Data Augmentation with Diffusion Models for Colon Polyp Localization on the Low Data Regime: How much real data is enough?

The scarcity of data in medical domains hinders the performance of Deep Learning models. Data augmentation techniques can alleviate that problem, but they usually rely on functional transformations of the data that do not guarantee to preserve the original tasks. To approximate the distribution of the data using generative models is a way of reducing that problem and also to obtain new samples that resemble the original data. Denoising Diffusion models is a promising Deep Learning technique that can learn good approximations of different kinds of data like images, time series or tabular data. Automatic colonoscopy analysis and specifically Polyp localization in colonoscopy videos is a task that can assist clinical diagnosis and treatment. The annotation of video frames for training a deep learning model is a time consuming task and usually only small datasets can be obtained. The fine tuning of application models using a large dataset of generated data could be an alternative to improve their performance. We conduct a set of experiments training different diffusion models that can generate jointly colonoscopy images with localization annotations using a combination of existing open datasets. The generated data is used on various transfer learning experiments in the task of polyp localization with a model based on YOLO v9 on the low data regime.

Present and Future Generalization of Synthetic Image Detectors

The continued release of new and better image generation models increases the demand for synthetic image detectors. In such a dynamic field, detectors need to be able to generalize widely and be robust to uncontrolled alterations. The present work is motivated by this setting, when looking at the role of time, image transformations and data sources, for detector generalization. In these experiments, none of the evaluated detectors is found universal, but results indicate an ensemble could be. Experiments on data collected in the wild show this task to be more challenging than the one defined by large-scale datasets, pointing to a gap between experimentation and actual practice. Finally, we observe a race equilibrium effect, where better generators lead to better detectors, and vice versa. We hypothesize this pushes the field towards a perpetually close race between generators and detectors.

Padding Aware Neurons

Convolutional layers are a fundamental component of most image-related models. These layers often implement by default a static padding policy (\eg zero padding), to control the scale of the internal representations, and to allow kernel activations centered on the border regions. In this work we identify Padding Aware Neurons (PANs), a type of filter that is found in most (if not all) convolutional models trained with static padding. PANs focus on the characterization and recognition of input border location, introducing a spatial inductive bias into the model (e.g., how close to the input's border a pattern typically is). We propose a method to identify PANs through their activations, and explore their presence in several popular pre-trained models, finding PANs on all models explored, from dozens to hundreds. We discuss and illustrate different types of PANs, their kernels and behaviour. To understand their relevance, we test their impact on model performance, and find padding and PANs to induce strong and characteristic biases in the data. Finally, we discuss whether or not PANs are desirable, as well as the potential side effects of their presence in the context of model performance, generalisation, efficiency and safety.

Exploring the Role of Explainability in AI-Assisted Embryo Selection

In Vitro Fertilization is among the most widespread treatments for infertility. One of its main challenges is the evaluation and selection of embryo for implantation, a process with large inter- and intra-clinician variability. Deep learning based methods are gaining attention, but their opaque nature compromises their acceptance in the clinical context, where transparency in the decision making is key. In this paper we analyze the current work in the explainability of AI-assisted embryo analysis models, identifying the limitations. We also discuss how these models could be integrated in the clinical context as decision support systems, considering the needs of clinicians and patients. Finally, we propose guidelines for the sake of increasing interpretability and trustworthiness, pushing this technology forward towards established clinical practice.

When & How to Transfer with Transfer Learning

In deep learning, transfer learning (TL) has become the de facto approach when dealing with image related tasks. Visual features learnt for one task have been shown to be reusable for other tasks, improving performance significantly. By reusing deep representations, TL enables the use of deep models in domains with limited data availability, limited computational resources and/or limited access to human experts. Domains which include the vast majority of real-life applications. This paper conducts an experimental evaluation of TL, exploring its trade-offs with respect to performance, environmental footprint, human hours and computational requirements. Results highlight the cases were a cheap feature extraction approach is preferable, and the situations where an expensive fine-tuning effort may be worth the added cost. Finally, a set of guidelines on the use of TL are proposed.

Healthy Twitter discussions? Time will tell

Studying misinformation and how to deal with unhealthy behaviours within online discussions has recently become an important field of research within social studies. With the rapid development of social media, and the increasing amount of available information and sources, rigorous manual analysis of such discourses has become unfeasible. Many approaches tackle the issue by studying the semantic and syntactic properties of discussions following a supervised approach, for example using natural language processing on a dataset labeled for abusive, fake or bot-generated content. Solutions based on the existence of a ground truth are limited to those domains which may have ground truth. However, within the context of misinformation, it may be difficult or even impossible to assign labels to instances. In this context, we consider the use of temporal dynamic patterns as an indicator of discussion health. Working in a domain for which ground truth was unavailable at the time (early COVID-19 pandemic discussions) we explore the characterization of discussions based on the the volume and time of contributions. First we explore the types of discussions in an unsupervised manner, and then characterize these types using the concept of ephemerality, which we formalize. In the end, we discuss the potential use of our ephemerality definition for labeling online discourses based on how desirable, healthy and constructive they are.

