Showing 1–31 of 31 results for author: Hicks, S

Beyond the Leaderboard: Design Lessons for Trustworthy Multimodal VQA

Authors: Sushant Gautam, Vajira Thambawita, Michael A. Riegler, Pål Halvorsen, Steven A. Hicks

Abstract: Healthcare multimodal AI must combine visual and textual evidence while remaining reliable and interpretable. Using MediaEval Medico 2025 as a retrospective GI endoscopy case study, we analyze design choices across nine documented systems for question answering and explanation quality. Parameter-efficient adaptation of pretrained backbones provides strong challenge performance, but answer-level ga… ▽ More Healthcare multimodal AI must combine visual and textual evidence while remaining reliable and interpretable. Using MediaEval Medico 2025 as a retrospective GI endoscopy case study, we analyze design choices across nine documented systems for question answering and explanation quality. Parameter-efficient adaptation of pretrained backbones provides strong challenge performance, but answer-level gains do not consistently translate into faithful and complete clinical reasoning. Methods enforcing structured reasoning and explicit grounding show more reliable behavior across heterogeneous question types, although the evidence is correlational rather than ablation-based. These results motivate evaluation beyond lexical overlap, standardized evidence-linked explanations, leakage-aware data governance, and lightweight robustness and calibration checks. The findings support trustworthy multimodal healthcare AI based on data fusion, explainability, and resilient evaluation. △ Less

Submitted 16 July, 2026; originally announced July 2026.

Comments: Accepted for presentation at the 39th IEEE International Symposium on Computer-Based Medical Systems (IEEE CBMS 2026) as a regular paper

MSC Class: 68T45; 68T07; 68U10 ACM Class: I.2.10; I.4.8; J.3

HealthBench Professional: Evaluating Large Language Models on Real Clinician Chats

Authors: Rebecca Soskin Hicks, Mikhail Trofimov, Dominick Lim, Rahul K. Arora, Foivos Tsimpourlas, Preston Bowman, Michael Sharman, Chi Tong, Kavin Karthik, Arnav Dugar, Akshay Jagadeesh, Khaled Saab, Johannes Heidecke, Ashley Alexander, Nate Gross, Karan Singhal

Abstract: Millions of clinicians use ChatGPT to support clinical care, but evaluations of the most common use cases in model-clinician conversations are limited. We introduce HealthBench Professional, an open benchmark for evaluating large language models on real tasks that clinicians bring to ChatGPT in the course of their work. The benchmark is organized around three common use cases central to clinical p… ▽ More Millions of clinicians use ChatGPT to support clinical care, but evaluations of the most common use cases in model-clinician conversations are limited. We introduce HealthBench Professional, an open benchmark for evaluating large language models on real tasks that clinicians bring to ChatGPT in the course of their work. The benchmark is organized around three common use cases central to clinical practice: care consult, writing and documentation, and medical research. Each example includes a physician-authored conversation with ChatGPT for Clinicians and is scored via rubrics written and iteratively adjudicated by three or more physicians across three phases. HealthBench Professional examples were carefully selected for quality, representativeness, and difficulty for OpenAI's current frontier models, to enable continued measurement of progress. Difficult examples for recent OpenAI models were enriched by roughly 3.5 times relative to the candidate pool of 15,079 examples. Additionally, about one-third of examples involve physicians conducting deliberate adversarial testing of models. As a strong baseline, we also collected human physician responses for all tasks (unbounded time, specialist-matched, web access). The best scoring system, GPT-5.4 in ChatGPT for Clinicians, outperforms base GPT-5.4, all other models, and human physicians. We hope HealthBench Professional provides the healthcare AI community a measure to track frontier model progress in real-world clinical tasks and build systems that clinicians can trust to improve care. △ Less

Submitted 30 April, 2026; originally announced April 2026.

Comments: Data link in paper; Blog: https://openai.com/index/making-chatgpt-better-for-clinicians/

Medical Imaging AI Competitions Lack Fairness

Authors: Annika Reinke, Evangelia Christodoulou, Sthuthi Sadananda, A. Emre Kavur, Khrystyna Faryna, Daan Schouten, Bennett A. Landman, Carole Sudre, Olivier Colliot, Nick Heller, Sophie Loizillon, Martin Maška, Maëlys Solal, Arya Yazdan-Panah, Vilma Bozgo, Ömer Sümer, Siem de Jong, Sophie Fischer, Michal Kozubek, Tim Rädsch, Nadim Hammoud, Fruzsina Molnár-Gábor, Steven Hicks, Michael A. Riegler, Anindo Saha , et al. (12 additional authors not shown)

Abstract: Benchmarking competitions are central to the development of artificial intelligence (AI) in medical imaging, defining performance standards and shaping methodological progress. However, it remains unclear whether these benchmarks provide data that are sufficiently representative, accessible, and reusable to support clinically meaningful AI. In this work, we assess fairness along two complementary… ▽ More Benchmarking competitions are central to the development of artificial intelligence (AI) in medical imaging, defining performance standards and shaping methodological progress. However, it remains unclear whether these benchmarks provide data that are sufficiently representative, accessible, and reusable to support clinically meaningful AI. In this work, we assess fairness along two complementary dimensions: (1) whether challenge datasets are representative of real-world clinical diversity, and (2) whether they are accessible and legally reusable in line with the FAIR principles. To address this question, we conducted a large-scale systematic study of 241 biomedical image analysis challenges comprising 458 tasks across 19 imaging modalities. Our findings show substantial biases in dataset composition, including geographic location, modality-, and problem type-related biases, indicating that current benchmarks do not adequately reflect real-world clinical diversity. Despite their widespread influence, challenge datasets were frequently constrained by restrictive or ambiguous access conditions, inconsistent or non-compliant licensing practices, and incomplete documentation, limiting reproducibility and long-term reuse. Together, these shortcomings expose foundational fairness limitations in our benchmarking ecosystem and highlight a disconnect between leaderboard success and clinical relevance. △ Less

Submitted 19 December, 2025; originally announced December 2025.

Comments: Submitted to Nature BME

Medico 2025: Visual Question Answering for Gastrointestinal Imaging

Authors: Sushant Gautam, Vajira Thambawita, Michael Riegler, Pål Halvorsen, Steven Hicks

Abstract: The Medico 2025 challenge addresses Visual Question Answering (VQA) for Gastrointestinal (GI) imaging, organized as part of the MediaEval task series. The challenge focuses on developing Explainable Artificial Intelligence (XAI) models that answer clinically relevant questions based on GI endoscopy images while providing interpretable justifications aligned with medical reasoning. It introduces tw… ▽ More The Medico 2025 challenge addresses Visual Question Answering (VQA) for Gastrointestinal (GI) imaging, organized as part of the MediaEval task series. The challenge focuses on developing Explainable Artificial Intelligence (XAI) models that answer clinically relevant questions based on GI endoscopy images while providing interpretable justifications aligned with medical reasoning. It introduces two subtasks: (1) answering diverse types of visual questions using the Kvasir-VQA-x1 dataset, and (2) generating multimodal explanations to support clinical decision-making. The Kvasir-VQA-x1 dataset, created from 6,500 images and 159,549 complex question-answer (QA) pairs, serves as the benchmark for the challenge. By combining quantitative performance metrics and expert-reviewed explainability assessments, this task aims to advance trustworthy Artificial Intelligence (AI) in medical image analysis. Instructions, data access, and an updated guide for participation are available in the official competition repository: https://github.com/simula/MediaEval-Medico-2025 △ Less

Submitted 14 August, 2025; originally announced August 2025.

