Imputation using training labels and classification via label imputation

Missing data is a common problem in practical settings. Various imputation methods have been developed to deal with missing data. However, even though the label is usually available in the training data, the common practice of imputation usually only relies on the input and ignores the label. In this work, we illustrate how stacking the label into the input can significantly improve the imputation of the input. In addition, we propose a classification strategy that initializes the predicted test label with missing values and stacks the label with the input for imputation. This allows imputing the label and the input at the same time. Also, the technique is capable of handling data training with missing labels without any prior imputation and is applicable to continuous, categorical, or mixed-type data. Experiments show promising results in terms of accuracy.

An objective validation of polyp and instrument segmentation methods in colonoscopy through Medico 2020 polyp segmentation and MedAI 2021 transparency challenges

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.

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

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 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 24 classes) from the GI tract. The dataset comprises 8,000 images acquired from B{\ae}rum Hospital in Norway and Karolinska University 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 https://osf.io/84e7f/.

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

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.

Correlation visualization under missing values: a comparison between imputation and direct parameter estimation methods

Correlation matrix visualization is essential for understanding the relationships between variables in a dataset, but missing data can pose a significant challenge in estimating correlation coefficients. In this paper, we compare the effects of various missing data methods on the correlation plot, focusing on two common missing patterns: random and monotone. We aim to provide practical strategies and recommendations for researchers and practitioners in creating and analyzing the correlation plot. Our experimental results suggest that while imputation is commonly used for missing data, using imputed data for plotting the correlation matrix may lead to a significantly misleading inference of the relation between the features. We recommend using DPER, a direct parameter estimation approach, for plotting the correlation matrix based on its performance in the experiments.

Mask-conditioned latent diffusion for generating gastrointestinal polyp images

In order to take advantage of AI solutions in endoscopy diagnostics, we must overcome the issue of limited annotations. These limitations are caused by the high privacy concerns in the medical field and the requirement of getting aid from experts for the time-consuming and costly medical data annotation process. In computer vision, image synthesis has made a significant contribution in recent years as a result of the progress of generative adversarial networks (GANs) and diffusion probabilistic models (DPM). Novel DPMs have outperformed GANs in text, image, and video generation tasks. Therefore, this study proposes a conditional DPM framework to generate synthetic GI polyp images conditioned on given generated segmentation masks. Our experimental results show that our system can generate an unlimited number of high-fidelity synthetic polyp images with the corresponding ground truth masks of polyps. To test the usefulness of the generated data, we trained binary image segmentation models to study the effect of using synthetic data. Results show that the best micro-imagewise IOU of 0.7751 was achieved from DeepLabv3+ when the training data consists of both real data and synthetic data. However, the results reflect that achieving good segmentation performance with synthetic data heavily depends on model architectures.

Understanding metric-related pitfalls in image analysis validation

Validation metrics are key for the reliable tracking of scientific progress and for bridging the current chasm between artificial intelligence (AI) research and its translation into practice. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately in relation to the underlying research problem. This could be attributed to a lack of accessibility of metric-related knowledge: While taking into account the individual strengths, weaknesses, and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. Focusing on biomedical image analysis but with the potential of transfer to other fields, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. To facilitate comprehension, illustrations and specific examples accompany each pitfall. As a structured body of information accessible to researchers of all levels of expertise, this work enhances global comprehension of a key topic in image analysis validation.

Conditional expectation for missing data imputation

Missing data is common in datasets retrieved in various areas, such as medicine, sports, and finance. In many cases, to enable proper and reliable analyses of such data, the missing values are often imputed, and it is necessary that the method used has a low root mean square error (RMSE) between the imputed and the true values. In addition, for some critical applications, it is also often a requirement that the logic behind the imputation is explainable, which is especially difficult for complex methods that are for example, based on deep learning. This motivates us to introduce a conditional Distribution based Imputation of Missing Values (DIMV) algorithm. This approach works based on finding the conditional distribution of a feature with missing entries based on the fully observed features. As will be illustrated in the paper, DIMV (i) gives a low RMSE for the imputed values compared to state-of-the-art methods under comparison; (ii) is explainable; (iii) can provide an approximated confidence region for the missing values in a given sample; (iv) works for both small and large scale data; (v) in many scenarios, does not require a huge number of parameters as deep learning approaches and therefore can be used for mobile devices or web browsers; and (vi) is robust to the normally distributed assumption that its theoretical grounds rely on. In addition to DIMV, we also introduce the DPER* algorithm improving the speed of DPER for estimating the mean and covariance matrix from the data, and we confirm the speed-up via experiments.

VISEM-Tracking: Human Spermatozoa Tracking Dataset

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 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 model trained on the VISEM-Tracking dataset. As a result, we show that the dataset can be used to train complex deep learning models to analyze spermatozoa. The dataset is publicly available at https://zenodo.org/record/7293726.

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

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.