Michael Roberts

Simon Deltadahl, Julian Gilbey, Christine Van Laer et al.

Accurate classification of haematological cells is critical for diagnosing blood disorders, but presents significant challenges for machine automation owing to the complexity of cell morphology, heterogeneities of biological, pathological, and imaging characteristics, and the imbalance of cell type frequencies. We introduce CytoDiffusion, a diffusion-based classifier that effectively models blood cell morphology, combining accurate classification with robust anomaly detection, resistance to distributional shifts, interpretability, data efficiency, and superhuman uncertainty quantification. Our approach outperforms state-of-the-art discriminative models in anomaly detection (AUC 0.990 vs. 0.918), resistance to domain shifts (85.85% vs. 74.38% balanced accuracy), and performance in low-data regimes (95.88% vs. 94.95% balanced accuracy). Notably, our model generates synthetic blood cell images that are nearly indistinguishable from real images, as demonstrated by an authenticity test in which expert haematologists achieved only 52.3% accuracy (95% CI: [50.5%, 54.2%]) in distinguishing real from generated images. Furthermore, we enhance model explainability through the generation of directly interpretable counterfactual heatmaps. Our comprehensive evaluation framework, encompassing these multiple performance dimensions, establishes a new benchmark for medical image analysis in haematology, ultimately enabling improved diagnostic accuracy in clinical settings. Our code is available at https://github.com/CambridgeCIA/CytoDiffusion.

Sayash Kapoor, Emily Cantrell, Kenny Peng et al. · princeton

Machine learning (ML) methods are proliferating in scientific research. However, the adoption of these methods has been accompanied by failures of validity, reproducibility, and generalizability. These failures can hinder scientific progress, lead to false consensus around invalid claims, and undermine the credibility of ML-based science. ML methods are often applied and fail in similar ways across disciplines. Motivated by this observation, our goal is to provide clear reporting standards for ML-based science. Drawing from an extensive review of past literature, we present the REFORMS checklist ($\textbf{Re}$porting Standards $\textbf{For}$ $\textbf{M}$achine Learning Based $\textbf{S}$cience). It consists of 32 questions and a paired set of guidelines. REFORMS was developed based on a consensus of 19 researchers across computer science, data science, mathematics, social sciences, and biomedical sciences. REFORMS can serve as a resource for researchers when designing and implementing a study, for referees when reviewing papers, and for journals when enforcing standards for transparency and reproducibility.

Tolou Shadbahr, Michael Roberts, Jan Stanczuk et al.

Classifying samples in incomplete datasets is a common aim for machine learning practitioners, but is non-trivial. Missing data is found in most real-world datasets and these missing values are typically imputed using established methods, followed by classification of the now complete, imputed, samples. The focus of the machine learning researcher is then to optimise the downstream classification performance. In this study, we highlight that it is imperative to consider the quality of the imputation. We demonstrate how the commonly used measures for assessing quality are flawed and propose a new class of discrepancy scores which focus on how well the method recreates the overall distribution of the data. To conclude, we highlight the compromised interpretability of classifier models trained using poorly imputed data.

Sören Dittmer, Michael Roberts, Julian Gilbey et al.

In this perspective, we argue that despite the democratization of powerful tools for data science and machine learning over the last decade, developing the code for a trustworthy and effective data science system (DSS) is getting harder. Perverse incentives and a lack of widespread software engineering (SE) skills are among many root causes we identify that naturally give rise to the current systemic crisis in reproducibility of DSSs. We analyze why SE and building large complex systems is, in general, hard. Based on these insights, we identify how SE addresses those difficulties and how we can apply and generalize SE methods to construct DSSs that are fit for purpose. We advocate two key development philosophies, namely that one should incrementally grow -- not biphasically plan and build -- DSSs, and one should always employ two types of feedback loops during development: one which tests the code's correctness and another that evaluates the code's efficacy.

Daniel Kreuter, Samuel Tull, Julian Gilbey et al.

Clinical data is often affected by clinically irrelevant factors such as discrepancies between measurement devices or differing processing methods between sites. In the field of machine learning (ML), these factors are known as domains and the distribution differences they cause in the data are known as domain shifts. ML models trained using data from one domain often perform poorly when applied to data from another domain, potentially leading to wrong predictions. As such, developing machine learning models that can generalise well across multiple domains is a challenging yet essential task in the successful application of ML in clinical practice. In this paper, we propose a novel disentangled autoencoder (Dis-AE) neural network architecture that can learn domain-invariant data representations for multi-label classification of medical measurements even when the data is influenced by multiple interacting domain shifts at once. The model utilises adversarial training to produce data representations from which the domain can no longer be determined. We evaluate the model's domain generalisation capabilities on synthetic datasets and full blood count (FBC) data from blood donors as well as primary and secondary care patients, showing that Dis-AE improves model generalisation on multiple domains simultaneously while preserving clinically relevant information.