MSC Class: 68T45; 92C55 ACM Class: I.2.10; I.4.9

AI-based Clinical Decision Support for Primary Care: A Real-World Study

Authors: Robert Korom, Sarah Kiptinness, Najib Adan, Kassim Said, Catherine Ithuli, Oliver Rotich, Boniface Kimani, Irene King'ori, Stellah Kamau, Elizabeth Atemba, Muna Aden, Preston Bowman, Michael Sharman, Rebecca Soskin Hicks, Rebecca Distler, Johannes Heidecke, Rahul K. Arora, Karan Singhal

Abstract: We evaluate the impact of large language model-based clinical decision support in live care. In partnership with Penda Health, a network of primary care clinics in Nairobi, Kenya, we studied AI Consult, a tool that serves as a safety net for clinicians by identifying potential documentation and clinical decision-making errors. AI Consult integrates into clinician workflows, activating only when ne… ▽ More We evaluate the impact of large language model-based clinical decision support in live care. In partnership with Penda Health, a network of primary care clinics in Nairobi, Kenya, we studied AI Consult, a tool that serves as a safety net for clinicians by identifying potential documentation and clinical decision-making errors. AI Consult integrates into clinician workflows, activating only when needed and preserving clinician autonomy. We conducted a quality improvement study, comparing outcomes for 39,849 patient visits performed by clinicians with or without access to AI Consult across 15 clinics. Visits were rated by independent physicians to identify clinical errors. Clinicians with access to AI Consult made relatively fewer errors: 16% fewer diagnostic errors and 13% fewer treatment errors. In absolute terms, the introduction of AI Consult would avert diagnostic errors in 22,000 visits and treatment errors in 29,000 visits annually at Penda alone. In a survey of clinicians with AI Consult, all clinicians said that AI Consult improved the quality of care they delivered, with 75% saying the effect was "substantial". These results required a clinical workflow-aligned AI Consult implementation and active deployment to encourage clinician uptake. We hope this study demonstrates the potential for LLM-based clinical decision support tools to reduce errors in real-world settings and provides a practical framework for advancing responsible adoption. △ Less

Submitted 22 July, 2025; originally announced July 2025.

Comments: Blog: https://openai.com/index/ai-clinical-copilot-penda-health/

HealthBench: Evaluating Large Language Models Towards Improved Human Health

Authors: Rahul K. Arora, Jason Wei, Rebecca Soskin Hicks, Preston Bowman, Joaquin Quiñonero-Candela, Foivos Tsimpourlas, Michael Sharman, Meghan Shah, Andrea Vallone, Alex Beutel, Johannes Heidecke, Karan Singhal

Abstract: We present HealthBench, an open-source benchmark measuring the performance and safety of large language models in healthcare. HealthBench consists of 5,000 multi-turn conversations between a model and an individual user or healthcare professional. Responses are evaluated using conversation-specific rubrics created by 262 physicians. Unlike previous multiple-choice or short-answer benchmarks, Healt… ▽ More We present HealthBench, an open-source benchmark measuring the performance and safety of large language models in healthcare. HealthBench consists of 5,000 multi-turn conversations between a model and an individual user or healthcare professional. Responses are evaluated using conversation-specific rubrics created by 262 physicians. Unlike previous multiple-choice or short-answer benchmarks, HealthBench enables realistic, open-ended evaluation through 48,562 unique rubric criteria spanning several health contexts (e.g., emergencies, transforming clinical data, global health) and behavioral dimensions (e.g., accuracy, instruction following, communication). HealthBench performance over the last two years reflects steady initial progress (compare GPT-3.5 Turbo's 16% to GPT-4o's 32%) and more rapid recent improvements (o3 scores 60%). Smaller models have especially improved: GPT-4.1 nano outperforms GPT-4o and is 25 times cheaper. We additionally release two HealthBench variations: HealthBench Consensus, which includes 34 particularly important dimensions of model behavior validated via physician consensus, and HealthBench Hard, where the current top score is 32%. We hope that HealthBench grounds progress towards model development and applications that benefit human health. △ Less

Submitted 13 May, 2025; originally announced May 2025.

Comments: Blog: https://openai.com/index/healthbench/ Code: https://github.com/openai/simple-evals

Prompt to Polyp: Medical Text-Conditioned Image Synthesis with Diffusion Models

Authors: Mikhail Chaichuk, Sushant Gautam, Steven Hicks, Elena Tutubalina

Abstract: The generation of realistic medical images from text descriptions has significant potential to address data scarcity challenges in healthcare AI while preserving patient privacy. This paper presents a comprehensive study of text-to-image synthesis in the medical domain, comparing two distinct approaches: (1) fine-tuning large pre-trained latent diffusion models and (2) training small, domain-speci… ▽ More The generation of realistic medical images from text descriptions has significant potential to address data scarcity challenges in healthcare AI while preserving patient privacy. This paper presents a comprehensive study of text-to-image synthesis in the medical domain, comparing two distinct approaches: (1) fine-tuning large pre-trained latent diffusion models and (2) training small, domain-specific models. We introduce a novel model named MSDM, an optimized architecture based on Stable Diffusion that integrates a clinical text encoder, variational autoencoder, and cross-attention mechanisms to better align medical text prompts with generated images. Our study compares two approaches: fine-tuning large pre-trained models (FLUX, Kandinsky) versus training compact domain-specific models (MSDM). Evaluation across colonoscopy (MedVQA-GI) and radiology (ROCOv2) datasets reveals that while large models achieve higher fidelity, our optimized MSDM delivers comparable quality with lower computational costs. Quantitative metrics and qualitative evaluations by medical experts reveal strengths and limitations of each approach. △ Less

Submitted 12 May, 2025; v1 submitted 8 May, 2025; originally announced May 2025.

Comments: code available at https://github.com/THunderCondOR/ImageCLEFmed-MEDVQA-GI-2024-MMCP-Team

MSC Class: 68T07; 68U10; 92C55 ACM Class: I.2.10; I.4.8; J.3

Interplay between Federated Learning and Explainable Artificial Intelligence: a Scoping Review

Authors: Luis M. Lopez-Ramos, Florian Leiser, Aditya Rastogi, Steven Hicks, Inga Strümke, Vince I. Madai, Tobias Budig, Ali Sunyaev, Adam Hilbert

Abstract: The joint implementation of federated learning (FL) and explainable artificial intelligence (XAI) could allow training models from distributed data and explaining their inner workings while preserving essential aspects of privacy. Toward establishing the benefits and tensions associated with their interplay, this scoping review maps the publications that jointly deal with FL and XAI, focusing on p… ▽ More The joint implementation of federated learning (FL) and explainable artificial intelligence (XAI) could allow training models from distributed data and explaining their inner workings while preserving essential aspects of privacy. Toward establishing the benefits and tensions associated with their interplay, this scoping review maps the publications that jointly deal with FL and XAI, focusing on publications that reported an interplay between FL and model interpretability or post-hoc explanations. Out of the 37 studies meeting our criteria, only one explicitly and quantitatively analyzed the influence of FL on model explanations, revealing a significant research gap. The aggregation of interpretability metrics across FL nodes created generalized global insights at the expense of node-specific patterns being diluted. Several studies proposed FL algorithms incorporating explanation methods to safeguard the learning process against defaulting or malicious nodes. Studies using established FL libraries or following reporting guidelines are a minority. More quantitative research and structured, transparent practices are needed to fully understand their mutual impact and under which conditions it happens. △ Less

Submitted 10 April, 2025; v1 submitted 7 November, 2024; originally announced November 2024.

