RAD-DINO: Exploring Scalable Medical Image Encoders Beyond Text Supervision

Language-supervised pre-training has proven to be a valuable method for extracting semantically meaningful features from images, serving as a foundational element in multimodal systems within the computer vision and medical imaging domains. However, resulting features are limited by the information contained within the text. This is particularly problematic in medical imaging, where radiologists' written findings focus on specific observations; a challenge compounded by the scarcity of paired imaging-text data due to concerns over leakage of personal health information. In this work, we fundamentally challenge the prevailing reliance on language supervision for learning general purpose biomedical imaging encoders. We introduce RAD-DINO, a biomedical image encoder pre-trained solely on unimodal biomedical imaging data that obtains similar or greater performance than state-of-the-art biomedical language supervised models on a diverse range of benchmarks. Specifically, the quality of learned representations is evaluated on standard imaging tasks (classification and semantic segmentation), and a vision-language alignment task (text report generation from images). To further demonstrate the drawback of language supervision, we show that features from RAD-DINO correlate with other medical records (e.g., sex or age) better than language-supervised models, which are generally not mentioned in radiology reports. Finally, we conduct a series of ablations determining the factors in RAD-DINO's performance; notably, we observe that RAD-DINO's downstream performance scales well with the quantity and diversity of training data, demonstrating that image-only supervision is a scalable approach for training a foundational biomedical image encoder.

MAIRA-1: A specialised large multimodal model for radiology report generation

We present a radiology-specific multimodal model for the task for generating radiological reports from chest X-rays (CXRs). Our work builds on the idea that large language model(s) can be equipped with multimodal capabilities through alignment with pre-trained vision encoders. On natural images, this has been shown to allow multimodal models to gain image understanding and description capabilities. Our proposed model (MAIRA-1) leverages a CXR-specific image encoder in conjunction with a fine-tuned large language model based on Vicuna-7B, and text-based data augmentation, to produce reports with state-of-the-art quality. In particular, MAIRA-1 significantly improves on the radiologist-aligned RadCliQ metric and across all lexical metrics considered. Manual review of model outputs demonstrates promising fluency and accuracy of generated reports while uncovering failure modes not captured by existing evaluation practices. More information and resources can be found on the project website: https://aka.ms/maira.

Compositional Zero-Shot Domain Transfer with Text-to-Text Models

Label scarcity is a bottleneck for improving task performance in specialised domains. We propose a novel compositional transfer learning framework (DoT5 - domain compositional zero-shot T5) for zero-shot domain transfer. Without access to in-domain labels, DoT5 jointly learns domain knowledge (from MLM of unlabelled in-domain free text) and task knowledge (from task training on more readily available general-domain data) in a multi-task manner. To improve the transferability of task training, we design a strategy named NLGU: we simultaneously train NLG for in-domain label-to-data generation which enables data augmentation for self-finetuning and NLU for label prediction. We evaluate DoT5 on the biomedical domain and the resource-lean subdomain of radiology, focusing on NLI, text summarisation and embedding learning. DoT5 demonstrates the effectiveness of compositional transfer learning through multi-task learning. In particular, DoT5 outperforms the current SOTA in zero-shot transfer by over 7 absolute points in accuracy on RadNLI. We validate DoT5 with ablations and a case study demonstrating its ability to solve challenging NLI examples requiring in-domain expertise.

Looking for Out-of-Distribution Environments in Critical Care: A case study with the eICU Database

Generalizing to new populations and domains in machine learning is still an open problem which has seen increased interest recently. In particular, clinical models show a significant performance drop when tested in settings not seen during training, e.g., new hospitals or population demographics. Recently proposed models for domain generalisation promise to alleviate this problem by learning invariant characteristics across environments, however, there is still scepticism about whether they improve over traditional training. In this work, we take a principled approach to identifying Out of Distribution (OoD) environments, motivated by the problem of cross-hospital generalization in critical care. We propose model-based and heuristic approaches to identify OoD environments and systematically compare models with different levels of held-out information. In particular, based on the assumption that models with access to OoD data should outperform other models, we train models across a range of experimental setups that include leave-one-hospital-out training and cross-sectional feature splits. We find that access to OoD data does not translate to increased performance, pointing to inherent limitations in defining potential OoD environments in the eICU Database potentially due to data harmonisation and sampling. Echoing similar results with other popular clinical benchmarks in the literature, new approaches are required to evaluate robust models in critical care.

