning Attention Network to alleviate these limitations. Specifically, we question candidate emotions and causes to the context independently through attention networks for a contextual and semantical answer. Also, we explore how weighted loss functions in controlling error propagation between steps. Empirical results show that our method performs better than baselines in terms of multiple evaluation metrics. The source code can be obtained at https://github.com/QixuanSun/DQAN.

Hongxuan Tang, Hongyu Li, Jing Liu et al.

Machine reading comprehension (MRC) is a crucial task in natural language processing and has achieved remarkable advancements. However, most of the neural MRC models are still far from robust and fail to generalize well in real-world applications. In order to comprehensively verify the robustness and generalization of MRC models, we introduce a real-world Chinese dataset -- DuReader_robust. It is designed to evaluate the MRC models from three aspects: over-sensitivity, over-stability and generalization. Comparing to previous work, the instances in DuReader_robust are natural texts, rather than the altered unnatural texts. It presents the challenges when applying MRC models to real-world applications. The experimental results show that MRC models do not perform well on the challenge test set. Moreover, we analyze the behavior of existing models on the challenge test set, which may provide suggestions for future model development. The dataset and codes are publicly available at https://github.com/baidu/DuReader.

Fei Li, Hong Yu

Automated ICD coding, which assigns the International Classification of Disease codes to patient visits, has attracted much research attention since it can save time and labor for billing. The previous state-of-the-art model utilized one convolutional layer to build document representations for predicting ICD codes. However, the lengths and grammar of text fragments, which are closely related to ICD coding, vary a lot in different documents. Therefore, a flat and fixed-length convolutional architecture may not be capable of learning good document representations. In this paper, we proposed a Multi-Filter Residual Convolutional Neural Network (MultiResCNN) for ICD coding. The innovations of our model are two-folds: it utilizes a multi-filter convolutional layer to capture various text patterns with different lengths and a residual convolutional layer to enlarge the receptive field. We evaluated the effectiveness of our model on the widely-used MIMIC dataset. On the full code set of MIMIC-III, our model outperformed the state-of-the-art model in 4 out of 6 evaluation metrics. On the top-50 code set of MIMIC-III and the full code set of MIMIC-II, our model outperformed all the existing and state-of-the-art models in all evaluation metrics. The code is available at https://github.com/foxlf823/Multi-Filter-Residual-Convolutional-Neural-Network.

Zhichao Yang, Avijit Mitra, Sunjae Kwon et al.

The advancement of natural language processing (NLP) systems in healthcare hinges on language model ability to interpret the intricate information contained within clinical notes. This process often requires integrating information from various time points in a patient's medical history. However, most earlier clinical language models were pretrained with a context length limited to roughly one clinical document. In this study, We introduce ClinicalMamba, a specialized version of the Mamba language model, pretrained on a vast corpus of longitudinal clinical notes to address the unique linguistic characteristics and information processing needs of the medical domain. ClinicalMamba, with 130 million and 2.8 billion parameters, demonstrates a superior performance in modeling clinical language across extended text lengths compared to Mamba and clinical Llama. With few-shot learning, ClinicalMamba achieves notable benchmarks in speed and accuracy, outperforming existing clinical language models and general domain large models like GPT-4 in longitudinal clinical notes information extraction tasks.

Rohan Pandey, Haijuan Yan, Hong Yu et al.