Comments: 16 pages, 10 figures, submitted in IEEE Access

Generative LLM Powered Conversational AI Application for Personalized Risk Assessment: A Case Study in COVID-19

Authors: Mohammad Amin Roshani, Xiangyu Zhou, Yao Qiang, Srinivasan Suresh, Steve Hicks, Usha Sethuraman, Dongxiao Zhu

Abstract: Large language models (LLMs) have shown remarkable capabilities in various natural language tasks and are increasingly being applied in healthcare domains. This work demonstrates a new LLM-powered disease risk assessment approach via streaming human-AI conversation, eliminating the need for programming required by traditional machine learning approaches. In a COVID-19 severity risk assessment case… ▽ More Large language models (LLMs) have shown remarkable capabilities in various natural language tasks and are increasingly being applied in healthcare domains. This work demonstrates a new LLM-powered disease risk assessment approach via streaming human-AI conversation, eliminating the need for programming required by traditional machine learning approaches. In a COVID-19 severity risk assessment case study, we fine-tune pre-trained generative LLMs (e.g., Llama2-7b and Flan-t5-xl) using a few shots of natural language examples, comparing their performance with traditional classifiers (i.e., Logistic Regression, XGBoost, Random Forest) that are trained de novo using tabular data across various experimental settings. We develop a mobile application that uses these fine-tuned LLMs as its generative AI (GenAI) core to facilitate real-time interaction between clinicians and patients, providing no-code risk assessment through conversational interfaces. This integration not only allows for the use of streaming Questions and Answers (QA) as inputs but also offers personalized feature importance analysis derived from the LLM's attention layers, enhancing the interpretability of risk assessments. By achieving high Area Under the Curve (AUC) scores with a limited number of fine-tuning samples, our results demonstrate the potential of generative LLMs to outperform discriminative classification methods in low-data regimes, highlighting their real-world adaptability and effectiveness. This work aims to fill the existing gap in leveraging generative LLMs for interactive no-code risk assessment and to encourage further research in this emerging field. △ Less

Submitted 23 September, 2024; originally announced September 2024.

Kvasir-VQA: A Text-Image Pair GI Tract Dataset

Authors: Sushant Gautam, Andrea Storås, Cise Midoglu, Steven A. Hicks, Vajira Thambawita, Pål Halvorsen, Michael A. Riegler

Abstract: We introduce Kvasir-VQA, an extended dataset derived from the HyperKvasir and Kvasir-Instrument datasets, augmented with question-and-answer annotations to facilitate advanced machine learning tasks in Gastrointestinal (GI) diagnostics. This dataset comprises 6,500 annotated images spanning various GI tract conditions and surgical instruments, and it supports multiple question types including yes/… ▽ More We introduce Kvasir-VQA, an extended dataset derived from the HyperKvasir and Kvasir-Instrument datasets, augmented with question-and-answer annotations to facilitate advanced machine learning tasks in Gastrointestinal (GI) diagnostics. This dataset comprises 6,500 annotated images spanning various GI tract conditions and surgical instruments, and it supports multiple question types including yes/no, choice, location, and numerical count. The dataset is intended for applications such as image captioning, Visual Question Answering (VQA), text-based generation of synthetic medical images, object detection, and classification. Our experiments demonstrate the dataset's effectiveness in training models for three selected tasks, showcasing significant applications in medical image analysis and diagnostics. We also present evaluation metrics for each task, highlighting the usability and versatility of our dataset. The dataset and supporting artifacts are available at https://datasets.simula.no/kvasir-vqa. △ Less

Submitted 2 September, 2024; originally announced September 2024.

Comments: to be published in VLM4Bio 2024, part of the ACM Multimedia (ACM MM) conference 2024

Validating polyp and instrument segmentation methods in colonoscopy through Medico 2020 and MedAI 2021 Challenges

Authors: Debesh Jha, Vanshali Sharma, Debapriya Banik, Debayan Bhattacharya, Kaushiki Roy, Steven A. Hicks, Nikhil Kumar Tomar, Vajira Thambawita, Adrian Krenzer, Ge-Peng Ji, Sahadev Poudel, George Batchkala, Saruar Alam, Awadelrahman M. A. Ahmed, Quoc-Huy Trinh, Zeshan Khan, Tien-Phat Nguyen, Shruti Shrestha, Sabari Nathan, Jeonghwan Gwak, Ritika K. Jha, Zheyuan Zhang, Alexander Schlaefer, Debotosh Bhattacharjee, M. K. Bhuyan , et al. (8 additional authors not shown)

Abstract: Automatic analysis of colonoscopy images has been an active field of research motivated by the importance of early detection of precancerous polyps. However, detecting polyps during the live examination can be challenging due to various factors such as variation of skills and experience among the endoscopists, lack of attentiveness, and fatigue leading to a high polyp miss-rate. Deep learning has… ▽ More Automatic analysis of colonoscopy images has been an active field of research motivated by the importance of early detection of precancerous polyps. However, detecting polyps during the live examination can be challenging due to various factors such as variation of skills and experience among the endoscopists, lack of attentiveness, and fatigue leading to a high polyp miss-rate. Deep learning has emerged as a promising solution to this challenge as it can assist endoscopists in detecting and classifying overlooked polyps and abnormalities in real time. In addition to the algorithm's accuracy, transparency and interpretability are crucial to explaining the whys and hows of the algorithm's prediction. Further, most algorithms are developed in private data, closed source, or proprietary software, and methods lack reproducibility. Therefore, to promote the development of efficient and transparent methods, we have organized the "Medico automatic polyp segmentation (Medico 2020)" and "MedAI: Transparency in Medical Image Segmentation (MedAI 2021)" competitions. We present a comprehensive summary and analyze each contribution, highlight the strength of the best-performing methods, and discuss the possibility of clinical translations of such methods into the clinic. For the transparency task, a multi-disciplinary team, including expert gastroenterologists, accessed each submission and evaluated the team based on open-source practices, failure case analysis, ablation studies, usability and understandability of evaluations to gain a deeper understanding of the models' credibility for clinical deployment. Through the comprehensive analysis of the challenge, we not only highlight the advancements in polyp and surgical instrument segmentation but also encourage qualitative evaluation for building more transparent and understandable AI-based colonoscopy systems. △ Less

Submitted 6 May, 2024; v1 submitted 30 July, 2023; originally announced July 2023.

