United Arab Emirates

Clinical coding is the task of transforming medical  documents into structured codes following a standard ontology. Since these terminologies are composed of hundreds of codes, this problem can be considered an Extreme Multi-label Classification task. This paper proposes a novel neural network-based architecture for clinical coding. First, we take full advantage of the hierarchical nature of ontologies to create clusters based on semantic relations. Then, we use a Matcher module to assign the probability of documents belonging to each cluster. Finally, the Ranker calculates the probability of each code considering only the documents in the cluster. This division allows a fine-grained differentiation within the cluster, which cannot be addressed using a single classifier. In addition, since most of the previous work has focused on solving this task in English, we conducted our experiments on three clinical coding corpora in Spanish. The experimental results demonstrate the effectiveness of our model, achieving state-of-the-art results on two of the three datasets. Specifically, we outperformed previous models on two subtasks of the CodiEsp shared task: CodiEsp-D (diseases) and CodiEsp-P (procedures). Automatic coding can profoundly impact healthcare by structuring critical information written in free text in electronic health records.

EMNLP 2022

Divide and Conquer: An Extreme Multi-Label Classification Approach for Coding Diseases and Procedures in Spanish

automatic coding

clinical natural language processing

text classification

information extraction

workshop paper

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EMNLP 2022 will take place in Abu Dhabi from December 7th to December 11th, 2022. And it will be held in hybrid mode, both online and offline.

Automatically generating short summaries from users' online mental health posts could save counselors' reading time and reduce their fatigue so that they can provide timely responses to those seeking help for improving their mental state. Recent Transformers-based summarization models have presented a promising approach to abstractive summarization. They go beyond sentence selection and extractive strategies to deal with more complicated tasks such as novel word generation and sentence paraphrasing. Nonetheless, these models have a prominent shortcoming; their training strategy is not quite efficient, which restricts the model's performance. In this paper, we include a curriculum learning approach to reweigh the training samples, bringing about an efficient learning procedure. We apply our model on extreme summarization dataset of MentSum posts ––a dataset of mental health related posts from Reddit social media. Compared to the state-of-the-art model, our proposed method makes substantial gains in terms of Rouge and Bertscore evaluation metrics, yielding 3.5% Rouge-1, 10.4% Rouge-2, and 4.7% Rouge-L, 1.5% Bertscore relative improvements.

Curriculum-guided Abstractive Summarization for Mental Health Online Posts

Clinical data often exists in different forms across the lifetime of a patient's interaction with the healthcare system - structured, unstructured or semi-structured data in the form of laboratory readings, clinical notes, diagnostic codes, imaging and audio data of various kinds, and other observational data. Formulating a representation model that aggregates information from these heterogeneous sources may allow us to jointly model on data with more predictive signal than noise and help inform our model with useful constraints learned from better data. Multimodal fusion approaches help produce representations combined from heterogeneous modalities, which can be used for clinical prediction tasks. Representations produced through different fusion techniques require different training strategies. We investigate the advantage of adding narrative clinical text to structured modalities to classification tasks in the clinical domain. We show that while there is a competitive advantage in combined representations of clinical data, the approach can be helped by training guidance customized to each modality. We show empirical results across binary/multiclass settings, single/multitask settings and unified/multimodal learning rate settings for early and late information fusion of clinical data.

Improving information fusion on multimodal clinical data in classification settings

Large pre-trained language models (LMs) have been widely adopted in biomedical and clinical domains, introducing many powerful LMs such as bio-lm and BioELECTRA. However, the applicability of these methods to real clinical use cases is hindered, due to the limitation of pre-trained LMs in processing long textual data with thousands of words, which is a common length for a clinical note. In this work, we explore long-range adaptation from such LMs with Longformer, allowing the LMs to capture longer clinical notes context. We conduct experiments on three n2c2 challenges datasets and a longitudinal clinical dataset from Hong Kong Hospital Authority electronic health record (EHR) system to show the effectiveness and generalizability of this concept, achieving ~10% F1-score improvement. Based on our experiments, we conclude that capturing a longer clinical note interval is beneficial to the model performance, but there are different cut-off intervals to achieve the optimal performance for different target variables.

How Long Is Enough? Exploring the Optimal Intervals of Long-Range Clinical Note Language Modeling

Schizophrenia is one of the most disabling mental health conditions to live with. Approximately one percent of the population has schizophrenia which makes it fairly common, and it affects many people and their families. Patients with schizophrenia suffer different symptoms: formal thought disorder (FTD), delusions, and emotional flatness. In this paper, we quantitatively and qualitatively analyze the language of patients with schizophrenia measuring various linguistic features in two modalities: speech and written text. We examine the following features: coherence and cohesion of thoughts, emotions, specificity, level of commit- ted belief (LCB), and personality traits. Our results show that patients with schizophrenia score high in fear and neuroticism compared to healthy controls. In addition, they are more committed to their beliefs, and their writing lacks details. They score lower in most of the linguistic features of cohesion with significant p-values.