Early prediction of respiratory failure in the intensive care unit

The development of respiratory failure is common among patients in intensive care units (ICU). Large data quantities from ICU patient monitoring systems make timely and comprehensive analysis by clinicians difficult but are ideal for automatic processing by machine learning algorithms. Early prediction of respiratory system failure could alert clinicians to patients at risk of respiratory failure and allow for early patient reassessment and treatment adjustment. We propose an early warning system that predicts moderate/severe respiratory failure up to 8 hours in advance. Our system was trained on HiRID-II, a data-set containing more than 60,000 admissions to a tertiary care ICU. An alarm is typically triggered several hours before the beginning of respiratory failure. Our system outperforms a clinical baseline mimicking traditional clinical decision-making based on pulse-oximetric oxygen saturation and the fraction of inspired oxygen. To provide model introspection and diagnostics, we developed an easy-to-use web browser-based system to explore model input data and predictions visually.

ML4H Abstract Track 2020

A collection of the accepted abstracts for the Machine Learning for Health (ML4H) workshop at NeurIPS 2020. This index is not complete, as some accepted abstracts chose to opt-out of inclusion.

On the Intrinsic Privacy of Stochastic Gradient Descent

Private learning algorithms have been proposed that ensure strong differential-privacy (DP) guarantees, however they often come at a cost to utility. Meanwhile, stochastic gradient descent (SGD) contains intrinsic randomness which has not been leveraged for privacy. In this work, we take the first step towards analysing the intrinsic privacy properties of SGD. Our primary contribution is a large-scale empirical analysis of SGD on convex and non-convex objectives. We evaluate the inherent variability due to the stochasticity in SGD on 3 datasets and calculate the $\epsilon$ values due to the intrinsic noise. First, we show that the variability in model parameters due to the random sampling almost always exceeds that due to changes in the data. We observe that SGD provides intrinsic $\epsilon$ values of 7.8, 6.9, and 2.8 on MNIST, Adult, and Forest Covertype datasets respectively. Next, we propose a method to augment the intrinsic noise of SGD to achieve the desired $\epsilon$. Our augmented SGD outputs models that outperform existing approaches with the same privacy guarantee, closing the gap to noiseless utility between 0.19% and 10.07%. Finally, we show that the existing theoretical bound on the sensitivity of SGD is not tight. By estimating the tightest bound empirically, we achieve near-noiseless performance at $\epsilon = 1$, closing the utility gap to the noiseless model between 3.13% and 100%. Our experiments provide concrete evidence that changing the seed in SGD is likely to have a far greater impact on the model than excluding any given training example. By accounting for this intrinsic randomness, higher utility can be achieved without sacrificing further privacy. With these results, we hope to inspire the research community to further explore and characterise the randomness in SGD, its impact on privacy, and the parallels with generalisation in machine learning.

Unsupervised Extraction of Phenotypes from Cancer Clinical Notes for Association Studies

The recent adoption of Electronic Health Records (EHRs) by health care providers has introduced an important source of data that provides detailed and highly specific insights into patient phenotypes over large cohorts. These datasets, in combination with machine learning and statistical approaches, generate new opportunities for research and clinical care. However, many methods require the patient representations to be in structured formats, while the information in the EHR is often locked in unstructured texts designed for human readability. In this work, we develop the methodology to automatically extract clinical features from clinical narratives from large EHR corpora without the need for prior knowledge. We consider medical terms and sentences appearing in clinical narratives as atomic information units. We propose an efficient clustering strategy suitable for the analysis of large text corpora and to utilize the clusters to represent information about the patient compactly. To demonstrate the utility of our approach, we perform an association study of clinical features with somatic mutation profiles from 4,007 cancer patients and their tumors. We apply the proposed algorithm to a dataset consisting of about 65 thousand documents with a total of about 3.2 million sentences. We identify 341 significant statistical associations between the presence of somatic mutations and clinical features. We annotated these associations according to their novelty, and report several known associations. We also propose 32 testable hypotheses where the underlying biological mechanism does not appear to be known but plausible. These results illustrate that the automated discovery of clinical features is possible and the joint analysis of clinical and genetic datasets can generate appealing new hypotheses.

Machine learning for early prediction of circulatory failure in the intensive care unit

Intensive care clinicians are presented with large quantities of patient information and measurements from a multitude of monitoring systems. The limited ability of humans to process such complex information hinders physicians to readily recognize and act on early signs of patient deterioration. We used machine learning to develop an early warning system for circulatory failure based on a high-resolution ICU database with 240 patient years of data. This automatic system predicts 90.0% of circulatory failure events (prevalence 3.1%), with 81.8% identified more than two hours in advance, resulting in an area under the receiver operating characteristic curve of 94.0% and area under the precision-recall curve of 63.0%. The model was externally validated in a large independent patient cohort.