Electronic health records (EHR) offer unprecedented opportunities for in-depth clinical phenotyping and prediction of clinical outcomes. Combining multiple data sources is crucial to generate a complete picture of disease prevalence, incidence and trajectories. The standard approach to combining clinical data involves collating clinical terms across different terminology systems using curated maps, which are often inaccurate and/or incomplete. Here, we propose sEHR-CE, a novel framework based on transformers to enable integrated phenotyping and analyses of heterogeneous clinical datasets without relying on these mappings. We unify clinical terminologies using textual descriptors of concepts, and represent individuals' EHR as sections of text. We then fine-tune pre-trained language models to predict disease phenotypes more accurately than non-text and single terminology approaches. We validate our approach using primary and secondary care data from the UK Biobank, a large-scale research study. Finally, we illustrate in a type 2 diabetes use case how sEHR-CE identifies individuals without diagnosis that share clinical characteristics with patients.
A recent trend in Natural Language Processing is the exponential growth in Language Model (LM) size, which prevents research groups without a necessary hardware infrastructure from participating in the development process. This study investigates methods for Knowledge Distillation (KD) to provide efficient alternatives to large-scale models. In this context, KD means extracting information about language encoded in a Neural Network and Lexical Knowledge Databases. We developed two methods to test our hypothesis that efficient architectures can gain knowledge from LMs and extract valuable information from lexical sources. First, we present a technique to learn confident probability distribution for Masked Language Modeling by prediction weighting of multiple teacher networks. Second, we propose a method for Word Sense Disambiguation (WSD) and lexical KD that is general enough to be adapted to many LMs. Our results show that KD with multiple teachers leads to improved training convergence. When using our lexical pre-training method, LM characteristics are not lost, leading to increased performance in Natural Language Understanding (NLU) tasks over the state-of-the-art while adding no parameters. Moreover, the improved semantic understanding of our model increased the task performance beyond WSD and NLU in a real-problem scenario (Plagiarism Detection). This study suggests that sophisticated training methods and network architectures can be superior over scaling trainable parameters. On this basis, we suggest the research area should encourage the development and use of efficient models and rate impacts resulting from growing LM size equally against task performance.
The causal revolution has spurred interest in understanding complex relationships in various fields. Most existing methods aim to discover causal relationships among all variables in a large-scale complex graph. However, in practice, only a small number of variables in the graph are relevant for the outcomes of interest. As a result, causal estimation with the full causal graph -- especially given limited data -- could lead to many falsely discovered, spurious variables that may be highly correlated with but have no causal impact on the target outcome. In this paper, we propose to learn a class of necessary and sufficient causal graphs (NSCG) that only contains causally relevant variables for an outcome of interest, which we term causal features. The key idea is to utilize probabilities of causation to systematically evaluate the importance of features in the causal graph, allowing us to identify a subgraph that is relevant to the outcome of interest. To learn NSCG from data, we develop a score-based necessary and sufficient causal structural learning (NSCSL) algorithm, by establishing theoretical relationships between probabilities of causation and causal effects of features. Across empirical studies of simulated and real data, we show that the proposed NSCSL algorithm outperforms existing algorithms and can reveal important yeast genes for target heritable traits of interest.
We introduce a framework for automatically defining and learning deep generative models with problem-specific structure. We tackle problem domains that are more traditionally solved by algorithms such as sorting, constraint satisfaction for Sudoku, and matrix factorization. Concretely, we train diffusion models with an architecture tailored to the problem specification. This problem specification should contain a graphical model describing relationships between variables, and often benefits from explicit representation of subcomputations. Permutation invariances can also be exploited. Across a diverse set of experiments we improve the scaling relationship between problem dimension and our model's performance, in terms of both training time and final accuracy.
Image reconstruction based on indirect, noisy, or incomplete data remains an important yet challenging task. While methods such as compressive sensing have demonstrated high-resolution image recovery in various settings, there remain issues of robustness due to parameter tuning. Moreover, since the recovery is limited to a point estimate, it is impossible to quantify the uncertainty, which is often desirable. Due to these inherent limitations, a sparse Bayesian learning approach is sometimes adopted to recover a posterior distribution of the unknown. Sparse Bayesian learning assumes that some linear transformation of the unknown is sparse. However, most of the methods developed are tailored to specific problems, with particular forward models and priors. Here, we present a generalized approach to sparse Bayesian learning. It has the advantage that it can be used for various types of data acquisitions and prior information. Some preliminary results on image reconstruction/recovery indicate its potential use for denoising, deblurring, and magnetic resonance imaging.