Homelessness among US veterans remains a critical public health challenge, yet risk prediction offers a pathway for proactive intervention. In this retrospective prognostic study, we analyzed electronic health record (EHR) data from 4,276,403 Veterans Affairs patients during a 2016 observation period to predict first-episode homelessness occurring 3-12 months later in 2017 (prevalence: 0.32-1.19%). We constructed static and time-varying EHR representations, utilizing clinician-informed logic to model the persistence of clinical conditions and social risks over time. We then compared the performance of classical machine learning, transformer-based masked language models, and fine-tuned large language models (LLMs). We demonstrate that incorporating social and behavioral factors into longitudinal models improved precision-recall area under the curve (PR-AUC) by 15-30%. In the top 1% risk tier, models yielded positive predictive values ranging from 3.93-4.72% at 3 months, 7.39-8.30% at 6 months, 9.84-11.41% at 9 months, and 11.65-13.80% at 12 months across model architectures. Large language models underperformed encoder-based models on discrimination but showed smaller performance disparities across racial groups. These results demonstrate that longitudinal, socially informed EHR modeling concentrates homelessness risk into actionable strata, enabling targeted and data-informed prevention strategies for at-risk veterans.

Rumeng Li, Xun Wang, Hong Yu

Synthetic clinical data are increasingly important for advancing AI in healthcare, given strict privacy constraints on real-world EHRs, limited availability of annotated rare-condition data, and systemic biases in observational datasets. While large language models (LLMs) can generate fluent clinical text, producing synthetic data that is both realistic and clinically meaningful remains challenging. We introduce DualAlign, a framework that enhances statistical fidelity and clinical plausibility through dual alignment: (1) statistical alignment, which conditions generation on patient demographics and risk factors; and (2) semantic alignment, which incorporates real-world symptom trajectories to guide content generation. Using Alzheimer's disease (AD) as a case study, DualAlign produces context-grounded symptom-level sentences that better reflect real-world clinical documentation. Fine-tuning an LLaMA 3.1-8B model with a combination of DualAlign-generated and human-annotated data yields substantial performance gains over models trained on gold data alone or unguided synthetic baselines. While DualAlign does not fully capture longitudinal complexity, it offers a practical approach for generating clinically grounded, privacy-preserving synthetic data to support low-resource clinical text analysis.

Zonghai Yao, Hong Yu

Models pre-trained on large-scale regular text corpora often do not work well for user-generated data where the language styles differ significantly from the mainstream text. Here we present Context-Aware Rule Injection (CARI), an innovative method for formality style transfer (FST). CARI injects multiple rules into an end-to-end BERT-based encoder and decoder model. It learns to select optimal rules based on context. The intrinsic evaluation showed that CARI achieved the new highest performance on the FST benchmark dataset. Our extrinsic evaluation showed that CARI can greatly improve the regular pre-trained models' performance on several tweet sentiment analysis tasks.

Abhyuday Jagannatha, Bhanu Pratap Singh Rawat, Hong Yu

Deep Neural Network (DNN) models have been shown to have high empirical privacy leakages. Clinical language models (CLMs) trained on clinical data have been used to improve performance in biomedical natural language processing tasks. In this work, we investigate the risks of training-data leakage through white-box or black-box access to CLMs. We design and employ membership inference attacks to estimate the empirical privacy leaks for model architectures like BERT and GPT2. We show that membership inference attacks on CLMs lead to non-trivial privacy leakages of up to 7%. Our results show that smaller models have lower empirical privacy leakages than larger ones, and masked LMs have lower leakages than auto-regressive LMs. We further show that differentially private CLMs can have improved model utility on clinical domain while ensuring low empirical privacy leakage. Lastly, we also study the effects of group-level membership inference and disease rarity on CLM privacy leakages.

John P. Lalor, Hong Yu

Curriculum learning methods typically rely on heuristics to estimate the difficulty of training examples or the ability of the model. In this work, we propose replacing difficulty heuristics with learned difficulty parameters. We also propose Dynamic Data selection for Curriculum Learning via Ability Estimation (DDaCLAE), a strategy that probes model ability at each training epoch to select the best training examples at that point. We show that models using learned difficulty and/or ability outperform heuristic-based curriculum learning models on the GLUE classification tasks.

Kai Chen, Fayuan Li, Baotian Hu et al.