GastroVision: A Multi-class Endoscopy Image Dataset for Computer Aided Gastrointestinal Disease Detection

Authors: Debesh Jha, Vanshali Sharma, Neethi Dasu, Nikhil Kumar Tomar, Steven Hicks, M. K. Bhuyan, Pradip K. Das, Michael A. Riegler, Pål Halvorsen, Ulas Bagci, Thomas de Lange

Abstract: Integrating real-time artificial intelligence (AI) systems in clinical practices faces challenges such as scalability and acceptance. These challenges include data availability, biased outcomes, data quality, lack of transparency, and underperformance on unseen datasets from different distributions. The scarcity of large-scale, precisely labeled, and diverse datasets are the major challenge for cl… ▽ More Integrating real-time artificial intelligence (AI) systems in clinical practices faces challenges such as scalability and acceptance. These challenges include data availability, biased outcomes, data quality, lack of transparency, and underperformance on unseen datasets from different distributions. The scarcity of large-scale, precisely labeled, and diverse datasets are the major challenge for clinical integration. This scarcity is also due to the legal restrictions and extensive manual efforts required for accurate annotations from clinicians. To address these challenges, we present \textit{GastroVision}, a multi-center open-access gastrointestinal (GI) endoscopy dataset that includes different anatomical landmarks, pathological abnormalities, polyp removal cases and normal findings (a total of 27 classes) from the GI tract. The dataset comprises 8,000 images acquired from Bærum Hospital in Norway and Karolinska University Hospital in Sweden and was annotated and verified by experienced GI endoscopists. Furthermore, we validate the significance of our dataset with extensive benchmarking based on the popular deep learning based baseline models. We believe our dataset can facilitate the development of AI-based algorithms for GI disease detection and classification. Our dataset is available at \url{https://osf.io/84e7f/}. △ Less

Submitted 17 August, 2023; v1 submitted 16 July, 2023; originally announced July 2023.

Blockwise Principal Component Analysis for monotone missing data imputation and dimensionality reduction

Authors: Tu T. Do, Mai Anh Vu, Tuan L. Vo, Hoang Thien Ly, Thu Nguyen, Steven A. Hicks, Michael A. Riegler, Pål Halvorsen, Binh T. Nguyen

Abstract: Monotone missing data is a common problem in data analysis. However, imputation combined with dimensionality reduction can be computationally expensive, especially with the increasing size of datasets. To address this issue, we propose a Blockwise principal component analysis Imputation (BPI) framework for dimensionality reduction and imputation of monotone missing data. The framework conducts Pri… ▽ More Monotone missing data is a common problem in data analysis. However, imputation combined with dimensionality reduction can be computationally expensive, especially with the increasing size of datasets. To address this issue, we propose a Blockwise principal component analysis Imputation (BPI) framework for dimensionality reduction and imputation of monotone missing data. The framework conducts Principal Component Analysis (PCA) on the observed part of each monotone block of the data and then imputes on merging the obtained principal components using a chosen imputation technique. BPI can work with various imputation techniques and can significantly reduce imputation time compared to conducting dimensionality reduction after imputation. This makes it a practical and efficient approach for large datasets with monotone missing data. Our experiments validate the improvement in speed. In addition, our experiments also show that while applying MICE imputation directly on missing data may not yield convergence, applying BPI with MICE for the data may lead to convergence. △ Less

Submitted 10 January, 2024; v1 submitted 10 May, 2023; originally announced May 2023.

Automated control and optimisation of laser driven ion acceleration

Authors: B. Loughran, M. J. V. Streeter, H. Ahmed, S. Astbury, M. Balcazar, M. Borghesi, N. Bourgeois, C. B. Curry, S. J. D. Dann, S. DiIorio, N. P. Dover, T. Dzelzanis, O. C. Ettlinger, M. Gauthier, L. Giuffrida, G. D. Glenn, S. H. Glenzer, J. S. Green, R. J. Gray, G. S. Hicks, C. Hyland, V. Istokskaia, M. King, D. Margarone, O. McCusker , et al. (10 additional authors not shown)

Abstract: The interaction of relativistically intense lasers with opaque targets represents a highly non-linear, multi-dimensional parameter space. This limits the utility of sequential 1D scanning of experimental parameters for the optimisation of secondary radiation, although to-date this has been the accepted methodology due to low data acquisition rates. High repetition-rate (HRR) lasers augmented by ma… ▽ More The interaction of relativistically intense lasers with opaque targets represents a highly non-linear, multi-dimensional parameter space. This limits the utility of sequential 1D scanning of experimental parameters for the optimisation of secondary radiation, although to-date this has been the accepted methodology due to low data acquisition rates. High repetition-rate (HRR) lasers augmented by machine learning present a valuable opportunity for efficient source optimisation. Here, an automated, HRR-compatible system produced high fidelity parameter scans, revealing the influence of laser intensity on target pre-heating and proton generation. A closed-loop Bayesian optimisation of maximum proton energy, through control of the laser wavefront and target position, produced proton beams with equivalent maximum energy to manually-optimized laser pulses but using only 60% of the laser energy. This demonstration of automated optimisation of laser-driven proton beams is a crucial step towards deeper physical insight and the construction of future radiation sources. △ Less

Submitted 1 March, 2023; originally announced March 2023.

Comments: 11 pages

VISEM-Tracking, a human spermatozoa tracking dataset

Authors: Vajira Thambawita, Steven A. Hicks, Andrea M. Storås, Thu Nguyen, Jorunn M. Andersen, Oliwia Witczak, Trine B. Haugen, Hugo L. Hammer, Pål Halvorsen, Michael A. Riegler

Abstract: A manual assessment of sperm motility requires microscopy observation, which is challenging due to the fast-moving spermatozoa in the field of view. To obtain correct results, manual evaluation requires extensive training. Therefore, computer-assisted sperm analysis (CASA) has become increasingly used in clinics. Despite this, more data is needed to train supervised machine learning approaches in… ▽ More A manual assessment of sperm motility requires microscopy observation, which is challenging due to the fast-moving spermatozoa in the field of view. To obtain correct results, manual evaluation requires extensive training. Therefore, computer-assisted sperm analysis (CASA) has become increasingly used in clinics. Despite this, more data is needed to train supervised machine learning approaches in order to improve accuracy and reliability in the assessment of sperm motility and kinematics. In this regard, we provide a dataset called VISEM-Tracking with 20 video recordings of 30 seconds (comprising 29,196 frames) of wet sperm preparations with manually annotated bounding-box coordinates and a set of sperm characteristics analyzed by experts in the domain. In addition to the annotated data, we provide unlabeled video clips for easy-to-use access and analysis of the data via methods such as self- or unsupervised learning. As part of this paper, we present baseline sperm detection performances using the YOLOv5 deep learning (DL) model trained on the VISEM-Tracking dataset. As a result, we show that the dataset can be used to train complex DL models to analyze spermatozoa. △ Less

Submitted 10 May, 2023; v1 submitted 6 December, 2022; originally announced December 2022.

