Jeremy Tan

Matthew Baugh, Jeremy Tan, Johanna P. Müller et al.

There is a growing interest in single-class modelling and out-of-distribution detection as fully supervised machine learning models cannot reliably identify classes not included in their training. The long tail of infinitely many out-of-distribution classes in real-world scenarios, e.g., for screening, triage, and quality control, means that it is often necessary to train single-class models that represent an expected feature distribution, e.g., from only strictly healthy volunteer data. Conventional supervised machine learning would require the collection of datasets that contain enough samples of all possible diseases in every imaging modality, which is not realistic. Self-supervised learning methods with synthetic anomalies are currently amongst the most promising approaches, alongside generative auto-encoders that analyse the residual reconstruction error. However, all methods suffer from a lack of structured validation, which makes calibration for deployment difficult and dataset-dependant. Our method alleviates this by making use of multiple visually-distinct synthetic anomaly learning tasks for both training and validation. This enables more robust training and generalisation. With our approach we can readily outperform state-of-the-art methods, which we demonstrate on exemplars in brain MRI and chest X-rays. Code is available at https://github.com/matt-baugh/many-tasks-make-light-work .

Johanna P. Müller, Matthew Baugh, Jeremy Tan et al.

Universal anomaly detection still remains a challenging problem in machine learning and medical image analysis. It is possible to learn an expected distribution from a single class of normative samples, e.g., through epistemic uncertainty estimates, auto-encoding models, or from synthetic anomalies in a self-supervised way. The performance of self-supervised anomaly detection approaches is still inferior compared to methods that use examples from known unknown classes to shape the decision boundary. However, outlier exposure methods often do not identify unknown unknowns. Here we discuss an improved self-supervised single-class training strategy that supports the approximation of probabilistic inference with loosen feature locality constraints. We show that up-scaling of gradients with histogram-equalised images is beneficial for recently proposed self-supervision tasks. Our method is integrated into several out-of-distribution (OOD) detection models and we show evidence that our method outperforms the state-of-the-art on various benchmark datasets.

Matthew Baugh, Jeremy Tan, Athanasios Vlontzos et al.

The wide variety of in-distribution and out-of-distribution data in medical imaging makes universal anomaly detection a challenging task. Recently a number of self-supervised methods have been developed that train end-to-end models on healthy data augmented with synthetic anomalies. However, it is difficult to compare these methods as it is not clear whether gains in performance are from the task itself or the training pipeline around it. It is also difficult to assess whether a task generalises well for universal anomaly detection, as they are often only tested on a limited range of anomalies. To assist with this we have developed nnOOD, a framework that adapts nnU-Net to allow for comparison of self-supervised anomaly localisation methods. By isolating the synthetic, self-supervised task from the rest of the training process we perform a more faithful comparison of the tasks, whilst also making the workflow for evaluating over a given dataset quick and easy. Using this we have implemented the current state-of-the-art tasks and evaluated them on a challenging X-ray dataset.

Clara Lebbos, Jen Barcroft, Jeremy Tan et al.

Ovarian cancer is the most lethal gynaecological malignancy. The disease is most commonly asymptomatic at its early stages and its diagnosis relies on expert evaluation of transvaginal ultrasound images. Ultrasound is the first-line imaging modality for characterising adnexal masses, it requires significant expertise and its analysis is subjective and labour-intensive, therefore open to error. Hence, automating processes to facilitate and standardise the evaluation of scans is desired in clinical practice. Using supervised learning, we have demonstrated that segmentation of adnexal masses is possible, however, prevalence and label imbalance restricts the performance on under-represented classes. To mitigate this we apply a novel pathology-specific data synthesiser. We create synthetic medical images with their corresponding ground truth segmentations by using Poisson image editing to integrate less common masses into other samples. Our approach achieves the best performance across all classes, including an improvement of up to 8% when compared with nnU-Net baseline approaches.

Hannah M. Schlüter, Jeremy Tan, Benjamin Hou et al.

We introduce a simple and intuitive self-supervision task, Natural Synthetic Anomalies (NSA), for training an end-to-end model for anomaly detection and localization using only normal training data. NSA integrates Poisson image editing to seamlessly blend scaled patches of various sizes from separate images. This creates a wide range of synthetic anomalies which are more similar to natural sub-image irregularities than previous data-augmentation strategies for self-supervised anomaly detection. We evaluate the proposed method using natural and medical images. Our experiments with the MVTec AD dataset show that a model trained to localize NSA anomalies generalizes well to detecting real-world a priori unknown types of manufacturing defects. Our method achieves an overall detection AUROC of 97.2 outperforming all previous methods that learn without the use of additional datasets. Code available at https://github.com/hmsch/natural-synthetic-anomalies.

Jeremy Tan, Benjamin Hou, Thomas Day et al.