Neural data-to-text generation models have achieved significant advancement in recent years. However, these models have two shortcomings: the generated texts tend to miss some vital information, and they often generate descriptions that are not consistent with the structured input data. To alleviate these problems, we propose a Neural data-to-text generation model with Dynamic content Planning, named NDP for abbreviation. The NDP can utilize the previously generated text to dynamically select the appropriate entry from the given structured data. We further design a reconstruction mechanism with a novel objective function that can reconstruct the whole entry of the used data sequentially from the hidden states of the decoder, which aids the accuracy of the generated text. Empirical results show that the NDP achieves superior performance over the state-of-the-art on ROTOWIRE dataset, in terms of relation generation (RG), content selection (CS), content ordering (CO) and BLEU metrics. The human evaluation result shows that the texts generated by the proposed NDP are better than the corresponding ones generated by NCP in most of time. And using the proposed reconstruction mechanism, the fidelity of the generated text can be further improved significantly.

Abhyuday Jagannatha, Hong Yu

We address the problem of calibrating prediction confidence for output entities of interest in natural language processing (NLP) applications. It is important that NLP applications such as named entity recognition and question answering produce calibrated confidence scores for their predictions, especially if the system is to be deployed in a safety-critical domain such as healthcare. However, the output space of such structured prediction models is often too large to adapt binary or multi-class calibration methods directly. In this study, we propose a general calibration scheme for output entities of interest in neural-network based structured prediction models. Our proposed method can be used with any binary class calibration scheme and a neural network model. Additionally, we show that our calibration method can also be used as an uncertainty-aware, entity-specific decoding step to improve the performance of the underlying model at no additional training cost or data requirements. We show that our method outperforms current calibration techniques for named-entity-recognition, part-of-speech and question answering. We also improve our model's performance from our decoding step across several tasks and benchmark datasets. Our method improves the calibration and model performance on out-of-domain test scenarios as well.

Subendhu Rongali, Abhyuday Jagannatha, Bhanu Pratap Singh Rawat et al.

Pre-trained language models (LM) such as BERT, DistilBERT, and RoBERTa can be tuned for different domains (domain-tuning) by continuing the pre-training phase on a new target domain corpus. This simple domain tuning (SDT) technique has been widely used to create domain-tuned models such as BioBERT, SciBERT and ClinicalBERT. However, during the pretraining phase on the target domain, the LM models may catastrophically forget the patterns learned from their source domain. In this work, we study the effects of catastrophic forgetting on domain-tuned LM models and investigate methods that mitigate its negative effects. We propose continual learning (CL) based alternatives for SDT, that aim to reduce catastrophic forgetting. We show that these methods may increase the performance of LM models on downstream target domain tasks. Additionally, we also show that constraining the LM model from forgetting the source domain leads to downstream task models that are more robust to domain shifts. We analyze the computational cost of using our proposed CL methods and provide recommendations for computationally lightweight and effective CL domain-tuning procedures.

Rumeng Li, Xun Wang, Hong Yu

Manipulating training data leads to robust neural models for MT.

John P. Lalor, Hao Wu, Hong Yu

Incorporating Item Response Theory (IRT) into NLP tasks can provide valuable information about model performance and behavior. Traditionally, IRT models are learned using human response pattern (RP) data, presenting a significant bottleneck for large data sets like those required for training deep neural networks (DNNs). In this work we propose learning IRT models using RPs generated from artificial crowds of DNN models. We demonstrate the effectiveness of learning IRT models using DNN-generated data through quantitative and qualitative analyses for two NLP tasks. Parameters learned from human and machine RPs for natural language inference and sentiment analysis exhibit medium to large positive correlations. We demonstrate a use-case for latent difficulty item parameters, namely training set filtering, and show that using difficulty to sample training data outperforms baseline methods. Finally, we highlight cases where human expectation about item difficulty does not match difficulty as estimated from the machine RPs.