Report number: Scientific Data volume 10

Journal ref: Sci Data 10, 260 (2023)

MLC at HECKTOR 2022: The Effect and Importance of Training Data when Analyzing Cases of Head and Neck Tumors using Machine Learning

Authors: Vajira Thambawita, Andrea M. Storås, Steven A. Hicks, Pål Halvorsen, Michael A. Riegler

Abstract: Head and neck cancers are the fifth most common cancer worldwide, and recently, analysis of Positron Emission Tomography (PET) and Computed Tomography (CT) images has been proposed to identify patients with a prognosis. Even though the results look promising, more research is needed to further validate and improve the results. This paper presents the work done by team MLC for the 2022 version of t… ▽ More Head and neck cancers are the fifth most common cancer worldwide, and recently, analysis of Positron Emission Tomography (PET) and Computed Tomography (CT) images has been proposed to identify patients with a prognosis. Even though the results look promising, more research is needed to further validate and improve the results. This paper presents the work done by team MLC for the 2022 version of the HECKTOR grand challenge held at MICCAI 2022. For Task 1, the automatic segmentation task, our approach was, in contrast to earlier solutions using 3D segmentation, to keep it as simple as possible using a 2D model, analyzing every slice as a standalone image. In addition, we were interested in understanding how different modalities influence the results. We proposed two approaches; one using only the CT scans to make predictions and another using a combination of the CT and PET scans. For Task 2, the prediction of recurrence-free survival, we first proposed two approaches, one where we only use patient data and one where we combined the patient data with segmentations from the image model. For the prediction of the first two approaches, we used Random Forest. In our third approach, we combined patient data and image data using XGBoost. Low kidney function might worsen cancer prognosis. In this approach, we therefore estimated the kidney function of the patients and included it as a feature. Overall, we conclude that our simple methods were not able to compete with the highest-ranking submissions, but we still obtained reasonably good scores. We also got interesting insights into how the combination of different modalities can influence the segmentation and predictions. △ Less

Submitted 30 November, 2022; originally announced November 2022.

Comments: Submitted to https://hecktor.grand-challenge.org/

Visual explanations for polyp detection: How medical doctors assess intrinsic versus extrinsic explanations

Authors: Steven Hicks, Andrea Storås, Michael Riegler, Cise Midoglu, Malek Hammou, Thomas de Lange, Sravanthi Parasa, Pål Halvorsen, Inga Strümke

Abstract: Deep learning has in recent years achieved immense success in all areas of computer vision and has the potential of assisting medical doctors in analyzing visual content for disease and other abnormalities. However, the current state of deep learning is very much a black box, making medical professionals highly skeptical about integrating these methods into clinical practice. Several methods have… ▽ More Deep learning has in recent years achieved immense success in all areas of computer vision and has the potential of assisting medical doctors in analyzing visual content for disease and other abnormalities. However, the current state of deep learning is very much a black box, making medical professionals highly skeptical about integrating these methods into clinical practice. Several methods have been proposed in order to shine some light onto these black boxes, but there is no consensus on the opinion of the medical doctors that will consume these explanations. This paper presents a study asking medical doctors about their opinion of current state-of-the-art explainable artificial intelligence methods when applied to a gastrointestinal disease detection use case. We compare two different categories of explanation methods, intrinsic and extrinsic, and gauge their opinion of the current value of these explanations. The results indicate that intrinsic explanations are preferred and that explanation. △ Less

Submitted 23 March, 2022; originally announced April 2022.

Assessing generalisability of deep learning-based polyp detection and segmentation methods through a computer vision challenge

Authors: Sharib Ali, Noha Ghatwary, Debesh Jha, Ece Isik-Polat, Gorkem Polat, Chen Yang, Wuyang Li, Adrian Galdran, Miguel-Ángel González Ballester, Vajira Thambawita, Steven Hicks, Sahadev Poudel, Sang-Woong Lee, Ziyi Jin, Tianyuan Gan, ChengHui Yu, JiangPeng Yan, Doyeob Yeo, Hyunseok Lee, Nikhil Kumar Tomar, Mahmood Haithmi, Amr Ahmed, Michael A. Riegler, Christian Daul, Pål Halvorsen , et al. (7 additional authors not shown)

Abstract: Polyps are well-known cancer precursors identified by colonoscopy. However, variability in their size, location, and surface largely affect identification, localisation, and characterisation. Moreover, colonoscopic surveillance and removal of polyps (referred to as polypectomy ) are highly operator-dependent procedures. There exist a high missed detection rate and incomplete removal of colonic pol… ▽ More Polyps are well-known cancer precursors identified by colonoscopy. However, variability in their size, location, and surface largely affect identification, localisation, and characterisation. Moreover, colonoscopic surveillance and removal of polyps (referred to as polypectomy ) are highly operator-dependent procedures. There exist a high missed detection rate and incomplete removal of colonic polyps due to their variable nature, the difficulties to delineate the abnormality, the high recurrence rates, and the anatomical topography of the colon. There have been several developments in realising automated methods for both detection and segmentation of these polyps using machine learning. However, the major drawback in most of these methods is their ability to generalise to out-of-sample unseen datasets that come from different centres, modalities and acquisition systems. To test this hypothesis rigorously we curated a multi-centre and multi-population dataset acquired from multiple colonoscopy systems and challenged teams comprising machine learning experts to develop robust automated detection and segmentation methods as part of our crowd-sourcing Endoscopic computer vision challenge (EndoCV) 2021. In this paper, we analyse the detection results of the four top (among seven) teams and the segmentation results of the five top teams (among 16). Our analyses demonstrate that the top-ranking teams concentrated on accuracy (i.e., accuracy > 80% on overall Dice score on different validation sets) over real-time performance required for clinical applicability. We further dissect the methods and provide an experiment-based hypothesis that reveals the need for improved generalisability to tackle diversity present in multi-centre datasets. △ Less

Submitted 24 February, 2022; originally announced February 2022.

Comments: 26 pages

MMSys'22 Grand Challenge on AI-based Video Production for Soccer

Authors: Cise Midoglu, Steven A. Hicks, Vajira Thambawita, Tomas Kupka, Pål Halvorsen

Abstract: Soccer has a considerable market share of the global sports industry, and the interest in viewing videos from soccer games continues to grow. In this respect, it is important to provide game summaries and highlights of the main game events. However, annotating and producing events and summaries often require expensive equipment and a lot of tedious, cumbersome, manual labor. Therefore, automating… ▽ More Soccer has a considerable market share of the global sports industry, and the interest in viewing videos from soccer games continues to grow. In this respect, it is important to provide game summaries and highlights of the main game events. However, annotating and producing events and summaries often require expensive equipment and a lot of tedious, cumbersome, manual labor. Therefore, automating the video production pipeline providing fast game highlights at a much lower cost is seen as the "holy grail". In this context, recent developments in Artificial Intelligence (AI) technology have shown great potential. Still, state-of-the-art approaches are far from being adequate for practical scenarios that have demanding real-time requirements, as well as strict performance criteria (where at least the detection of official events such as goals and cards must be 100% accurate). In addition, event detection should be thoroughly enhanced by annotation and classification, proper clipping, generating short descriptions, selecting appropriate thumbnails for highlight clips, and finally, combining the event highlights into an overall game summary, similar to what is commonly aired during sports news. Even though the event tagging operation has by far received the most attention, an end-to-end video production pipeline also includes various other operations which serve the overall purpose of automated soccer analysis. This challenge aims to assist the automation of such a production pipeline using AI. In particular, we focus on the enhancement operations that take place after an event has been detected, namely event clipping (Task 1), thumbnail selection (Task 2), and game summarization (Task 3). Challenge website: https://mmsys2022.ie/authors/grand-challenge. △ Less

Submitted 2 February, 2022; originally announced February 2022.

