Clinical Relation Extraction Using Transformer-based Models

The newly emerged transformer technology has a tremendous impact on NLP research. In the general English domain, transformer-based models have achieved state-of-the-art performances on various NLP benchmarks. In the clinical domain, researchers also have investigated transformer models for clinical applications. The goal of this study is to systematically explore three widely used transformer-based models (i.e., BERT, RoBERTa, and XLNet) for clinical relation extraction and develop an open-source package with clinical pre-trained transformer-based models to facilitate information extraction in the clinical domain. We developed a series of clinical RE models based on three transformer architectures, namely BERT, RoBERTa, and XLNet. We evaluated these models using 2 publicly available datasets from 2018 MADE1.0 and 2018 n2c2 challenges. We compared two classification strategies (binary vs. multi-class classification) and investigated two approaches to generate candidate relations in different experimental settings. In this study, we compared three transformer-based (BERT, RoBERTa, and XLNet) models for relation extraction. We demonstrated that the RoBERTa-clinical RE model achieved the best performance on the 2018 MADE1.0 dataset with an F1-score of 0.8958. On the 2018 n2c2 dataset, the XLNet-clinical model achieved the best F1-score of 0.9610. Our results indicated that the binary classification strategy consistently outperformed the multi-class classification strategy for clinical relation extraction. Our methods and models are publicly available at https://github.com/uf-hobi-informatics-lab/ClinicalTransformerRelationExtraction. We believe this work will improve current practice on clinical relation extraction and other related NLP tasks in the biomedical domain.

A Study of Social and Behavioral Determinants of Health in Lung Cancer Patients Using Transformers-based Natural Language Processing Models

Social and behavioral determinants of health (SBDoH) have important roles in shaping people's health. In clinical research studies, especially comparative effectiveness studies, failure to adjust for SBDoH factors will potentially cause confounding issues and misclassification errors in either statistical analyses and machine learning-based models. However, there are limited studies to examine SBDoH factors in clinical outcomes due to the lack of structured SBDoH information in current electronic health record (EHR) systems, while much of the SBDoH information is documented in clinical narratives. Natural language processing (NLP) is thus the key technology to extract such information from unstructured clinical text. However, there is not a mature clinical NLP system focusing on SBDoH. In this study, we examined two state-of-the-art transformer-based NLP models, including BERT and RoBERTa, to extract SBDoH concepts from clinical narratives, applied the best performing model to extract SBDoH concepts on a lung cancer screening patient cohort, and examined the difference of SBDoH information between NLP extracted results and structured EHRs (SBDoH information captured in standard vocabularies such as the International Classification of Diseases codes). The experimental results show that the BERT-based NLP model achieved the best strict/lenient F1-score of 0.8791 and 0.8999, respectively. The comparison between NLP extracted SBDoH information and structured EHRs in the lung cancer patient cohort of 864 patients with 161,933 various types of clinical notes showed that much more detailed information about smoking, education, and employment were only captured in clinical narratives and that it is necessary to use both clinical narratives and structured EHRs to construct a more complete picture of patients' SBDoH factors.

W2v-BERT: Combining Contrastive Learning and Masked Language Modeling for Self-Supervised Speech Pre-Training

Motivated by the success of masked language modeling~(MLM) in pre-training natural language processing models, we propose w2v-BERT that explores MLM for self-supervised speech representation learning. w2v-BERT is a framework that combines contrastive learning and MLM, where the former trains the model to discretize input continuous speech signals into a finite set of discriminative speech tokens, and the latter trains the model to learn contextualized speech representations via solving a masked prediction task consuming the discretized tokens. In contrast to existing MLM-based speech pre-training frameworks such as HuBERT, which relies on an iterative re-clustering and re-training process, or vq-wav2vec, which concatenates two separately trained modules, w2v-BERT can be optimized in an end-to-end fashion by solving the two self-supervised tasks~(the contrastive task and MLM) simultaneously. Our experiments show that w2v-BERT achieves competitive results compared to current state-of-the-art pre-trained models on the LibriSpeech benchmarks when using the Libri-Light~60k corpus as the unsupervised data. In particular, when compared to published models such as conformer-based wav2vec~2.0 and HuBERT, our model shows~5\% to~10\% relative WER reduction on the test-clean and test-other subsets. When applied to the Google's Voice Search traffic dataset, w2v-BERT outperforms our internal conformer-based wav2vec~2.0 by more than~30\% relatively.

GSPMD: General and Scalable Parallelization for ML Computation Graphs

We present GSPMD, an automatic, compiler-based parallelization system for common machine learning computation graphs. It allows users to write programs in the same way as for a single device, then give hints through a few annotations on how to distribute tensors, based on which GSPMD will parallelize the computation. Its representation of partitioning is simple yet general, allowing it to express different or mixed paradigms of parallelism on a wide variety of models. GSPMD infers the partitioning for every operator in the graph based on limited user annotations, making it convenient to scale up existing single-device programs. It solves several technical challenges for production usage, such as static shape constraints, uneven partitioning, exchange of halo data, and nested operator partitioning. These techniques allow GSPMD to achieve 50% to 62% compute utilization on 128 to 2048 Cloud TPUv3 cores for models with up to one trillion parameters. GSPMD produces a single program for all devices, which adjusts its behavior based on a run-time partition ID, and uses collective operators for cross-device communication. This property allows the system itself to be scalable: the compilation time stays constant with increasing number of devices.

Parallel Tacotron 2: A Non-Autoregressive Neural TTS Model with Differentiable Duration Modeling

This paper introduces Parallel Tacotron 2, a non-autoregressive neural text-to-speech model with a fully differentiable duration model which does not require supervised duration signals. The duration model is based on a novel attention mechanism and an iterative reconstruction loss based on Soft Dynamic Time Warping, this model can learn token-frame alignments as well as token durations automatically. Experimental results show that Parallel Tacotron 2 outperforms baselines in subjective naturalness in several diverse multi speaker evaluations. Its duration control capability is also demonstrated.

PnG BERT: Augmented BERT on Phonemes and Graphemes for Neural TTS

This paper introduces PnG BERT, a new encoder model for neural TTS. This model is augmented from the original BERT model, by taking both phoneme and grapheme representations of text as input, as well as the word-level alignment between them. It can be pre-trained on a large text corpus in a self-supervised manner, and fine-tuned in a TTS task. Experimental results show that a neural TTS model using a pre-trained PnG BERT as its encoder yields more natural prosody and more accurate pronunciation than a baseline model using only phoneme input with no pre-training. Subjective side-by-side preference evaluations show that raters have no statistically significant preference between the speech synthesized using a PnG BERT and ground truth recordings from professional speakers.