Identifying Health Risks from Family History: A Survey of Natural Language Processing Techniques

Electronic health records include information on patients' status and medical history, which could cover the history of diseases and disorders that could be hereditary. One important use of family history information is in precision health, where the goal is to keep the population healthy with preventative measures. Natural Language Processing (NLP) and machine learning techniques can assist with identifying information that could assist health professionals in identifying health risks before a condition is developed in their later years, saving lives and reducing healthcare costs. We survey the literature on the techniques from the NLP field that have been developed to utilise digital health records to identify risks of familial diseases. We highlight that rule-based methods are heavily investigated and are still actively used for family history extraction. Still, more recent efforts have been put into building neural models based on large-scale pre-trained language models. In addition to the areas where NLP has successfully been utilised, we also identify the areas where more research is needed to unlock the value of patients' records regarding data collection, task formulation and downstream applications.

Tensorial tomographic Fourier Ptychography with applications to muscle tissue imaging

We report Tensorial tomographic Fourier Ptychography (ToFu), a new non-scanning label-free tomographic microscopy method for simultaneous imaging of quantitative phase and anisotropic specimen information in 3D. Built upon Fourier Ptychography, a quantitative phase imaging technique, ToFu additionally highlights the vectorial nature of light. The imaging setup consists of a standard microscope equipped with an LED matrix, a polarization generator, and a polarization-sensitive camera. Permittivity tensors of anisotropic samples are computationally recovered from polarized intensity measurements across three dimensions. We demonstrate ToFu's efficiency through volumetric reconstructions of refractive index, birefringence, and orientation for various validation samples, as well as tissue samples from muscle fibers and diseased heart tissue. Our reconstructions of muscle fibers resolve their 3D fine-filament structure and yield consistent morphological measurements compared to gold-standard second harmonic generation scanning confocal microscope images found in the literature. Additionally, we demonstrate reconstructions of a heart tissue sample that carries important polarization information for detecting cardiac amyloidosis.

Detecting Entities in the Astrophysics Literature: A Comparison of Word-based and Span-based Entity Recognition Methods

Information Extraction from scientific literature can be challenging due to the highly specialised nature of such text. We describe our entity recognition methods developed as part of the DEAL (Detecting Entities in the Astrophysics Literature) shared task. The aim of the task is to build a system that can identify Named Entities in a dataset composed by scholarly articles from astrophysics literature. We planned our participation such that it enables us to conduct an empirical comparison between word-based tagging and span-based classification methods. When evaluated on two hidden test sets provided by the organizer, our best-performing submission achieved $F_1$ scores of 0.8307 (validation phase) and 0.7990 (testing phase).

An Exploration of Hierarchical Attention Transformers for Efficient Long Document Classification

Non-hierarchical sparse attention Transformer-based models, such as Longformer and Big Bird, are popular approaches to working with long documents. There are clear benefits to these approaches compared to the original Transformer in terms of efficiency, but Hierarchical Attention Transformer (HAT) models are a vastly understudied alternative. We develop and release fully pre-trained HAT models that use segment-wise followed by cross-segment encoders and compare them with Longformer models and partially pre-trained HATs. In several long document downstream classification tasks, our best HAT model outperforms equally-sized Longformer models while using 10-20% less GPU memory and processing documents 40-45% faster. In a series of ablation studies, we find that HATs perform best with cross-segment contextualization throughout the model than alternative configurations that implement either early or late cross-segment contextualization. Our code is on GitHub: https://github.com/coastalcph/hierarchical-transformers.

Tensorial tomographic differential phase-contrast microscopy

We report Tensorial Tomographic Differential Phase-Contrast microscopy (T2DPC), a quantitative label-free tomographic imaging method for simultaneous measurement of phase and anisotropy. T2DPC extends differential phase-contrast microscopy, a quantitative phase imaging technique, to highlight the vectorial nature of light. The method solves for permittivity tensor of anisotropic samples from intensity measurements acquired with a standard microscope equipped with an LED matrix, a circular polarizer, and a polarization-sensitive camera. We demonstrate accurate volumetric reconstructions of refractive index, birefringence, and orientation for various validation samples, and show that the reconstructed polarization structures of a biological specimen are predictive of pathology.

