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High resolution micro-ultrasound has demonstrated promise in real-time prostate cancer detection, with deep learning becoming a prominent tool for learning complex tissue properties reflected on ultrasound. However, a significant roadblock to real-world deployment remains, which prior works often overlook: model performance suffers when applied to data from different clinical centers due to variations in data distribution. This distribution shift significantly impacts the model's robustness, posing major challenge to clinical deployment. Domain adaptation and specifically its test-time adaption (TTA) variant offer a promising solution to address this challenge. In a setting designed to reflect real-world conditions, we compare existing methods to state-of-the-art TTA approaches adopted for cancer detection, demonstrating the lack of robustness to distribution shifts in the former. We then propose Diverse Ensemble Entropy Minimization (DEnEM), questioning the effectiveness of current TTA methods on ultrasound data. We show that these methods, although outperforming baselines, are suboptimal due to relying on neural networks output probabilities, which could be uncalibrated, or relying on data augmentation, which is not straightforward to define on ultrasound data. Our results show a significant improvement of $5\%$ to $7\%$ in AUROC over the existing methods and $3\%$ to $5\%$ over TTA methods, demonstrating the advantage of DEnEM in addressing distribution shift. \keywords{Ultrasound Imaging \and Prostate Cancer \and Computer-aided Diagnosis \and Distribution Shift Robustness \and Test-time Adaptation.}

We propose a categorical semantics for machine learning algorithms in terms of lenses, parametric maps, and reverse derivative categories. This foundation provides a powerful explanatory and unifying framework: it encompasses a variety of gradient descent algorithms such as ADAM, AdaGrad, and Nesterov momentum, as well as a variety of loss functions such as MSE and Softmax cross-entropy, and different architectures, shedding new light on their similarities and differences. Furthermore, our approach to learning has examples generalising beyond the familiar continuous domains (modelled in categories of smooth maps) and can be realised in the discrete setting of Boolean and polynomial circuits. We demonstrate the practical significance of our framework with an implementation in Python., Comment: arXiv admin note: text overlap with arXiv:2403.13001

PURPOSE: Deep learning methods for classifying prostate cancer (PCa) in ultrasound images typically employ convolutional networks (CNNs) to detect cancer in small regions of interest (ROI) along a needle trace region. However, this approach suffers from weak labelling, since the ground-truth histopathology labels do not describe the properties of individual ROIs. Recently, multi-scale approaches have sought to mitigate this issue by combining the context awareness of transformers with a CNN feature extractor to detect cancer from multiple ROIs using multiple-instance learning (MIL). In this work, we present a detailed study of several image transformer architectures for both ROI-scale and multi-scale classification, and a comparison of the performance of CNNs and transformers for ultrasound-based prostate cancer classification. We also design a novel multi-objective learning strategy that combines both ROI and core predictions to further mitigate label noise. METHODS: We evaluate 3 image transformers on ROI-scale cancer classification, then use the strongest model to tune a multi-scale classifier with MIL. We train our MIL models using our novel multi-objective learning strategy and compare our results to existing baselines. RESULTS: We find that for both ROI-scale and multi-scale PCa detection, image transformer backbones lag behind their CNN counterparts. This deficit in performance is even more noticeable for larger models. When using multi-objective learning, we can improve performance of MIL, with a 77.9% AUROC, a sensitivity of 75.9%, and a specificity of 66.3%. CONCLUSION: Convolutional networks are better suited for modelling sparse datasets of prostate ultrasounds, producing more robust features than transformers in PCa detection. Multi-scale methods remain the best architecture for this task, with multi-objective learning presenting an effective way to improve performance., Comment: early draft, 7 pages; Accepted to SPIE Medical Imaging 2024

We give parallel algorithms for string diagrams represented as structured cospans of ACSets. Specifically, we give linear (sequential) and logarithmic (parallel) time algorithms for composition, tensor product, construction of diagrams from arbitrary $\Sigma$-terms, and application of functors to diagrams. Our datastructure can represent morphisms of both the free symmetric monoidal category over an arbitrary signature as well as those with a chosen Special Frobenius structure. We show how this additional (hypergraph) structure can be used to map diagrams to diagrams of optics. This leads to a case study in which we define an algorithm for efficiently computing symbolic representations of gradient-based learners based on reverse derivatives. The work we present here is intended to be useful as a general purpose datastructure. Implementation requires only integer arrays and well-known algorithms, and is data-parallel by constuction. We therefore expect it to be applicable to a wide variety of settings, including embedded and parallel hardware and low-level languages.

