Color Flow Imaging Microscopy Improves Identification of Stress Sources of Protein Aggregates in Biopharmaceuticals

Protein-based therapeutics play a pivotal role in modern medicine targeting various diseases. Despite their therapeutic importance, these products can aggregate and form subvisible particles (SvPs), which can compromise their efficacy and trigger immunological responses, emphasizing the critical need for robust monitoring techniques. Flow Imaging Microscopy (FIM) has been a significant advancement in detecting SvPs, evolving from monochrome to more recently incorporating color imaging. Complementing SvP images obtained via FIM, deep learning techniques have recently been employed successfully for stress source identification of monochrome SvPs. In this study, we explore the potential of color FIM to enhance the characterization of stress sources in SvPs. To achieve this, we curate a new dataset comprising 16,000 SvPs from eight commercial monoclonal antibodies subjected to heat and mechanical stress. Using both supervised and self-supervised convolutional neural networks, as well as vision transformers in large-scale experiments, we demonstrate that deep learning with color FIM images consistently outperforms monochrome images, thus highlighting the potential of color FIM in stress source classification compared to its monochrome counterparts.

Self-supervised Benchmark Lottery on ImageNet: Do Marginal Improvements Translate to Improvements on Similar Datasets?

Machine learning (ML) research strongly relies on benchmarks in order to determine the relative effectiveness of newly proposed models. Recently, a number of prominent research effort argued that a number of models that improve the state-of-the-art by a small margin tend to do so by winning what they call a "benchmark lottery". An important benchmark in the field of machine learning and computer vision is the ImageNet where newly proposed models are often showcased based on their performance on this dataset. Given the large number of self-supervised learning (SSL) frameworks that has been proposed in the past couple of years each coming with marginal improvements on the ImageNet dataset, in this work, we evaluate whether those marginal improvements on ImageNet translate to improvements on similar datasets or not. To do so, we investigate twelve popular SSL frameworks on five ImageNet variants and discover that models that seem to perform well on ImageNet may experience significant performance declines on similar datasets. Specifically, state-of-the-art frameworks such as DINO and Swav, which are praised for their performance, exhibit substantial drops in performance while MoCo and Barlow Twins displays comparatively good results. As a result, we argue that otherwise good and desirable properties of models remain hidden when benchmarking is only performed on the ImageNet validation set, making us call for more adequate benchmarking. To avoid the "benchmark lottery" on ImageNet and to ensure a fair benchmarking process, we investigate the usage of a unified metric that takes into account the performance of models on other ImageNet variant datasets.

Re-assessing ImageNet: How aligned is its single-label assumption with its multi-label nature?

ImageNet, an influential dataset in computer vision, is traditionally evaluated using single-label classification, which assumes that an image can be adequately described by a single concept or label. However, this approach may not fully capture the complex semantics within the images available in ImageNet, potentially hindering the development of models that effectively learn these intricacies. This study critically examines the prevalent single-label benchmarking approach and advocates for a shift to multi-label benchmarking for ImageNet. This shift would enable a more comprehensive assessment of the capabilities of deep neural network (DNN) models. We analyze the effectiveness of pre-trained state-of-the-art DNNs on ImageNet and one of its variants, ImageNetV2. Studies in the literature have reported unexpected accuracy drops of 11% to 14% on ImageNetV2. Our findings show that these reported declines are largely attributable to a characteristic of the dataset that has not received sufficient attention -- the proportion of images with multiple labels. Taking this characteristic into account, the results of our experiments provide evidence that there is no substantial degradation in effectiveness on ImageNetV2. Furthermore, we acknowledge that ImageNet pre-trained models exhibit some capability at capturing the multi-label nature of the dataset even though they were trained under the single-label assumption. Consequently, we propose a new evaluation approach to augment existing approaches that assess this capability. Our findings highlight the importance of considering the multi-label nature of the ImageNet dataset during benchmarking. Failing to do so could lead to incorrect conclusions regarding the effectiveness of DNNs and divert research efforts from addressing other substantial challenges related to the reliability and robustness of these models.

Leveraging Human-Machine Interactions for Computer Vision Dataset Quality Enhancement

Large-scale datasets for single-label multi-class classification, such as \emph{ImageNet-1k}, have been instrumental in advancing deep learning and computer vision. However, a critical and often understudied aspect is the comprehensive quality assessment of these datasets, especially regarding potential multi-label annotation errors. In this paper, we introduce a lightweight, user-friendly, and scalable framework that synergizes human and machine intelligence for efficient dataset validation and quality enhancement. We term this novel framework \emph{Multilabelfy}. Central to Multilabelfy is an adaptable web-based platform that systematically guides annotators through the re-evaluation process, effectively leveraging human-machine interactions to enhance dataset quality. By using Multilabelfy on the ImageNetV2 dataset, we found that approximately $47.88\%$ of the images contained at least two labels, underscoring the need for more rigorous assessments of such influential datasets. Furthermore, our analysis showed a negative correlation between the number of potential labels per image and model top-1 accuracy, illuminating a crucial factor in model evaluation and selection. Our open-source framework, Multilabelfy, offers a convenient, lightweight solution for dataset enhancement, emphasizing multi-label proportions. This study tackles major challenges in dataset integrity and provides key insights into model performance evaluation. Moreover, it underscores the advantages of integrating human expertise with machine capabilities to produce more robust models and trustworthy data development. The source code for Multilabelfy will be available at https://github.com/esla/Multilabelfy. \keywords{Computer Vision \and Dataset Quality Enhancement \and Dataset Validation \and Human-Computer Interaction \and Multi-label Annotation.}