Visual Sentiment Analysis: A Natural DisasterUse-case Task at MediaEval 2021

Authors: Syed Zohaib Hassan, Kashif Ahmad, Michael A. Riegler, Steven Hicks, Nicola Conci, Paal Halvorsen, Ala Al-Fuqaha

Abstract: The Visual Sentiment Analysis task is being offered for the first time at MediaEval. The main purpose of the task is to predict the emotional response to images of natural disasters shared on social media. Disaster-related images are generally complex and often evoke an emotional response, making them an ideal use case of visual sentiment analysis. We believe being able to perform meaningful analy… ▽ More The Visual Sentiment Analysis task is being offered for the first time at MediaEval. The main purpose of the task is to predict the emotional response to images of natural disasters shared on social media. Disaster-related images are generally complex and often evoke an emotional response, making them an ideal use case of visual sentiment analysis. We believe being able to perform meaningful analysis of natural disaster-related data could be of great societal importance, and a joint effort in this regard can open several interesting directions for future research. The task is composed of three sub-tasks, each aiming to explore a different aspect of the challenge. In this paper, we provide a detailed overview of the task, the general motivation of the task, and an overview of the dataset and the metrics to be used for the evaluation of the proposed solutions. △ Less

Submitted 22 November, 2021; originally announced November 2021.

Comments: 3 pages

SinGAN-Seg: Synthetic training data generation for medical image segmentation

Authors: Vajira Thambawita, Pegah Salehi, Sajad Amouei Sheshkal, Steven A. Hicks, Hugo L. Hammer, Sravanthi Parasa, Thomas de Lange, Pål Halvorsen, Michael A. Riegler

Abstract: Analyzing medical data to find abnormalities is a time-consuming and costly task, particularly for rare abnormalities, requiring tremendous efforts from medical experts. Artificial intelligence has become a popular tool for the automatic processing of medical data, acting as a supportive tool for doctors. However, the machine learning models used to build these tools are highly dependent on the da… ▽ More Analyzing medical data to find abnormalities is a time-consuming and costly task, particularly for rare abnormalities, requiring tremendous efforts from medical experts. Artificial intelligence has become a popular tool for the automatic processing of medical data, acting as a supportive tool for doctors. However, the machine learning models used to build these tools are highly dependent on the data used to train them. Large amounts of data can be difficult to obtain in medicine due to privacy, expensive and time-consuming annotations, and a general lack of data samples for infrequent lesions. Here, we present a novel synthetic data generation pipeline, called SinGAN-Seg, to produce synthetic medical images with corresponding masks using a single training image. Our method is different from the traditional GANs because our model needs only a single image and the corresponding ground truth to train. Our method produces alternative artificial segmentation datasets with ground truth masks when real datasets are not allowed to share. The pipeline is evaluated using qualitative and quantitative comparisons between real and synthetic data to show that the style transfer technique used in our pipeline significantly improves the quality of the generated data and our method is better than other state-of-the-art GANs to prepare synthetic images when the size of training datasets are limited. By training UNet++ using both real and the synthetic data generated from the SinGAN-Seg pipeline, we show that models trained with synthetic data have very close performances to those trained on real data when the datasets have a considerable amount of data. In contrast, Synthetic data generated from the SinGAN-Seg pipeline can improve the performance of segmentation models when training datasets do not have a considerable amount of data. The code is available on GitHub. △ Less

Submitted 25 April, 2022; v1 submitted 29 June, 2021; originally announced July 2021.

DivergentNets: Medical Image Segmentation by Network Ensemble

Authors: Vajira Thambawita, Steven A. Hicks, Pål Halvorsen, Michael A. Riegler

Abstract: Detection of colon polyps has become a trending topic in the intersecting fields of machine learning and gastrointestinal endoscopy. The focus has mainly been on per-frame classification. More recently, polyp segmentation has gained attention in the medical community. Segmentation has the advantage of being more accurate than per-frame classification or object detection as it can show the affected… ▽ More Detection of colon polyps has become a trending topic in the intersecting fields of machine learning and gastrointestinal endoscopy. The focus has mainly been on per-frame classification. More recently, polyp segmentation has gained attention in the medical community. Segmentation has the advantage of being more accurate than per-frame classification or object detection as it can show the affected area in greater detail. For our contribution to the EndoCV 2021 segmentation challenge, we propose two separate approaches. First, a segmentation model named TriUNet composed of three separate UNet models. Second, we combine TriUNet with an ensemble of well-known segmentation models, namely UNet++, FPN, DeepLabv3, and DeepLabv3+, into a model called DivergentNets to produce more generalizable medical image segmentation masks. In addition, we propose a modified Dice loss that calculates loss only for a single class when performing multiclass segmentation, forcing the model to focus on what is most important. Overall, the proposed methods achieved the best average scores for each respective round in the challenge, with TriUNet being the winning model in Round I and DivergentNets being the winning model in Round II of the segmentation generalization challenge at EndoCV 2021. The implementation of our approach is made publicly available on GitHub. △ Less

Submitted 1 July, 2021; originally announced July 2021.

Comments: the winning model of the segmentation generalization challenge at EndoCV 2021

Journal ref: Proceedings of the 3rd International Workshop and Challenge on Computer Vision in Endoscopy (EndoCV 2021) colocated with with the 17th IEEE International Symposium on Biomedical Imaging (ISBI 2021)

Meta-learning with implicit gradients in a few-shot setting for medical image segmentation

Authors: Rabindra Khadga, Debesh Jha, Steven Hicks, Vajira Thambawita, Michael A. Riegler, Sharib Ali, Pål Halvorsen

Abstract: Widely used traditional supervised deep learning methods require a large number of training samples but often fail to generalize on unseen datasets. Therefore, a more general application of any trained model is quite limited for medical imaging for clinical practice. Using separately trained models for each unique lesion category or a unique patient population will require sufficiently large curat… ▽ More Widely used traditional supervised deep learning methods require a large number of training samples but often fail to generalize on unseen datasets. Therefore, a more general application of any trained model is quite limited for medical imaging for clinical practice. Using separately trained models for each unique lesion category or a unique patient population will require sufficiently large curated datasets, which is not practical to use in a real-world clinical set-up. Few-shot learning approaches can not only minimize the need for an enormous number of reliable ground truth labels that are labour-intensive and expensive but can also be used to model on a dataset coming from a new population. To this end, we propose to exploit an optimization-based implicit model agnostic meta-learning (iMAML) algorithm under few-shot settings for medical image segmentation. Our approach can leverage the learned weights from diverse but small training samples to perform analysis on unseen datasets with high accuracy. We show that, unlike classical few-shot learning approaches, our method improves generalization capability. To our knowledge, this is the first work that exploits iMAML for medical image segmentation and explores the strength of the model on scenarios such as meta-training on unique and mixed instances of lesion datasets. Our quantitative results on publicly available skin and polyp datasets show that the proposed method outperforms the naive supervised baseline model and two recent few-shot segmentation approaches by large margins. In addition, our iMAML approach shows an improvement of 2%-4% in dice score compared to its counterpart MAML for most experiments. △ Less

Submitted 30 January, 2022; v1 submitted 6 June, 2021; originally announced June 2021.