Supervised learning of every possible pathology is unrealistic for many primary care applications like health screening. Image anomaly detection methods that learn normal appearance from only healthy data have shown promising results recently. We propose an alternative to image reconstruction-based and image embedding-based methods and propose a new self-supervised method to tackle pathological anomaly detection. Our approach originates in the foreign patch interpolation (FPI) strategy that has shown superior performance on brain MRI and abdominal CT data. We propose to use a better patch interpolation strategy, Poisson image interpolation (PII), which makes our method suitable for applications in challenging data regimes. PII outperforms state-of-the-art methods by a good margin when tested on surrogate tasks like identifying common lung anomalies in chest X-rays or hypo-plastic left heart syndrome in prenatal, fetal cardiac ultrasound images. Code available at https://github.com/jemtan/PII.

Daniel C. Castro, Jeremy Tan, Bernhard Kainz et al.

Revealing latent structure in data is an active field of research, having introduced exciting technologies such as variational autoencoders and adversarial networks, and is essential to push machine learning towards unsupervised knowledge discovery. However, a major challenge is the lack of suitable benchmarks for an objective and quantitative evaluation of learned representations. To address this issue we introduce Morpho-MNIST, a framework that aims to answer: "to what extent has my model learned to represent specific factors of variation in the data?" We extend the popular MNIST dataset by adding a morphometric analysis enabling quantitative comparison of trained models, identification of the roles of latent variables, and characterisation of sample diversity. We further propose a set of quantifiable perturbations to assess the performance of unsupervised and supervised methods on challenging tasks such as outlier detection and domain adaptation. Data and code are available at https://github.com/dccastro/Morpho-MNIST.

Yuhan Hou, Tianji Rao, Jeremy Tan et al.

The Federal Open Market Committee (FOMC) sets the federal funds rate, shaping monetary policy and the broader economy. We introduce \emph{FedSight AI}, a multi-agent framework that uses large language models (LLMs) to simulate FOMC deliberations and predict policy outcomes. Member agents analyze structured indicators and unstructured inputs such as the Beige Book, debate options, and vote, replicating committee reasoning. A Chain-of-Draft (CoD) extension further improves efficiency and accuracy by enforcing concise multistage reasoning. Evaluated at 2023-2024 meetings, FedSight CoD achieved accuracy of 93.75\% and stability of 93.33\%, outperforming baselines including MiniFed and Ordinal Random Forest (RF), while offering transparent reasoning aligned with real FOMC communications.

Samuel Budd, Matthew Sinclair, Thomas Day et al.

Fetal ultrasound screening during pregnancy plays a vital role in the early detection of fetal malformations which have potential long-term health impacts. The level of skill required to diagnose such malformations from live ultrasound during examination is high and resources for screening are often limited. We present an interpretable, atlas-learning segmentation method for automatic diagnosis of Hypo-plastic Left Heart Syndrome (HLHS) from a single `4 Chamber Heart' view image. We propose to extend the recently introduced Image-and-Spatial Transformer Networks (Atlas-ISTN) into a framework that enables sensitising atlas generation to disease. In this framework we can jointly learn image segmentation, registration, atlas construction and disease prediction while providing a maximum level of clinical interpretability compared to direct image classification methods. As a result our segmentation allows diagnoses competitive with expert-derived manual diagnosis and yields an AUC-ROC of 0.978 (1043 cases for training, 260 for validation and 325 for testing).

Elisa Chotzoglou, Thomas Day, Jeremy Tan et al.

Congenital heart disease is considered as one the most common groups of congenital malformations which affects $6-11$ per $1000$ newborns. In this work, an automated framework for detection of cardiac anomalies during ultrasound screening is proposed and evaluated on the example of Hypoplastic Left Heart Syndrome (HLHS), a sub-category of congenital heart disease. We propose an unsupervised approach that learns healthy anatomy exclusively from clinically confirmed normal control patients. We evaluate a number of known anomaly detection frameworks together with a model architecture based on the $α$-GAN network and find evidence that the proposed model performs significantly better than the state-of-the-art in image-based anomaly detection, yielding average $0.81$ AUC \emph{and} a better robustness towards initialisation compared to previous works.

Jeremy Tan, Benjamin Hou, James Batten et al.

In medical imaging, outliers can contain hypo/hyper-intensities, minor deformations, or completely altered anatomy. To detect these irregularities it is helpful to learn the features present in both normal and abnormal images. However this is difficult because of the wide range of possible abnormalities and also the number of ways that normal anatomy can vary naturally. As such, we leverage the natural variations in normal anatomy to create a range of synthetic abnormalities. Specifically, the same patch region is extracted from two independent samples and replaced with an interpolation between both patches. The interpolation factor, patch size, and patch location are randomly sampled from uniform distributions. A wide residual encoder decoder is trained to give a pixel-wise prediction of the patch and its interpolation factor. This encourages the network to learn what features to expect normally and to identify where foreign patterns have been introduced. The estimate of the interpolation factor lends itself nicely to the derivation of an outlier score. Meanwhile the pixel-wise output allows for pixel- and subject- level predictions using the same model.

Jeremy Tan, Anselm Au, Qingjie Meng et al.