A large body of previous machine learning methods for ultrasound-based prostate cancer detection classify small regions of interest (ROIs) of ultrasound signals that lie within a larger needle trace corresponding to a prostate tissue biopsy (called biopsy core). These ROI-scale models suffer from weak labeling as histopathology results available for biopsy cores only approximate the distribution of cancer in the ROIs. ROI-scale models do not take advantage of contextual information that are normally considered by pathologists, i.e. they do not consider information about surrounding tissue and larger-scale trends when identifying cancer. We aim to improve cancer detection by taking a multi-scale, i.e. ROI-scale and biopsy core-scale, approach. Methods: Our multi-scale approach combines (i) an "ROI-scale" model trained using self-supervised learning to extract features from small ROIs and (ii) a "core-scale" transformer model that processes a collection of extracted features from multiple ROIs in the needle trace region to predict the tissue type of the corresponding core. Attention maps, as a byproduct, allow us to localize cancer at the ROI scale. We analyze this method using a dataset of micro-ultrasound acquired from 578 patients who underwent prostate biopsy, and compare our model to baseline models and other large-scale studies in the literature. Results and Conclusions: Our model shows consistent and substantial performance improvements compared to ROI-scale-only models. It achieves 80.3% AUROC, a statistically significant improvement over ROI-scale classification. We also compare our method to large studies on prostate cancer detection, using other imaging modalities. Our code is publicly available at www.github.com/med-i-lab/TRUSFormer

Systematic evaluations of publicly funded research typically employ a combination of bibliometrics and peer review, but it is not known whether the bibliometric component introduces biases. This article compares three alternative mechanisms for scoring 73,612 UK Research Excellence Framework (REF) journal articles from all 34 field-based Units of Assessment (UoAs) 2014-17: peer review, field normalised citations, and journal average field normalised citation impact. All three were standardised into a four-point scale. The results suggest that in almost all academic fields, bibliometric scoring can disadvantage departments publishing high quality research, with the main exception of article citation rates in chemistry. Thus, introducing journal or article level citation information into peer review exercises may have a regression to the mean effect. Bibliometric scoring slightly advantaged women compared to men, but this varied between UoAs and was most evident in the physical sciences, engineering, and social sciences. In contrast, interdisciplinary research gained from bibliometric scoring in about half of the UoAs, but relatively substantially in two. In conclusion, out of the three potential source of bias examined, the most serious seems to be the tendency for bibliometric scores to work against high quality departments, assuming that the peer review scores are correct. This is almost a paradox: although high quality departments tend to get the highest bibliometric scores, bibliometrics conceal the full extent of departmental quality advantages. This should be considered when using bibliometrics or bibliometric informed peer review.

Altmetrics are web-based quantitative impact or attention indicators for academic articles that have been proposed to supplement citation counts. This article reports the first assessment of the extent to which mature altmetrics from Altmetric.com and Mendeley associate with journal article quality. It exploits expert norm-referenced peer review scores from the UK Research Excellence Framework 2021 for 67,030+ journal articles in all fields 2014-17/18, split into 34 Units of Assessment (UoAs). The results show that altmetrics are better indicators of research quality than previously thought, although not as good as raw and field normalised Scopus citation counts. Surprisingly, field normalising citation counts can reduce their strength as a quality indicator for articles in a single field. For most UoAs, Mendeley reader counts are the best, tweet counts are also a relatively strong indicator in many fields, and Facebook, blogs and news citations are moderately strong indicators in some UoAs, at least in the UK. In general, altmetrics are the strongest indicators of research quality in the health and physical sciences and weakest in the arts and humanities. The Altmetric Attention Score, although hybrid, is almost as good as Mendeley reader counts as a quality indicator and reflects more non-scholarly impacts.

Collaborative research causes problems for research assessments because of the difficulty in fairly crediting its authors. Whilst splitting the rewards for an article amongst its authors has the greatest surface-level fairness, many important evaluations assign full credit to each author, irrespective of team size. The underlying rationales for this are labour reduction and the need to incentivise collaborative work because it is necessary to solve many important societal problems. This article assesses whether full counting changes results compared to fractional counting in the case of the UK's Research Excellence Framework (REF) 2021. For this assessment, fractional counting reduces the number of journal articles to as little as 10% of the full counting value, depending on the Unit of Assessment (UoA). Despite this large difference, allocating an overall grade point average (GPA) based on full counting or fractional counting give results with a median Pearson correlation within UoAs of 0.98. The largest changes are for Archaeology (r=0.84) and Physics (r=0.88). There is a weak tendency for higher scoring institutions to lose from fractional counting, with the loss being statistically significant in 5 of the 34 UoAs. Thus, whilst the apparent over-weighting of contributions to collaboratively authored outputs does not seem too problematic from a fairness perspective overall, it may be worth examining in the few UoAs in which it makes the most difference.