Journal ref: Computers in Biology and Medicine, 2022

Medico Multimedia Task at MediaEval 2020: Automatic Polyp Segmentation

Authors: Debesh Jha, Steven A. Hicks, Krister Emanuelsen, Håvard Johansen, Dag Johansen, Thomas de Lange, Michael A. Riegler, Pål Halvorsen

Abstract: Colorectal cancer is the third most common cause of cancer worldwide. According to Global cancer statistics 2018, the incidence of colorectal cancer is increasing in both developing and developed countries. Early detection of colon anomalies such as polyps is important for cancer prevention, and automatic polyp segmentation can play a crucial role for this. Regardless of the recent advancement in… ▽ More Colorectal cancer is the third most common cause of cancer worldwide. According to Global cancer statistics 2018, the incidence of colorectal cancer is increasing in both developing and developed countries. Early detection of colon anomalies such as polyps is important for cancer prevention, and automatic polyp segmentation can play a crucial role for this. Regardless of the recent advancement in early detection and treatment options, the estimated polyp miss rate is still around 20\%. Support via an automated computer-aided diagnosis system could be one of the potential solutions for the overlooked polyps. Such detection systems can help low-cost design solutions and save doctors time, which they could for example use to perform more patient examinations. In this paper, we introduce the 2020 Medico challenge, provide some information on related work and the dataset, describe the task and evaluation metrics, and discuss the necessity of organizing the Medico challenge. △ Less

Submitted 30 December, 2020; originally announced December 2020.

Comments: MediaEval 2020

Pyramid-Focus-Augmentation: Medical Image Segmentation with Step-Wise Focus

Authors: Vajira Thambawita, Steven Hicks, Pål Halvorsen, Michael A. Riegler

Abstract: Segmentation of findings in the gastrointestinal tract is a challenging but also an important task which is an important building stone for sufficient automatic decision support systems. In this work, we present our solution for the Medico 2020 task, which focused on the problem of colon polyp segmentation. We present our simple but efficient idea of using an augmentation method that uses grids in… ▽ More Segmentation of findings in the gastrointestinal tract is a challenging but also an important task which is an important building stone for sufficient automatic decision support systems. In this work, we present our solution for the Medico 2020 task, which focused on the problem of colon polyp segmentation. We present our simple but efficient idea of using an augmentation method that uses grids in a pyramid-like manner (large to small) for segmentation. Our results show that the proposed methods work as indented and can also lead to comparable results when competing with other methods. △ Less

Submitted 14 December, 2020; originally announced December 2020.

Kvasir-Instrument: Diagnostic and therapeutic tool segmentation dataset in gastrointestinal endoscopy

Authors: Debesh Jha, Sharib Ali, Krister Emanuelsen, Steven A. Hicks, VajiraThambawita, Enrique Garcia-Ceja, Michael A. Riegler, Thomas de Lange, Peter T. Schmidt, Håvard D. Johansen, Dag Johansen, Pål Halvorsen

Abstract: Gastrointestinal (GI) pathologies are periodically screened, biopsied, and resected using surgical tools. Usually the procedures and the treated or resected areas are not specifically tracked or analysed during or after colonoscopies. Information regarding disease borders, development and amount and size of the resected area get lost. This can lead to poor follow-up and bothersome reassessment dif… ▽ More Gastrointestinal (GI) pathologies are periodically screened, biopsied, and resected using surgical tools. Usually the procedures and the treated or resected areas are not specifically tracked or analysed during or after colonoscopies. Information regarding disease borders, development and amount and size of the resected area get lost. This can lead to poor follow-up and bothersome reassessment difficulties post-treatment. To improve the current standard and also to foster more research on the topic we have released the ``Kvasir-Instrument'' dataset which consists of $590$ annotated frames containing GI procedure tools such as snares, balloons and biopsy forceps, etc. Beside of the images, the dataset includes ground truth masks and bounding boxes and has been verified by two expert GI endoscopists. Additionally, we provide a baseline for the segmentation of the GI tools to promote research and algorithm development. We obtained a dice coefficient score of 0.9158 and a Jaccard index of 0.8578 using a classical U-Net architecture. A similar dice coefficient score was observed for DoubleUNet. The qualitative results showed that the model did not work for the images with specularity and the frames with multiple instruments, while the best result for both methods was observed on all other types of images. Both, qualitative and quantitative results show that the model performs reasonably good, but there is a large potential for further improvements. Benchmarking using the dataset provides an opportunity for researchers to contribute to the field of automatic endoscopic diagnostic and therapeutic tool segmentation for GI endoscopy. △ Less

Submitted 23 October, 2020; originally announced November 2020.

Visual Sentiment Analysis from Disaster Images in Social Media

Authors: Syed Zohaib Hassan, Kashif Ahmad, Steven Hicks, Paal Halvorsen, Ala Al-Fuqaha, Nicola Conci, Michael Riegler

Abstract: The increasing popularity of social networks and users' tendency towards sharing their feelings, expressions, and opinions in text, visual, and audio content, have opened new opportunities and challenges in sentiment analysis. While sentiment analysis of text streams has been widely explored in literature, sentiment analysis from images and videos is relatively new. This article focuses on visual… ▽ More The increasing popularity of social networks and users' tendency towards sharing their feelings, expressions, and opinions in text, visual, and audio content, have opened new opportunities and challenges in sentiment analysis. While sentiment analysis of text streams has been widely explored in literature, sentiment analysis from images and videos is relatively new. This article focuses on visual sentiment analysis in a societal important domain, namely disaster analysis in social media. To this aim, we propose a deep visual sentiment analyzer for disaster related images, covering different aspects of visual sentiment analysis starting from data collection, annotation, model selection, implementation, and evaluations. For data annotation, and analyzing peoples' sentiments towards natural disasters and associated images in social media, a crowd-sourcing study has been conducted with a large number of participants worldwide. The crowd-sourcing study resulted in a large-scale benchmark dataset with four different sets of annotations, each aiming a separate task. The presented analysis and the associated dataset will provide a baseline/benchmark for future research in the domain. We believe the proposed system can contribute toward more livable communities by helping different stakeholders, such as news broadcasters, humanitarian organizations, as well as the general public. △ Less

Submitted 4 September, 2020; originally announced September 2020.