Objective: Clinical knowledge enriched transformer models (e.g., ClinicalBERT) have state-of-the-art results on clinical NLP (natural language processing) tasks. One of the core limitations of these transformer models is the substantial memory consumption due to their full self-attention mechanism, which leads to the performance degradation in long clinical texts. To overcome this, we propose to leverage long-sequence transformer models (e.g., Longformer and BigBird), which extend the maximum input sequence length from 512 to 4096, to enhance the ability to model long-term dependencies in long clinical texts. Materials and Methods: Inspired by the success of long sequence transformer models and the fact that clinical notes are mostly long, we introduce two domain enriched language models, Clinical-Longformer and Clinical-BigBird, which are pre-trained on a large-scale clinical corpus. We evaluate both language models using 10 baseline tasks including named entity recognition, question answering, natural language inference, and document classification tasks. Results: The results demonstrate that Clinical-Longformer and Clinical-BigBird consistently and significantly outperform ClinicalBERT and other short-sequence transformers in all 10 downstream tasks and achieve new state-of-the-art results. Discussion: Our pre-trained language models provide the bedrock for clinical NLP using long texts. We have made our source code available at //github.com/luoyuanlab/Clinical-Longformer, and the pre-trained models available for public download at: //huggingface.co/yikuan8/Clinical-Longformer. Conclusion: This study demonstrates that clinical knowledge enriched long-sequence transformers are able to learn long-term dependencies in long clinical text. Our methods can also inspire the development of other domain-enriched long-sequence transformers.
The rapid development of diagnostic technologies in healthcare is leading to higher requirements for physicians to handle and integrate the heterogeneous, yet complementary data that are produced during routine practice. For instance, the personalized diagnosis and treatment planning for a single cancer patient relies on the various images (e.g., radiological, pathological, and camera images) and non-image data (e.g., clinical data and genomic data). However, such decision-making procedures can be subjective, qualitative, and have large inter-subject variabilities. With the recent advances in multi-modal deep learning technologies, an increasingly large number of efforts have been devoted to a key question: how do we extract and aggregate multi-modal information to ultimately provide more objective, quantitative computer-aided clinical decision making? This paper reviews the recent studies on dealing with such a question. Briefly, this review will include the (1) overview of current multi-modal learning workflows, (2) summarization of multi-modal fusion methods, (3) discussion of the performance, (4) applications in disease diagnosis and prognosis, and (5) challenges and future directions.
A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark.
External knowledge is often useful for natural language understanding tasks. We introduce a contextual text representation model called Conceptual-Contextual (CC) embeddings, which incorporates structured knowledge into text representations. Unlike entity embedding methods, our approach encodes a knowledge graph into a context model. CC embeddings can be easily reused for a wide range of tasks just like pre-trained language models. Our model effectively encodes the huge UMLS database by leveraging semantic generalizability. Experiments on electronic health records (EHRs) and medical text processing benchmarks showed our model gives a major boost to the performance of supervised medical NLP tasks.
The era of big data provides researchers with convenient access to copious data. However, people often have little knowledge about it. The increasing prevalence of big data is challenging the traditional methods of learning causality because they are developed for the cases with limited amount of data and solid prior causal knowledge. This survey aims to close the gap between big data and learning causality with a comprehensive and structured review of traditional and frontier methods and a discussion about some open problems of learning causality. We begin with preliminaries of learning causality. Then we categorize and revisit methods of learning causality for the typical problems and data types. After that, we discuss the connections between learning causality and machine learning. At the end, some open problems are presented to show the great potential of learning causality with data.
We study the problem of named entity recognition (NER) from electronic medical records, which is one of the most fundamental and critical problems for medical text mining. Medical records which are written by clinicians from different specialties usually contain quite different terminologies and writing styles. The difference of specialties and the cost of human annotation makes it particularly difficult to train a universal medical NER system. In this paper, we propose a label-aware double transfer learning framework (La-DTL) for cross-specialty NER, so that a medical NER system designed for one specialty could be conveniently applied to another one with minimal annotation efforts. The transferability is guaranteed by two components: (i) we propose label-aware MMD for feature representation transfer, and (ii) we perform parameter transfer with a theoretical upper bound which is also label aware. We conduct extensive experiments on 12 cross-specialty NER tasks. The experimental results demonstrate that La-DTL provides consistent accuracy improvement over strong baselines. Besides, the promising experimental results on non-medical NER scenarios indicate that La-DTL is potential to be seamlessly adapted to a wide range of NER tasks.