Prenatal screening with ultrasound can lower neonatal mortality significantly for selected cardiac abnormalities. However, the need for human expertise, coupled with the high volume of screening cases, limits the practically achievable detection rates. In this paper we discuss the potential for deep learning techniques to aid in the detection of congenital heart disease (CHD) in fetal ultrasound. We propose a pipeline for automated data curation and classification. During both training and inference, we exploit an auxiliary view classification task to bias features toward relevant cardiac structures. This bias helps to improve in F1-scores from 0.72 and 0.77 to 0.87 and 0.85 for healthy and CHD classes respectively.

Payel Das, Tom Sercu, Kahini Wadhawan et al.

De novo therapeutic design is challenged by a vast chemical repertoire and multiple constraints, e.g., high broad-spectrum potency and low toxicity. We propose CLaSS (Controlled Latent attribute Space Sampling) - an efficient computational method for attribute-controlled generation of molecules, which leverages guidance from classifiers trained on an informative latent space of molecules modeled using a deep generative autoencoder. We screen the generated molecules for additional key attributes by using deep learning classifiers in conjunction with novel features derived from atomistic simulations. The proposed approach is demonstrated for designing non-toxic antimicrobial peptides (AMPs) with strong broad-spectrum potency, which are emerging drug candidates for tackling antibiotic resistance. Synthesis and testing of only twenty designed sequences identified two novel and minimalist AMPs with high potency against diverse Gram-positive and Gram-negative pathogens, including one multidrug-resistant and one antibiotic-resistant K. pneumoniae, via membrane pore formation. Both antimicrobials exhibit low in vitro and in vivo toxicity and mitigate the onset of drug resistance. The proposed approach thus presents a viable path for faster and efficient discovery of potent and selective broad-spectrum antimicrobials.

Tianrui Liu, Qingjie Meng, Athanasios Vlontzos et al.

Video is an essential imaging modality for diagnostics, e.g. in ultrasound imaging, for endoscopy, or movement assessment. However, video hasn't received a lot of attention in the medical image analysis community. In the clinical practice, it is challenging to utilise raw diagnostic video data efficiently as video data takes a long time to process, annotate or audit. In this paper we introduce a novel, fully automatic video summarization method that is tailored to the needs of medical video data. Our approach is framed as reinforcement learning problem and produces agents focusing on the preservation of important diagnostic information. We evaluate our method on videos from fetal ultrasound screening, where commonly only a small amount of the recorded data is used diagnostically. We show that our method is superior to alternative video summarization methods and that it preserves essential information required by clinical diagnostic standards.

Jeremy Tan, Bernhard Kainz

When data is unlabelled and the target task is not known a priori, divergent search offers a strategy for learning a wide range of skills. Having such a repertoire allows a system to adapt to new, unforeseen tasks. Unlabelled image data is plentiful, but it is not always known which features will be required for downstream tasks. We propose a method for divergent search in the few-shot image classification setting and evaluate with Omniglot and Mini-ImageNet. This high-dimensional behavior space includes all possible ways of partitioning the data. To manage divergent search in this space, we rely on a meta-learning framework to integrate useful features from diverse tasks into a single model. The final layer of this model is used as an index into the `archive' of all past behaviors. We search for regions in the behavior space that the current archive cannot reach. As expected, divergent search is outperformed by models with a strong bias toward the evaluation tasks. But it is able to match and sometimes exceed the performance of models that have a weak bias toward the target task or none at all. This demonstrates that divergent search is a viable approach, even in high-dimensional behavior spaces.

Jeremy Tan, Anselm Au, Qingjie Meng et al.

Semi-supervised learning methods have achieved excellent performance on standard benchmark datasets using very few labelled images. Anatomy classification in fetal 2D ultrasound is an ideal problem setting to test whether these results translate to non-ideal data. Our results indicate that inclusion of a challenging background class can be detrimental and that semi-supervised learning mostly benefits classes that are already distinct, sometimes at the expense of more similar classes.

Ahmet Tuysuzoglu, Jeremy Tan, Kareem Eissa et al.

Real-time localization of prostate gland in trans-rectal ultrasound images is a key technology that is required to automate the ultrasound guided prostate biopsy procedures. In this paper, we propose a new deep learning based approach which is aimed at localizing several prostate landmarks efficiently and robustly. We propose a multitask learning approach primarily to make the overall algorithm more contextually aware. In this approach, we not only consider the explicit learning of landmark locations, but also build-in a mechanism to learn the contour of the prostate. This multitask learning is further coupled with an adversarial arm to promote the generation of feasible structures. We have trained this network using ~4000 labeled trans-rectal ultrasound images and tested on an independent set of images with ground truth landmark locations. We have achieved an overall Dice score of 92.6% for the adversarially trained multitask approach, which is significantly better than the Dice score of 88.3% obtained by only learning of landmark locations. The overall mean distance error using the adversarial multitask approach has also improved by 20% while reducing the standard deviation of the error compared to learning landmark locations only. In terms of computational complexity both approaches can process the images in real-time using standard computer with a standard CUDA enabled GPU.