Clemens Karner, Janek Gröhl, Ian Selby et al.

When developing machine learning models, image quality assessment (IQA) measures are a crucial component for the evaluation of obtained output images. However, commonly used full-reference IQA (FR-IQA) measures have been primarily developed and optimized for natural images. In many specialized settings, such as medical images, this poses an often overlooked problem regarding suitability. In previous studies, the FR-IQA measure HaarPSI showed promising behavior regarding generalizability. The measure is based on Haar wavelet representations and the framework allows optimization of two parameters. So far, these parameters have been aligned for natural images. Here, we optimize these parameters for two medical image data sets, a photoacoustic and a chest X-ray data set, with IQA expert ratings. We observe that they lead to similar parameter values, different to the natural image data, and are more sensitive to parameter changes. We denote the novel optimized setting as HaarPSI$_{MED}$, which improves the performance of the employed medical images significantly (p<0.05). Additionally, we include an independent CT test data set that illustrates the generalizability of HaarPSI$_{MED}$, as well as visual examples that qualitatively demonstrate the improvement. The results suggest that adapting common IQA measures within their frameworks for medical images can provide a valuable, generalizable addition to employment of more specific task-based measures.

Mary Chriselda Antony Oliver, Michael Roberts, Carola-Bibiane Schönlieb et al.

The manifold hypothesis posits that high-dimensional data typically resides on low-dimensional sub spaces. In this paper, we assume manifold hypothesis to investigate graph-based semi-supervised learning methods. In particular, we examine Laplace Learning in the Wasserstein space, extending the classical notion of graph-based semi-supervised learning algorithms from finite-dimensional Euclidean spaces to an infinite-dimensional setting. To achieve this, we prove variational convergence of a discrete graph p- Dirichlet energy to its continuum counterpart. In addition, we characterize the Laplace-Beltrami operator on asubmanifold of the Wasserstein space. Finally, we validate the proposed theoretical framework through numerical experiments conducted on benchmark datasets, demonstrating the consistency of our classification performance in high-dimensional settings.

Xu Chen, Yuan Huang, Benn Jessney et al.

Artificial intelligence (AI) methodologies hold great promise for the rapid and accurate diagnosis of coronary artery disease (CAD) from intravascular optical coherent tomography (IVOCT) images. Numerous papers have been published describing AI-based models for different diagnostic tasks, yet it remains unclear which models have potential clinical utility and have been properly validated. This systematic review considered published literature between January 2015 and February 2023 describing AI-based diagnosis of CAD using IVOCT. Our search identified 5,576 studies, with 513 included after initial screening and 35 studies included in the final systematic review after quality screening. Our findings indicate that most of the identified models are not currently suitable for clinical use, primarily due to methodological flaws and underlying biases. To address these issues, we provide recommendations to improve model quality and research practices to enhance the development of clinically useful AI products.

Michael Roberts, Indranil SenGupta

In this paper we present a sequential hypothesis test for the detection of general jump size distrubution. Infinitesimal generators for the corresponding log-likelihood ratios are presented and analyzed. Bounds for infinitesimal generators in terms of super-solutions and sub-solutions are computed. This is shown to be implementable in relation to various classification problems for a crude oil price data set. Machine and deep learning algorithms are implemented to extract a specific deterministic component from the crude oil data set, and the deterministic component is implemented to improve the Barndorff-Nielsen and Shephard model, a commonly used stochastic model for derivative and commodity market analysis.

Michael Roberts, Jack Spencer

Selective segmentation involves incorporating user input to partition an image into foreground and background, by discriminating between objects of a similar type. Typically, such methods involve introducing additional constraints to generic segmentation approaches. However, we show that this is often inconsistent with respect to common assumptions about the image. The proposed method introduces a new fitting term that is more useful in practice than the Chan-Vese framework. In particular, the idea is to define a term that allows for the background to consist of multiple regions of inhomogeneity. We provide comparitive experimental results to alternative approaches to demonstrate the advantages of the proposed method, broadening the possible application of these methods.