Revisiting Transformer-based Models for Long Document Classification

The recent literature in text classification is biased towards short text sequences (e.g., sentences or paragraphs). In real-world applications, multi-page multi-paragraph documents are common and they cannot be efficiently encoded by vanilla Transformer-based models. We compare different Transformer-based Long Document Classification (TrLDC) approaches that aim to mitigate the computational overhead of vanilla transformers to encode much longer text, namely sparse attention and hierarchical encoding methods. We examine several aspects of sparse attention (e.g., size of local attention window, use of global attention) and hierarchical (e.g., document splitting strategy) transformers on four document classification datasets covering different domains. We observe a clear benefit from being able to process longer text, and, based on our results, we derive practical advice of applying Transformer-based models on long document classification tasks.

Quantitative Jones matrix imaging using vectorial Fourier ptychography

This paper presents a microscopic imaging technique that uses variable-angle illumination to recover the complex polarimetric properties of a specimen at high resolution and over a large field-of-view. The approach extends Fourier ptychography, which is a synthetic aperture-based imaging approach to improve resolution with phaseless measurements, to additionally account for the vectorial nature of light. After images are acquired using a standard microscope outfitted with an LED illumination array and two polarizers, our vectorial Fourier Ptychography (vFP) algorithm solves for the complex 2x2 Jones matrix of the anisotropic specimen of interest at each resolved spatial location. We introduce a new sequential Gauss-Newton-based solver that additionally jointly estimates and removes polarization-dependent imaging system aberrations. We demonstrate effective vFP performance by generating large-area (29 mm$^2$), high-resolution (1.24 $\mu$m full-pitch) reconstructions of sample absorption, phase, orientation, diattenuation, and retardance for a variety of calibration samples and biological specimens.

MDAPT: Multilingual Domain Adaptive Pretraining in a Single Model

Domain adaptive pretraining, i.e. the continued unsupervised pretraining of a language model on domain-specific text, improves the modelling of text for downstream tasks within the domain. Numerous real-world applications are based on domain-specific text, e.g. working with financial or biomedical documents, and these applications often need to support multiple languages. However, large-scale domain-specific multilingual pretraining data for such scenarios can be difficult to obtain, due to regulations, legislation, or simply a lack of language- and domain-specific text. One solution is to train a single multilingual model, taking advantage of the data available in as many languages as possible. In this work, we explore the benefits of domain adaptive pretraining with a focus on adapting to multiple languages within a specific domain. We propose different techniques to compose pretraining corpora that enable a language model to both become domain-specific and multilingual. Evaluation on nine domain-specific datasets-for biomedical named entity recognition and financial sentence classification-covering seven different languages show that a single multilingual domain-specific model can outperform the general multilingual model, and performs close to its monolingual counterpart. This finding holds across two different pretraining methods, adapter-based pretraining and full model pretraining.

Recognising Biomedical Names: Challenges and Solutions

The growth rate in the amount of biomedical documents is staggering. Unlocking information trapped in these documents can enable researchers and practitioners to operate confidently in the information world. Biomedical NER, the task of recognising biomedical names, is usually employed as the first step of the NLP pipeline. Standard NER models, based on sequence tagging technique, are good at recognising short entity mentions in the generic domain. However, there are several open challenges of applying these models to recognise biomedical names: 1) Biomedical names may contain complex inner structure (discontinuity and overlapping) which cannot be recognised using standard sequence tagging technique; 2) The training of NER models usually requires large amount of labelled data, which are difficult to obtain in the biomedical domain; and, 3) Commonly used language representation models are pre-trained on generic data; a domain shift therefore exists between these models and target biomedical data. To deal with these challenges, we explore several research directions and make the following contributions: 1) we propose a transition-based NER model which can recognise discontinuous mentions; 2) We develop a cost-effective approach that nominates the suitable pre-training data; and, 3) We design several data augmentation methods for NER. Our contributions have obvious practical implications, especially when new biomedical applications are needed. Our proposed data augmentation methods can help the NER model achieve decent performance, requiring only a small amount of labelled data. Our investigation regarding selecting pre-training data can improve the model by incorporating language representation models, which are pre-trained using in-domain data. Finally, our proposed transition-based NER model can further improve the performance by recognising discontinuous mentions.