Comments: 10 pages, 6 figures, 6 tables. arXiv admin note: substantial text overlap with arXiv:2002.03773

Machine Learning-Based Analysis of Sperm Videos and Participant Data for Male Fertility Prediction

Authors: Steven A. Hicks, Jorunn M. Andersen, Oliwia Witczak, Vajira Thambawita, Påll Halvorsen, Hugo L. Hammer, Trine B. Haugen, Michael A. Riegler

Abstract: Methods for automatic analysis of clinical data are usually targeted towards a specific modality and do not make use of all relevant data available. In the field of male human reproduction, clinical and biological data are not used to its fullest potential. Manual evaluation of a semen sample using a microscope is time-consuming and requires extensive training. Furthermore, the validity of manual… ▽ More Methods for automatic analysis of clinical data are usually targeted towards a specific modality and do not make use of all relevant data available. In the field of male human reproduction, clinical and biological data are not used to its fullest potential. Manual evaluation of a semen sample using a microscope is time-consuming and requires extensive training. Furthermore, the validity of manual semen analysis has been questioned due to limited reproducibility, and often high inter-personnel variation. The existing computer-aided sperm analyzer systems are not recommended for routine clinical use due to methodological challenges caused by the consistency of the semen sample. Thus, there is a need for an improved methodology. We use modern and classical machine learning techniques together with a dataset consisting of 85 videos of human semen samples and related participant data to automatically predict sperm motility. Used techniques include simple linear regression and more sophisticated methods using convolutional neural networks. Our results indicate that sperm motility prediction based on deep learning using sperm motility videos is rapid to perform and consistent. The algorithms performed worse when participant data was added. In conclusion, machine learning-based automatic analysis may become a valuable tool in male infertility investigation and research. △ Less

Submitted 29 October, 2019; originally announced October 2019.

Comments: Preprint, accepted by Nature Scientific Reports for publication 24.10.2019

A Guide to Teaching Data Science

Authors: Stephanie C. Hicks, Rafael A. Irizarry

Abstract: Demand for data science education is surging and traditional courses offered by statistics departments are not meeting the needs of those seeking training. This has led to a number of opinion pieces advocating for an update to the Statistics curriculum. The unifying recommendation is computing should play a more prominent role. We strongly agree with this recommendation, but advocate the main prio… ▽ More Demand for data science education is surging and traditional courses offered by statistics departments are not meeting the needs of those seeking training. This has led to a number of opinion pieces advocating for an update to the Statistics curriculum. The unifying recommendation is computing should play a more prominent role. We strongly agree with this recommendation, but advocate the main priority is to bring applications to the forefront as proposed by Nolan and Speed (1999). We also argue that the individuals tasked with developing data science courses should not only have statistical training, but also have experience analyzing data with the main objective of solving real-world problems. Here, we share a set of general principles and offer a detailed guide derived from our successful experience developing and teaching a graduate-level, introductory data science course centered entirely on case studies. We argue for the importance of statistical thinking, as defined by Wild and Pfannkuck (1999) and describe how our approach teaches students three key skills needed to succeed in data science, which we refer to as creating, connecting, and computing. This guide can also be used for statisticians wanting to gain more practical knowledge about data science before embarking on teaching an introductory course. △ Less

Submitted 15 May, 2017; v1 submitted 21 December, 2016; originally announced December 2016.

Comments: 2 tables, 3 figures, 2 supplemental figures

Relational Grid Monitoring Architecture (R-GMA)

Authors: Rob Byrom, Brian Coghlan, Andrew W Cooke, Roney Cordenonsi, Linda Cornwall, Abdeslem Djaoui, Laurence Field, Steve Fisher, Steve Hicks, Stuart Kenny, Jason Leake, James Magowan, Werner Nutt, David O'Callaghan, Norbert Podhorszki, John Ryan, Manish Soni, Paul Taylor, Antony J Wilson

Abstract: We describe R-GMA (Relational Grid Monitoring Architecture) which has been developed within the European DataGrid Project as a Grid Information and Monitoring System. Is is based on the GMA from GGF, which is a simple Consumer-Producer model. The special strength of this implementation comes from the power of the relational model. We offer a global view of the information as if each Virtual Orga… ▽ More We describe R-GMA (Relational Grid Monitoring Architecture) which has been developed within the European DataGrid Project as a Grid Information and Monitoring System. Is is based on the GMA from GGF, which is a simple Consumer-Producer model. The special strength of this implementation comes from the power of the relational model. We offer a global view of the information as if each Virtual Organisation had one large relational database. We provide a number of different Producer types with different characteristics; for example some support streaming of information. We also provide combined Consumer/Producers, which are able to combine information and republish it. At the heart of the system is the mediator, which for any query is able to find and connect to the best Producers for the job. We have developed components to allow a measure of inter-working between MDS and R-GMA. We have used it both for information about the grid (primarily to find out about what services are available at any one time) and for application monitoring. R-GMA has been deployed in various testbeds; we describe some preliminary results and experiences of this deployment. △ Less

Submitted 15 August, 2003; originally announced August 2003.

Comments: Talk given at UK e-Science All-Hands meeting, Nottingham, UK, September 2-4, 2003. 7 pages of LaTeX and 5 PNG figures

ACM Class: H.2.4; H.m

R-GMA: First results after deployment

Authors: Rob Byrom, Brian Coghlan, Andrew W Cooke, Roney Cordenonsi, Linda Cornwall, Ari Datta, Abdeslem Djaoui, Laurence Field, Steve Fisher, Steve Hicks, Stuart Kenny, James Magowan, Werner Nutt, David O'Callaghan, Manfred Oevers, Norbert Podhorszki, John Ryan, Manish Soni, Paul Taylor, Antony J. Wilson, Xiaomei Zhu

Abstract: We describe R-GMA (Relational Grid Monitoring Architecture) which is being developed within the European DataGrid Project as an Grid Information and Monitoring System. Is is based on the GMA from GGF, which is a simple Consumer-Producer model. The special strength of this implementation comes from the power of the relational model. We offer a global view of the information as if each VO had one… ▽ More We describe R-GMA (Relational Grid Monitoring Architecture) which is being developed within the European DataGrid Project as an Grid Information and Monitoring System. Is is based on the GMA from GGF, which is a simple Consumer-Producer model. The special strength of this implementation comes from the power of the relational model. We offer a global view of the information as if each VO had one large relational database. We provide a number of different Producer types with different characteristics; for example some support streaming of information. We also provide combined Consumer/Producers, which are able to combine information and republish it. At the heart of the system is the mediator, which for any query is able to find and connect to the best Producers to do the job. We are able to invoke MDS info-provider scripts and publish the resulting information via R-GMA in addition to having some of our own sensors. APIs are available which allow the user to deploy monitoring and information services for any application that may be needed in the future. We have used it both for information about the grid (primarily to find what services are available at any one time) and for application monitoring. R-GMA has been deployed in Grid testbeds, we describe the results and experiences of this deployment. △ Less

Submitted 12 June, 2003; v1 submitted 30 May, 2003; originally announced June 2003.

Comments: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, 5 pages, LaTeX, 3 eps figures. PSN MOET004

ACM Class: H.2.4; H.m