Conceptualizing Machine Learning for Dynamic Information Retrieval of Electronic Health Record Notes
The large amount of time clinicians spend sifting through patient notes and documenting in electronic health records (EHRs) is a leading cause of clinician burnout. By proactively and dynamically retrieving relevant notes during the documentation process, we can reduce the effort required to find relevant patient history. In this work, we conceptualize the use of EHR audit logs for machine learning as a source of supervision of note relevance in a specific clinical context, at a particular point in time. Our evaluation focuses on the dynamic retrieval in the emergency department, a high acuity setting with unique patterns of information retrieval and note writing. We show that our methods can achieve an AUC of 0.963 for predicting which notes will be read in an individual note writing session. We additionally conduct a user study with several clinicians and find that our framework can help clinicians retrieve relevant information more efficiently. Demonstrating that our framework and methods can perform well in this demanding setting is a promising proof of concept that they will translate to other clinical settings and data modalities (e.g., labs, medications, imaging).
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Clinical texts, represented in electronic medical records (EMRs), contain rich medical information and are essential for disease prediction, personalised information recommendation, clinical decision support, and medication pattern mining and measurement. Relation extractions between medication mentions and temporal information can further help clinicians better understand the patients' treatment history. To evaluate the performances of deep learning (DL) and large language models (LLMs) in medication extraction and temporal relations classification, we carry out an empirical investigation of \textbf{MedTem} project using several advanced learning structures including BiLSTM-CRF and CNN-BiLSTM for a clinical domain named entity recognition (NER), and BERT-CNN for temporal relation extraction (RE), in addition to the exploration of different word embedding techniques. Furthermore, we also designed a set of post-processing roles to generate structured output on medications and the temporal relation. Our experiments show that CNN-BiLSTM slightly wins the BiLSTM-CRF model on the i2b2-2009 clinical NER task yielding 75.67, 77.83, and 78.17 for precision, recall, and F1 scores using Macro Average. BERT-CNN model also produced reasonable evaluation scores 64.48, 67.17, and 65.03 for P/R/F1 using Macro Avg on the temporal relation extraction test set from i2b2-2012 challenges. Code and Tools from MedTem will be hosted at \url{//github.com/HECTA-UoM/MedTem}
Diabetic Retinopathy (DR), a prevalent and severe complication of diabetes, affects millions of individuals globally, underscoring the need for accurate and timely diagnosis. Recent advancements in imaging technologies, such as Ultra-WideField Color Fundus Photography (UWF-CFP) imaging and Optical Coherence Tomography Angiography (OCTA), provide opportunities for the early detection of DR but also pose significant challenges given the disparate nature of the data they produce. This study introduces a novel multimodal approach that leverages these imaging modalities to notably enhance DR classification. Our approach integrates 2D UWF-CFP images and 3D high-resolution 6x6 mm$^3$ OCTA (both structure and flow) images using a fusion of ResNet50 and 3D-ResNet50 models, with Squeeze-and-Excitation (SE) blocks to amplify relevant features. Additionally, to increase the model's generalization capabilities, a multimodal extension of Manifold Mixup, applied to concatenated multimodal features, is implemented. Experimental results demonstrate a remarkable enhancement in DR classification performance with the proposed multimodal approach compared to methods relying on a single modality only. The methodology laid out in this work holds substantial promise for facilitating more accurate, early detection of DR, potentially improving clinical outcomes for patients.
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as sequences of nucleotides - offers a promising storage medium. DNA is nature's information-storage molecule of choice and has a number of key properties: it is extremely dense, offering the theoretical possibility of storing 455 EB/g; it is durable, with a half-life of approximately 520 years that can be increased to thousands of years when DNA is chilled and stored dry; and it is amenable to automated synthesis and sequencing. Furthermore, biochemical processes that act on DNA potentially enable highly parallel data manipulation. Whilst biological information is encoded in DNA via a specific mapping from triplet sequences of nucleotides to amino acids, DNA storage is not limited to a single encoding scheme, and there are many possible ways to map data to chemical sequences of nucleotides for synthesis, storage, retrieval and data manipulation. However, there are several biological, error-tolerance and information-retrieval considerations that an encoding scheme needs to address to be viable. This comprehensive review focuses on comparing existing work done in encoding arbitrary data within DNA in terms of their encoding schemes, methods to address biological constraints and measures to provide error correction. We compare encoding approaches on the overall information density and coverage they achieve, as well as the data-retrieval method they use (i.e., sequential or random access). We also discuss the background and evolution of the encoding schemes.
Mathematical reasoning is a fundamental aspect of human intelligence and is applicable in various fields, including science, engineering, finance, and everyday life. The development of artificial intelligence (AI) systems capable of solving math problems and proving theorems has garnered significant interest in the fields of machine learning and natural language processing. For example, mathematics serves as a testbed for aspects of reasoning that are challenging for powerful deep learning models, driving new algorithmic and modeling advances. On the other hand, recent advances in large-scale neural language models have opened up new benchmarks and opportunities to use deep learning for mathematical reasoning. In this survey paper, we review the key tasks, datasets, and methods at the intersection of mathematical reasoning and deep learning over the past decade. We also evaluate existing benchmarks and methods, and discuss future research directions in this domain.