Co-authored articles tend to be more cited in many academic fields, but is this because they tend to be higher quality or is it an audience effect: increased awareness through multiple author networks? We address this unknown with the largest investigation yet into whether author numbers associate with research quality, using expert peer quality judgements for 122,331 non-review journal articles submitted by UK academics for the 2014-20 national assessment process. Spearman correlations between the number of authors and the quality scores show moderately strong positive associations (0.2-0.4) in the health, life, and physical sciences, but weak or no positive associations in engineering, and social sciences. In contrast, we found little or no association in the arts and humanities, and a possible negative association for decision sciences. This gives reasonably conclusive evidence that greater numbers of authors associates with higher quality journal articles in the majority of academia outside the arts and humanities, at least for the UK. Positive associations between team size and citation counts in areas with little association between team size and quality also show that audience effects or other non-quality factors account for the higher citation rates of co-authored articles in some fields.

The Journal Impact Factor and other indicators that assess the average citation rate of articles in a journal are consulted by many academics and research evaluators, despite initiatives against overreliance on them. Despite this, there is limited evidence about the extent to which journal impact indicators in any field relates to human judgements about the journals or their articles. In response, we compared average citation rates of journals against expert judgements of their articles in all fields of science. We used preliminary quality scores for 96,031 articles published 2014-18 from the UK Research Excellence Framework (REF) 2021. We show that whilst there is a positive correlation between expert judgements of article quality and average journal impact in all fields of science, it is very weak in many fields and is never strong. The strength of the correlation varies from 0.11 to 0.43 for the 27 broad fields of Scopus. The highest correlation for the 94 Scopus narrow fields with at least 750 articles was only 0.54, for Infectious Diseases, and there was only one negative correlation, for the mixed category Computer Science (all). The results suggest that the average citation impact of a Scopus-indexed journal is never completely irrelevant to the quality of an article, even though it is never a strong indicator of article quality.

Purpose: Scholars often aim to conduct high quality research and their success is judged primarily by peer reviewers. Research quality is difficult for either group to identify, however, and misunderstandings can reduce the efficiency of the scientific enterprise. In response, we use a novel term association strategy to seek quantitative evidence of aspects of research that associate with high or low quality. Design/methodology/approach: We extracted the words and 2-5-word phrases most strongly associating with different quality scores in each of 34 Units of Assessment (UoAs) in the Research Excellence Framework (REF) 2021. We extracted the terms from 122,331 journal articles 2014-2020 with individual REF2021 quality scores. Findings: The terms associating with high- or low-quality scores vary between fields but relate to writing styles, methods, and topics. We show that the first-person writing style strongly associates with higher quality research in many areas because it is the norm for a set of large prestigious journals. We found methods and topics that associate with both high- and low-quality scores. Worryingly, terms associating with educational and qualitative research attract lower quality scores in multiple areas. REF experts may rarely give high scores to qualitative or educational research because the authors tend to be less competent, because it is harder to make world leading research with these themes, or because they do not value them. Originality: This is the first investigation of journal article terms associating with research quality.

The search for and management of external funding now occupies much valuable researcher time. Whilst funding is essential for some types of research and beneficial for others, it may also constrain academic choice and creativity. Thus, it is important to assess whether it is ever detrimental or unnecessary. Here we investigate whether funded research tends to be higher quality in all fields and for all major research funders. Based on peer review quality scores for 113,877 articles from all fields in the UK's Research Excellence Framework (REF) 2021, we estimate that there are substantial disciplinary differences in the proportion of funded journal articles, from Theology and Religious Studies (16%+) to Biological Sciences (91%+). The results suggest that funded research is likely to be higher quality overall, for all the largest research funders, and for all fields, even after factoring out research team size. There are differences between funders in the average quality of the research they support, however. Funding seems particularly beneficial in health-related fields. The results do not show cause and effect and do not take into account the amount of funding received but are consistent with funding either improving research quality or being won by high quality researchers or projects. In summary, there are no broad fields of research in which funding is irrelevant, so no fields can afford to ignore it. The results also show that citations are not effective proxies for research quality in the arts and humanities and most social sciences for evaluating research funding.

