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Add to EdgeVoice EHR: Introducing Multimodal Audio Data for Health
Apr 02, 2024
Large AI models trained on audio data may have the potential to rapidly classify patients, enhancing medical decision-making and potentially improving outcomes through early detection. Existing technologies depend on limited datasets using expensive recording equipment in high-income, English-speaking countries. This challenges deployment in resource-constrained, high-volume settings where audio data may have a profound impact. This report introduces a novel data type and a corresponding collection system that captures health data through guided questions using only a mobile/web application. This application ultimately results in an audio electronic health record (voice EHR) which may contain complex biomarkers of health from conventional voice/respiratory features, speech patterns, and language with semantic meaning - compensating for the typical limitations of unimodal clinical datasets. This report introduces a consortium of partners for global work, presents the application used for data collection, and showcases the potential of informative voice EHR to advance the scalability and diversity of audio AI.
Efficiency at Scale: Investigating the Performance of Diminutive Language Models in Clinical Tasks
Feb 16, 2024
The entry of large language models (LLMs) into research and commercial spaces has led to a trend of ever-larger models, with initial promises of generalisability, followed by a widespread desire to downsize and create specialised models without the need for complete fine-tuning, using Parameter Efficient Fine-tuning (PEFT) methods. We present an investigation into the suitability of different PEFT methods to clinical decision-making tasks, across a range of model sizes, including extremely small models with as few as $25$ million parameters. Our analysis shows that the performance of most PEFT approaches varies significantly from one task to another, with the exception of LoRA, which maintains relatively high performance across all model sizes and tasks, typically approaching or matching full fine-tuned performance. The effectiveness of PEFT methods in the clinical domain is evident, particularly for specialised models which can operate on low-cost, in-house computing infrastructure. The advantages of these models, in terms of speed and reduced training costs, dramatically outweighs any performance gain from large foundation LLMs. Furthermore, we highlight how domain-specific pre-training interacts with PEFT methods and model size, and discuss how these factors interplay to provide the best efficiency-performance trade-off. Full code available at: tbd.
All models are local: time to replace external validation with recurrent local validation
May 13, 2023External validation is often recommended to ensure the generalizability of ML models. However, it neither guarantees generalizability nor equates to a model's clinical usefulness (the ultimate goal of any clinical decision-support tool). External validation is misaligned with current healthcare ML needs. First, patient data changes across time, geography, and facilities. These changes create significant volatility in the performance of a single fixed model (especially for deep learning models, which dominate clinical ML). Second, newer ML techniques, current market forces, and updated regulatory frameworks are enabling frequent updating and monitoring of individual deployed model instances. We submit that external validation is insufficient to establish ML models' safety or utility. Proposals to fix the external validation paradigm do not go far enough. Continued reliance on it as the ultimate test is likely to lead us astray. We propose the MLOps-inspired paradigm of recurring local validation as an alternative that ensures the validity of models while protecting against performance-disruptive data variability. This paradigm relies on site-specific reliability tests before every deployment, followed by regular and recurrent checks throughout the life cycle of the deployed algorithm. Initial and recurrent reliability tests protect against performance-disruptive distribution shifts, and concept drifts that jeopardize patient safety.
Is dataset condensation a silver bullet for healthcare data sharing?
May 05, 2023
Safeguarding personal information is paramount for healthcare data sharing, a challenging issue without any silver bullet thus far. We study the prospect of a recent deep-learning advent, dataset condensation (DC), in sharing healthcare data for AI research, and the results are promising. The condensed data abstracts original records and irreversibly conceals individual-level knowledge to achieve a bona fide de-identification, which permits free sharing. Moreover, the original deep-learning utilities are well preserved in the condensed data with compressed volume and accelerated model convergences. In PhysioNet-2012, a condensed dataset of 20 samples can orient deep models attaining 80.3% test AUC of mortality prediction (versus 85.8% of 5120 original records), an inspiring discovery generalised to MIMIC-III and Coswara datasets. We also interpret the inhere privacy protections of DC through theoretical analysis and empirical evidence. Dataset condensation opens a new gate to sharing healthcare data for AI research with multiple desirable traits.
Adversarial De-confounding in Individualised Treatment Effects Estimation
Oct 19, 2022
Observational studies have recently received significant attention from the machine learning community due to the increasingly available non-experimental observational data and the limitations of the experimental studies, such as considerable cost, impracticality, small and less representative sample sizes, etc. In observational studies, de-confounding is a fundamental problem of individualised treatment effects (ITE) estimation. This paper proposes disentangled representations with adversarial training to selectively balance the confounders in the binary treatment setting for the ITE estimation. The adversarial training of treatment policy selectively encourages treatment-agnostic balanced representations for the confounders and helps to estimate the ITE in the observational studies via counterfactual inference. Empirical results on synthetic and real-world datasets, with varying degrees of confounding, prove that our proposed approach improves the state-of-the-art methods in achieving lower error in the ITE estimation.