Yonghao Jin, Fei Li, Hong Yu

Hypoglycemia is common and potentially dangerous among those treated for diabetes. Electronic health records (EHRs) are important resources for hypoglycemia surveillance. In this study, we report the development and evaluation of deep learning-based natural language processing systems to automatically detect hypoglycemia events from the EHR narratives. Experts in Public Health annotated 500 EHR notes from patients with diabetes. We used this annotated dataset to train and evaluate HYPE, supervised NLP systems for hypoglycemia detection. In our experiment, the convolutional neural network model yielded promising performance $Precision=0.96 \pm 0.03, Recall=0.86 \pm 0.03, F1=0.91 \pm 0.03$ in a 10-fold cross-validation setting. Despite the annotated data is highly imbalanced, our CNN-based HYPE system still achieved a high performance for hypoglycemia detection. HYPE could be used for EHR-based hypoglycemia surveillance and to facilitate clinicians for timely treatment of high-risk patients.

Tu Vu, Baotian Hu, Tsendsuren Munkhdalai et al.

Sentence simplification aims to simplify the content and structure of complex sentences, and thus make them easier to interpret for human readers, and easier to process for downstream NLP applications. Recent advances in neural machine translation have paved the way for novel approaches to the task. In this paper, we adapt an architecture with augmented memory capacities called Neural Semantic Encoders (Munkhdalai and Yu, 2017) for sentence simplification. Our experiments demonstrate the effectiveness of our approach on different simplification datasets, both in terms of automatic evaluation measures and human judgments.

Jinying Chen, Hong Yu

Background: Electronic health record (EHR) notes contain abundant medical jargon that can be difficult for patients to comprehend. One way to help patients is to reduce information overload and help them focus on medical terms that matter most to them. Objective: The aim of this work was to develop FIT (Finding Important Terms for patients), an unsupervised natural language processing (NLP) system that ranks medical terms in EHR notes based on their importance to patients. Methods: We built FIT on a new unsupervised ensemble ranking model derived from the biased random walk algorithm to combine heterogeneous information resources for ranking candidate terms from each EHR note. Specifically, FIT integrates four single views for term importance: patient use of medical concepts, document-level term salience, word-occurrence based term relatedness, and topic coherence. It also incorporates partial information of term importance as conveyed by terms' unfamiliarity levels and semantic types. We evaluated FIT on 90 expert-annotated EHR notes and compared it with three benchmark unsupervised ensemble ranking methods. Results: FIT achieved 0.885 AUC-ROC for ranking candidate terms from EHR notes to identify important terms. When including term identification, the performance of FIT for identifying important terms from EHR notes was 0.813 AUC-ROC. It outperformed the three ensemble rankers for most metrics. Its performance is relatively insensitive to its parameter. Conclusions: FIT can automatically identify EHR terms important to patients and may help develop personalized interventions to improve quality of care. By using unsupervised learning as well as a robust and flexible framework for information fusion, FIT can be readily applied to other domains and applications.

John P. Lalor, Hao Wu, Tsendsuren Munkhdalai et al.

Interpreting the performance of deep learning models beyond test set accuracy is challenging. Characteristics of individual data points are often not considered during evaluation, and each data point is treated equally. We examine the impact of a test set question's difficulty to determine if there is a relationship between difficulty and performance. We model difficulty using well-studied psychometric methods on human response patterns. Experiments on Natural Language Inference (NLI) and Sentiment Analysis (SA) show that the likelihood of answering a question correctly is impacted by the question's difficulty. As DNNs are trained with more data, easy examples are learned more quickly than hard examples.

Jinying Chen, Abhyuday N. Jagannatha, Samah J. Jarad et al.