A Quantitative and Qualitative Analysis of Schizophrenia Language

In recent years, there has been a surge of interest in research on automatic mental health detection (MHD) from social media data leveraging advances in natural language processing and machine learning techniques. While significant progress has been achieved in this interdisciplinary research area, the vast majority of work has treated MHD as a binary classification task.  The multiclass classification setup is, however, essential if we are to uncover the subtle differences among the statistical patterns of language use associated with particular mental health conditions. Here, we report on experiments aimed at predicting six conditions (anxiety, attention deficit hyperactivity disorder, bipolar disorder, post-traumatic stress disorder, depression, and psychological stress) from Reddit social media posts. We explore and compare the performance of hybrid and ensemble models leveraging transformer-based architectures (BERT and RoBERTa) and BiLSTM neural networks trained on within-text distributions of a diverse set of linguistic features. This set encompasses measures of syntactic complexity, lexical sophistication and diversity, readability, and register-specific ngram frequencies, as well as sentiment and emotion lexicons. In addition, we conduct feature ablation experiments to investigate which types of features are most indicative of particular mental health conditions.

Exploring Hybrid and Ensemble Models for Multiclass Prediction of Mental Health Status on Social Media

Using language models created from large data sources has improved the performance of several deep learning-based architectures, obtaining state-of-the-art results in several NLP extrinsic tasks. However, little research is related to creating intrinsic tests that allow us to compare the quality of different language models when obtaining contextualized embeddings. This gap increases even more when working on specific domains in languages other than English. This paper proposes a novel graph-based intrinsic test that allows us to measure the quality of different language models in clinical and biomedical domains in Spanish. Our results show that our intrinsic test performs better for clinical and biomedical language models than a general one. Also, it correlates with better outcomes for a NER task using a probing model over contextualized embeddings. We hope our work will help the clinical NLP research community to evaluate and compare new language models in other languages and find the most suitable models for solving downstream tasks.

A Knowledge-Graph-Based Intrinsic Test for Benchmarking Medical Concept Embeddings and Pretrained Language Models

Empathy is a vital component of health care and plays  a key role in the training of future doctors. Paying attention to medical students' self-reflective stories of their interactions with patients can encourage empathy and the formation of professional identities that embody desirable values such as integrity and respect. We present a computational approach and linguistic analysis of empathic language in a large corpus of 440 essays written by pre-med students as narrated simulated patient -- doctor interactions. We analyze the discourse of three kinds of empathy: cognitive, affective, and prosocial as highlighted by expert annotators. We also present various experiments with state-of-the-art recurrent neural networks and transformer models for classifying these forms of empathy. To further improve over these results, we develop a novel system architecture that makes use of frame semantics to enrich our state-of-the-art models. We show that this novel framework leads to significant improvement on the empathy classification task for this dataset.

Enriching Deep Learning with Frame Semantics for Empathy Classification in Medical Narrative Essays

Social media has become a popular platform where people share information about personal healthcare conditions, diagnostic histories, and medical plans. Analyzing posts on social media depicting such realistic information can help improve quality and clinical decision-making; however, the lack of structured resources in this genre limits us to build robust NLP models for meaningful analysis. This paper presents a new corpus annotating relations among many types of conditions, treatments, and their attributes illustrated in social media posts by patients and caregivers. For experiments, a transformer encoder is pretrained on 1M raw posts and used to train several document-level relation extraction models using our corpus. Our best-performing model achieves the F1 scores of 70.9 and 51.7 for Entity Recognition and Relation Extraction, respectively. These results are encouraging as it is the first neural model extracting complex relations of this kind on social media data.

Condition-Treatment Relation Extraction on Disease-related Social Media Data

Recently, research into bringing outside knowledge sources into current neural NLP models has been increasing. Most approaches that leverage external knowledge sources require laborious and non-trivial designs, as well as tailoring the system through intensive ablation of different knowledge sources, an effort that discourages users to use quality ontological resources. In this paper, we show that multiple large heterogeneous KSs can be easily integrated using a decoupled approach, allowing for an automatic ablation of irrelevant KSs, while keeping the overall parameter space tractable. We experiment with BERT and pre-trained graph embeddings, and show that they interoperate well without performance degradation, even when some do not contribute to the task.

Integration of Heterogeneous Knowledge Sources for Biomedical Text Processing

Recent literature has demonstrated the potential of multilingual Neural Machine Translation (mNMT) models. However, the most efficient models are not well suited to specialized industries. In these cases, internal data is scarce and expensive to find in all language pairs. Therefore, fine-tuning a mNMT model on a specialized domain is hard. In this context, we decided to focus on a new task: Domain Adaptation of a pre-trained mNMT model on a single pair of language while trying to maintain model quality on generic domain data for all language pairs. The risk of loss on generic domain and on other pairs is high. This task is key for mNMT model adoption in the industry and is at the border of many others. We propose a fine-tuning procedure for the generic mNMT that combines embeddings freezing and adversarial loss. Our experiments demonstrated that the procedure improves performances on specialized data with a minimal loss in initial performances on generic domain for all languages pairs, compared to a naive standard approach (+10.0 BLEU score on specialized data,  -0.01 to -0.5 BLEU on WMT and Tatoeba datasets on the other pairs with M2M100).

Divide and Conquer: An Extreme Multi-Label Classification Approach for Coding Diseases and Procedures in Spanish

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Curriculum-guided Abstractive Summarization for Mental Health Online Posts

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