Using Bottleneck Adapters to Identify Cancer in Clinical Notes under Low-Resource Constraints
Oct 17, 2022
Processing information locked within clinical health records is a challenging task that remains an active area of research in biomedical NLP. In this work, we evaluate a broad set of machine learning techniques ranging from simple RNNs to specialised transformers such as BioBERT on a dataset containing clinical notes along with a set of annotations indicating whether a sample is cancer-related or not. Furthermore, we specifically employ efficient fine-tuning methods from NLP, namely, bottleneck adapters and prompt tuning, to adapt the models to our specialised task. Our evaluations suggest that fine-tuning a frozen BERT model pre-trained on natural language and with bottleneck adapters outperforms all other strategies, including full fine-tuning of the specialised BioBERT model. Based on our findings, we suggest that using bottleneck adapters in low-resource situations with limited access to labelled data or processing capacity could be a viable strategy in biomedical text mining. The code used in the experiments are going to be made available at https://github.com/omidrohanian/bottleneck-adapters.
Nowruz at SemEval-2022 Task 7: Tackling Cloze Tests with Transformers and Ordinal Regression
Apr 01, 2022
This paper outlines the system using which team Nowruz participated in SemEval 2022 Task 7 Identifying Plausible Clarifications of Implicit and Underspecified Phrases for both subtasks A and B. Using a pre-trained transformer as a backbone, the model targeted the task of multi-task classification and ranking in the context of finding the best fillers for a cloze task related to instructional texts on the website Wikihow. The system employed a combination of two ordinal regression components to tackle this task in a multi-task learning scenario. According to the official leaderboard of the shared task, this system was ranked 5th in the ranking and 7th in the classification subtasks out of 21 participating teams. With additional experiments, the models have since been further optimised.
Assessing the risk of re-identification arising from an attack on anonymised data
Mar 31, 2022
Objective: The use of routinely-acquired medical data for research purposes requires the protection of patient confidentiality via data anonymisation. The objective of this work is to calculate the risk of re-identification arising from a malicious attack to an anonymised dataset, as described below. Methods: We first present an analytical means of estimating the probability of re-identification of a single patient in a k-anonymised dataset of Electronic Health Record (EHR) data. Second, we generalize this solution to obtain the probability of multiple patients being re-identified. We provide synthetic validation via Monte Carlo simulations to illustrate the accuracy of the estimates obtained. Results: The proposed analytical framework for risk estimation provides re-identification probabilities that are in agreement with those provided by simulation in a number of scenarios. Our work is limited by conservative assumptions which inflate the re-identification probability. Discussion: Our estimates show that the re-identification probability increases with the proportion of the dataset maliciously obtained and that it has an inverse relationship with the equivalence class size. Our recursive approach extends the applicability domain to the general case of a multi-patient re-identification attack in an arbitrary k-anonymisation scheme. Conclusion: We prescribe a systematic way to parametrize the k-anonymisation process based on a pre-determined re-identification probability. We observed that the benefits of a reduced re-identification risk that come with increasing k-size may not be worth the reduction in data granularity when one is considering benchmarking the re-identification probability on the size of the portion of the dataset maliciously obtained by the adversary.
Privacy-aware Early Detection of COVID-19 through Adversarial Training
Jan 09, 2022
Early detection of COVID-19 is an ongoing area of research that can help with triage, monitoring and general health assessment of potential patients and may reduce operational strain on hospitals that cope with the coronavirus pandemic. Different machine learning techniques have been used in the literature to detect coronavirus using routine clinical data (blood tests, and vital signs). Data breaches and information leakage when using these models can bring reputational damage and cause legal issues for hospitals. In spite of this, protecting healthcare models against leakage of potentially sensitive information is an understudied research area. In this work, we examine two machine learning approaches, intended to predict a patient's COVID-19 status using routinely collected and readily available clinical data. We employ adversarial training to explore robust deep learning architectures that protect attributes related to demographic information about the patients. The two models we examine in this work are intended to preserve sensitive information against adversarial attacks and information leakage. In a series of experiments using datasets from the Oxford University Hospitals, Bedfordshire Hospitals NHS Foundation Trust, University Hospitals Birmingham NHS Foundation Trust, and Portsmouth Hospitals University NHS Trust we train and test two neural networks that predict PCR test results using information from basic laboratory blood tests, and vital signs performed on a patients' arrival to hospital. We assess the level of privacy each one of the models can provide and show the efficacy and robustness of our proposed architectures against a comparable baseline. One of our main contributions is that we specifically target the development of effective COVID-19 detection models with built-in mechanisms in order to selectively protect sensitive attributes against adversarial attacks.
Let Your Heart Speak in its Mother Tongue: Multilingual Captioning of Cardiac Signals
Mar 19, 2021
Cardiac signals, such as the electrocardiogram, convey a significant amount of information about the health status of a patient which is typically summarized by a clinician in the form of a clinical report, a cumbersome process that is prone to errors. To streamline this routine process, we propose a deep neural network capable of captioning cardiac signals; it receives a cardiac signal as input and generates a clinical report as output. We extend this further to generate multilingual reports. To that end, we create and make publicly available a multilingual clinical report dataset. In the absence of sufficient labelled data, deep neural networks can benefit from a warm-start, or pre-training, procedure in which parameters are first learned in an arbitrary task. We propose such a task in the form of discriminative multilingual pre-training where tokens from clinical reports are randomly replaced with those from other languages and the network is tasked with predicting the language of all tokens. We show that our method performs on par with state-of-the-art pre-training methods such as MLM, ELECTRA, and MARGE, while simultaneously generating diverse and plausible clinical reports. We also demonstrate that multilingual models can outperform their monolingual counterparts, informally terming this beneficial phenomenon as the blessing of multilinguality.