Who Explains the Explanation? Quantitatively Assessing Feature Attribution Methods

AI explainability seeks to increase the transparency of models, making them more trustworthy in the process. The need for transparency has been recently motivated by the emergence of deep learning models, which are particularly obscure by nature. Even in the domain of images, where deep learning has succeeded the most, explainability is still poorly assessed. Multiple feature attribution methods have been proposed in the literature with the purpose of explaining a DL model's behavior using visual queues, but no standardized metrics to assess or select these methods exist. In this paper we propose a novel evaluation metric -- the Focus -- designed to quantify the faithfulness of explanations provided by feature attribution methods, such as LRP or GradCAM. First, we show the robustness of the metric through randomization experiments, and then use Focus to evaluate and compare three popular explainability techniques using multiple architectures and datasets. Our results find LRP and GradCAM to be consistent and reliable, the former being more accurate for high performing models, while the latter remains most competitive even when applied to poorly performing models. Finally, we identify a strong relation between Focus and factors like model architecture and task, unveiling a new unsupervised approach for the assessment of models.

A Closer Look at Art Mediums: The MAMe Image Classification Dataset

Art is an expression of human creativity, skill and technology. An exceptionally rich source of visual content. In the context of AI image processing systems, artworks represent one of the most challenging domains conceivable: Properly perceiving art requires attention to detail, a huge generalization capacity, and recognizing both simple and complex visual patterns. To challenge the AI community, this work introduces a novel image classification task focused on museum art mediums, the MAMe dataset. Data is gathered from three different museums, and aggregated by art experts into 29 classes of medium (i.e. materials and techniques). For each class, MAMe provides a minimum of 850 images (700 for training) of high-resolution and variable shape. The combination of volume, resolution and shape allows MAMe to fill a void in current image classification challenges, empowering research in aspects so far overseen by the research community. After reviewing the singularity of MAMe in the context of current image classification tasks, a thorough description of the task is provided, together with dataset statistics. Baseline experiments are conducted using well-known architectures, to highlight both the feasibility and complexity of the task proposed. Finally, these baselines are inspected using explainability methods and expert knowledge, to gain insight on the challenges that remain ahead.

Recommendations for machine learning validation in biology

Modern biology frequently relies on machine learning to provide predictions and improve decision processes. There have been recent calls for more scrutiny on machine learning performance and possible limitations. Here we present a set of community-wide recommendations aiming to help establish standards of machine learning validation in biology. Adopting a structured methods description for machine learning based on DOME (data, optimization, model, evaluation) will allow both reviewers and readers to better understand and assess the performance and limitations of a method or outcome. The recommendations are complemented by a machine learning summary table which can be easily included in the supplementary material of published papers.

Global Data Science Project for COVID-19 Summary Report

This paper aims at providing the summary of the Global Data Science Project (GDSC) for COVID-19. as on May 31 2020. COVID-19 has largely impacted on our societies through both direct and indirect effects transmitted by the policy measures to counter the spread of viruses. We quantitatively analysed the multifaceted impacts of the COVID-19 pandemic on our societies including people's mobility, health, and social behaviour changes. People's mobility has changed significantly due to the implementation of travel restriction and quarantine measurements. Indeed, the physical distance has widened at international (cross-border), national and regional level. At international level, due to the travel restrictions, the number of international flights has plunged overall at around 88 percent during March. In particular, the number of flights connecting Europe dropped drastically in mid of March after the United States announced travel restrictions to Europe and the EU and participating countries agreed to close borders, at 84 percent decline compared to March 10th. Similarly, we examined the impacts of quarantine measures in the major city: Tokyo (Japan), New York City (the United States), and Barcelona (Spain). Within all three cities, we found the significant decline in traffic volume. We also identified the increased concern for mental health through the analysis of posts on social networking services such as Twitter and Instagram. Notably, in the beginning of April 2020, the number of post with #depression on Instagram doubled, which might reflect the rise in mental health awareness among Instagram users. Besides, we identified the changes in a wide range of people's social behaviors, as well as economic impacts through the analysis of Instagram data and primary survey data.