Objective: Allowing patients to access their own electronic health record (EHR) notes through online patient portals has the potential to improve patient-centered care. However, medical jargon, which abounds in EHR notes, has been shown to be a barrier for patient EHR comprehension. Existing knowledge bases that link medical jargon to lay terms or definitions play an important role in alleviating this problem but have low coverage of medical jargon in EHRs. We developed a data-driven approach that mines EHRs to identify and rank medical jargon based on its importance to patients, to support the building of EHR-centric lay language resources. Methods: We developed an innovative adapted distant supervision (ADS) model based on support vector machines to rank medical jargon from EHRs. For distant supervision, we utilized the open-access, collaborative consumer health vocabulary, a large, publicly available resource that links lay terms to medical jargon. We explored both knowledge-based features from the Unified Medical Language System and distributed word representations learned from unlabeled large corpora. We evaluated the ADS model using physician-identified important medical terms. Results: Our ADS model significantly surpassed two state-of-the-art automatic term recognition methods, TF*IDF and C-Value, yielding 0.810 ROC-AUC versus 0.710 and 0.667, respectively. Our model identified 10K important medical jargon terms after ranking over 100K candidate terms mined from over 7,500 EHR narratives. Conclusion: Our work is an important step towards enriching lexical resources that link medical jargon to lay terms/definitions to support patient EHR comprehension. The identified medical jargon terms and their rankings are available upon request.

Tsendsuren Munkhdalai, Hong Yu

Hypothesis testing is an important cognitive process that supports human reasoning. In this paper, we introduce a computational hypothesis testing approach based on memory augmented neural networks. Our approach involves a hypothesis testing loop that reconsiders and progressively refines a previously formed hypothesis in order to generate new hypotheses to test. We apply the proposed approach to language comprehension task by using Neural Semantic Encoders (NSE). Our NSE models achieve the state-of-the-art results showing an absolute improvement of 1.2% to 2.6% accuracy over previous results obtained by single and ensemble systems on standard machine comprehension benchmarks such as the Children's Book Test (CBT) and Who-Did-What (WDW) news article datasets.

Tsendsuren Munkhdalai, Hong Yu

Recurrent neural networks (RNNs) process input text sequentially and model the conditional transition between word tokens. In contrast, the advantages of recursive networks include that they explicitly model the compositionality and the recursive structure of natural language. However, the current recursive architecture is limited by its dependence on syntactic tree. In this paper, we introduce a robust syntactic parsing-independent tree structured model, Neural Tree Indexers (NTI) that provides a middle ground between the sequential RNNs and the syntactic treebased recursive models. NTI constructs a full n-ary tree by processing the input text with its node function in a bottom-up fashion. Attention mechanism can then be applied to both structure and node function. We implemented and evaluated a binarytree model of NTI, showing the model achieved the state-of-the-art performance on three different NLP tasks: natural language inference, answer sentence selection, and sentence classification, outperforming state-of-the-art recurrent and recursive neural networks.

Abhyuday Jagannatha, Hong Yu

Sequence labeling for extraction of medical events and their attributes from unstructured text in Electronic Health Record (EHR) notes is a key step towards semantic understanding of EHRs. It has important applications in health informatics including pharmacovigilance and drug surveillance. The state of the art supervised machine learning models in this domain are based on Conditional Random Fields (CRFs) with features calculated from fixed context windows. In this application, we explored various recurrent neural network frameworks and show that they significantly outperformed the CRF models.

John P. Lalor, Hao Wu, Hong Yu

Evaluation of NLP methods requires testing against a previously vetted gold-standard test set and reporting standard metrics (accuracy/precision/recall/F1). The current assumption is that all items in a given test set are equal with regards to difficulty and discriminating power. We propose Item Response Theory (IRT) from psychometrics as an alternative means for gold-standard test-set generation and NLP system evaluation. IRT is able to describe characteristics of individual items - their difficulty and discriminating power - and can account for these characteristics in its estimation of human intelligence or ability for an NLP task. In this paper, we demonstrate IRT by generating a gold-standard test set for Recognizing Textual Entailment. By collecting a large number of human responses and fitting our IRT model, we show that our IRT model compares NLP systems with the performance in a human population and is able to provide more insight into system performance than standard evaluation metrics. We show that a high accuracy score does not always imply a high IRT score, which depends on the item characteristics and the response pattern.