International collaboration is sometimes encouraged in the belief that it generates higher quality research or is more capable of addressing societal problems. Nevertheless, while there is evidence that the journal articles of international teams tend to be more cited than average, perhaps from increased international audiences, there is no science-wide direct academic evidence of a connection between international collaboration and research quality. This article empirically investigates the connection between international collaboration and research quality for the first time, with 148,977 UK-based journal articles with post publication expert review scores from the 2021 Research Excellence Framework (REF). Using an ordinal regression model controlling for collaboration, international partners increased the odds of higher quality scores in 27 out of 34 Units of Assessment (UoAs) and all Main Panels. The results therefore give the first large scale evidence of the fields in which international co-authorship for articles is usually apparently beneficial. At the country level, the results suggests that UK collaboration with other high research-expenditure economies generates higher quality research, even when the countries produce lower citation impact journal articles than the United Kingdom. Worryingly, collaborations with lower research-expenditure economies tend to be judged lower quality, possibly through misunderstanding Global South research goals., Comment: Journal of the American Society for Information Science and Technology

Citation counts are widely used as indicators of research quality to support or replace human peer review and for lists of top cited papers, researchers, and institutions. Nevertheless, the relationship between citations and research quality is poorly evidenced. We report the first large-scale science-wide academic evaluation of the relationship between research quality and citations (field normalised citation counts), correlating them for 87,739 journal articles in 34 field-based UK Units of Assessment (UoAs). The two correlate positively in all academic fields, from very weak (0.1) to strong (0.5), reflecting broadly linear relationships in all fields. We give the first evidence that the correlations are positive even across the arts and humanities. The patterns are similar for the field classification schemes of Scopus and Dimensions.ai, although varying for some individual subjects and therefore more uncertain for these. We also show for the first time that no field has a citation threshold beyond which all articles are excellent quality, so lists of top cited articles are not pure collections of excellence, and neither is any top citation percentile indicator. Thus, whilst appropriately field normalised citations associate positively with research quality in all fields, they never perfectly reflect it, even at high values.

National research evaluation initiatives and incentive schemes have previously chosen between simplistic quantitative indicators and time-consuming peer review, sometimes supported by bibliometrics. Here we assess whether artificial intelligence (AI) could provide a third alternative, estimating article quality using more multiple bibliometric and metadata inputs. We investigated this using provisional three-level REF2021 peer review scores for 84,966 articles submitted to the UK Research Excellence Framework 2021, matching a Scopus record 2014-18 and with a substantial abstract. We found that accuracy is highest in the medical and physical sciences Units of Assessment (UoAs) and economics, reaching 42% above the baseline (72% overall) in the best case. This is based on 1000 bibliometric inputs and half of the articles used for training in each UoA. Prediction accuracies above the baseline for the social science, mathematics, engineering, arts, and humanities UoAs were much lower or close to zero. The Random Forest Classifier (standard or ordinal) and Extreme Gradient Boosting Classifier algorithms performed best from the 32 tested. Accuracy was lower if UoAs were merged or replaced by Scopus broad categories. We increased accuracy with an active learning strategy and by selecting articles with higher prediction probabilities, as estimated by the algorithms, but this substantially reduced the number of scores predicted.

This document describes strategies for using Artificial Intelligence (AI) to predict some journal article scores in future research assessment exercises. Five strategies have been assessed.

Deep learning-based analysis of high-frequency, high-resolution micro-ultrasound data shows great promise for prostate cancer detection. Previous approaches to analysis of ultrasound data largely follow a supervised learning paradigm. Ground truth labels for ultrasound images used for training deep networks often include coarse annotations generated from the histopathological analysis of tissue samples obtained via biopsy. This creates inherent limitations on the availability and quality of labeled data, posing major challenges to the success of supervised learning methods. On the other hand, unlabeled prostate ultrasound data are more abundant. In this work, we successfully apply self-supervised representation learning to micro-ultrasound data. Using ultrasound data from 1028 biopsy cores of 391 subjects obtained in two clinical centres, we demonstrate that feature representations learnt with this method can be used to classify cancer from non-cancer tissue, obtaining an AUROC score of 91% on an independent test set. To the best of our knowledge, this is the first successful end-to-end self-supervised learning approach for prostate cancer detection using ultrasound data. Our method outperforms baseline supervised learning approaches, generalizes well between different data centers, and scale well in performance as more unlabeled data are added, making it a promising approach for future research using large volumes of unlabeled data.