In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.
The dominating NLP paradigm of training a strong neural predictor to perform one task on a specific dataset has led to state-of-the-art performance in a variety of applications (eg. sentiment classification, span-prediction based question answering or machine translation). However, it builds upon the assumption that the data distribution is stationary, ie. that the data is sampled from a fixed distribution both at training and test time. This way of training is inconsistent with how we as humans are able to learn from and operate within a constantly changing stream of information. Moreover, it is ill-adapted to real-world use cases where the data distribution is expected to shift over the course of a model's lifetime. The first goal of this thesis is to characterize the different forms this shift can take in the context of natural language processing, and propose benchmarks and evaluation metrics to measure its effect on current deep learning architectures. We then proceed to take steps to mitigate the effect of distributional shift on NLP models. To this end, we develop methods based on parametric reformulations of the distributionally robust optimization framework. Empirically, we demonstrate that these approaches yield more robust models as demonstrated on a selection of realistic problems. In the third and final part of this thesis, we explore ways of efficiently adapting existing models to new domains or tasks. Our contribution to this topic takes inspiration from information geometry to derive a new gradient update rule which alleviate catastrophic forgetting issues during adaptation.
Translational distance-based knowledge graph embedding has shown progressive improvements on the link prediction task, from TransE to the latest state-of-the-art RotatE. However, N-1, 1-N and N-N predictions still remain challenging. In this work, we propose a novel translational distance-based approach for knowledge graph link prediction. The proposed method includes two-folds, first we extend the RotatE from 2D complex domain to high dimension space with orthogonal transforms to model relations for better modeling capacity. Second, the graph context is explicitly modeled via two directed context representations. These context representations are used as part of the distance scoring function to measure the plausibility of the triples during training and inference. The proposed approach effectively improves prediction accuracy on the difficult N-1, 1-N and N-N cases for knowledge graph link prediction task. The experimental results show that it achieves better performance on two benchmark data sets compared to the baseline RotatE, especially on data set (FB15k-237) with many high in-degree connection nodes.
Deep neural networks (DNNs) are successful in many computer vision tasks. However, the most accurate DNNs require millions of parameters and operations, making them energy, computation and memory intensive. This impedes the deployment of large DNNs in low-power devices with limited compute resources. Recent research improves DNN models by reducing the memory requirement, energy consumption, and number of operations without significantly decreasing the accuracy. This paper surveys the progress of low-power deep learning and computer vision, specifically in regards to inference, and discusses the methods for compacting and accelerating DNN models. The techniques can be divided into four major categories: (1) parameter quantization and pruning, (2) compressed convolutional filters and matrix factorization, (3) network architecture search, and (4) knowledge distillation. We analyze the accuracy, advantages, disadvantages, and potential solutions to the problems with the techniques in each category. We also discuss new evaluation metrics as a guideline for future research.
Deep convolutional neural networks (CNNs) have recently achieved great success in many visual recognition tasks. However, existing deep neural network models are computationally expensive and memory intensive, hindering their deployment in devices with low memory resources or in applications with strict latency requirements. Therefore, a natural thought is to perform model compression and acceleration in deep networks without significantly decreasing the model performance. During the past few years, tremendous progress has been made in this area. In this paper, we survey the recent advanced techniques for compacting and accelerating CNNs model developed. These techniques are roughly categorized into four schemes: parameter pruning and sharing, low-rank factorization, transferred/compact convolutional filters, and knowledge distillation. Methods of parameter pruning and sharing will be described at the beginning, after that the other techniques will be introduced. For each scheme, we provide insightful analysis regarding the performance, related applications, advantages, and drawbacks etc. Then we will go through a few very recent additional successful methods, for example, dynamic capacity networks and stochastic depths networks. After that, we survey the evaluation matrix, the main datasets used for evaluating the model performance and recent benchmarking efforts. Finally, we conclude this paper, discuss remaining challenges and possible directions on this topic.
Deep Convolutional Neural Networks have pushed the state-of-the art for semantic segmentation provided that a large amount of images together with pixel-wise annotations is available. Data collection is expensive and a solution to alleviate it is to use transfer learning. This reduces the amount of annotated data required for the network training but it does not get rid of this heavy processing step. We propose a method of transfer learning without annotations on the target task for datasets with redundant content and distinct pixel distributions. Our method takes advantage of the approximate content alignment of the images between two datasets when the approximation error prevents the reuse of annotation from one dataset to another. Given the annotations for only one dataset, we train a first network in a supervised manner. This network autonomously learns to generate deep data representations relevant to the semantic segmentation. Then the images in the new dataset, we train a new network to generate a deep data representation that matches the one from the first network on the previous dataset. The training consists in a regression between feature maps and does not require any annotations on the new dataset. We show that this method reaches performances similar to a classic transfer learning on the PASCAL VOC dataset with synthetic transformations.
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