Towards Abdominal 3-D Scene Rendering from Laparoscopy Surgical Videos using NeRFs

Given that a conventional laparoscope only provides a two-dimensional (2-D) view, the detection and diagnosis of medical ailments can be challenging. To overcome the visual constraints associated with laparoscopy, the use of laparoscopic images and videos to reconstruct the three-dimensional (3-D) anatomical structure of the abdomen has proven to be a promising approach. Neural Radiance Fields (NeRFs) have recently gained attention thanks to their ability to generate photorealistic images from a 3-D static scene, thus facilitating a more comprehensive exploration of the abdomen through the synthesis of new views. This distinguishes NeRFs from alternative methods such as Simultaneous Localization and Mapping (SLAM) and depth estimation. In this paper, we present a comprehensive examination of NeRFs in the context of laparoscopy surgical videos, with the goal of rendering abdominal scenes in 3-D. Although our experimental results are promising, the proposed approach encounters substantial challenges, which require further exploration in future research.

Know Your Self-supervised Learning: A Survey on Image-based Generative and Discriminative Training

Although supervised learning has been highly successful in improving the state-of-the-art in the domain of image-based computer vision in the past, the margin of improvement has diminished significantly in recent years, indicating that a plateau is in sight. Meanwhile, the use of self-supervised learning (SSL) for the purpose of natural language processing (NLP) has seen tremendous successes during the past couple of years, with this new learning paradigm yielding powerful language models. Inspired by the excellent results obtained in the field of NLP, self-supervised methods that rely on clustering, contrastive learning, distillation, and information-maximization, which all fall under the banner of discriminative SSL, have experienced a swift uptake in the area of computer vision. Shortly afterwards, generative SSL frameworks that are mostly based on masked image modeling, complemented and surpassed the results obtained with discriminative SSL. Consequently, within a span of three years, over $100$ unique general-purpose frameworks for generative and discriminative SSL, with a focus on imaging, were proposed. In this survey, we review a plethora of research efforts conducted on image-oriented SSL, providing a historic view and paying attention to best practices as well as useful software packages. While doing so, we discuss pretext tasks for image-based SSL, as well as techniques that are commonly used in image-based SSL. Lastly, to aid researchers who aim at contributing to image-focused SSL, we outline a number of promising research directions.

A Principled Evaluation Protocol for Comparative Investigation of the Effectiveness of DNN Classification Models on Similar-but-non-identical Datasets

Deep Neural Network (DNN) models are increasingly evaluated using new replication test datasets, which have been carefully created to be similar to older and popular benchmark datasets. However, running counter to expectations, DNN classification models show significant, consistent, and largely unexplained degradation in accuracy on these replication test datasets. While the popular evaluation approach is to assess the accuracy of a model by making use of all the datapoints available in the respective test datasets, we argue that doing so hinders us from adequately capturing the behavior of DNN models and from having realistic expectations about their accuracy. Therefore, we propose a principled evaluation protocol that is suitable for performing comparative investigations of the accuracy of a DNN model on multiple test datasets, leveraging subsets of datapoints that can be selected using different criteria, including uncertainty-related information. By making use of this new evaluation protocol, we determined the accuracy of $564$ DNN models on both (1) the CIFAR-10 and ImageNet datasets and (2) their replication datasets. Our experimental results indicate that the observed accuracy degradation between established benchmark datasets and their replications is consistently lower (that is, models do perform better on the replication test datasets) than the accuracy degradation reported in published works, with these published works relying on conventional evaluation approaches that do not utilize uncertainty-related information.

Exact Feature Collisions in Neural Networks

Predictions made by deep neural networks were shown to be highly sensitive to small changes made in the input space where such maliciously crafted data points containing small perturbations are being referred to as adversarial examples. On the other hand, recent research suggests that the same networks can also be extremely insensitive to changes of large magnitude, where predictions of two largely different data points can be mapped to approximately the same output. In such cases, features of two data points are said to approximately collide, thus leading to the largely similar predictions. Our results improve and extend the work of Li et al.(2019), laying out theoretical grounds for the data points that have colluding features from the perspective of weights of neural networks, revealing that neural networks not only suffer from features that approximately collide but also suffer from features that exactly collide. We identify the necessary conditions for the existence of such scenarios, hereby investigating a large number of DNNs that have been used to solve various computer vision problems. Furthermore, we propose the Null-space search, a numerical approach that does not rely on heuristics, to create data points with colliding features for any input and for any task, including, but not limited to, classification, localization, and segmentation.

Evaluating Adversarial Attacks on ImageNet: A Reality Check on Misclassification Classes

Although ImageNet was initially proposed as a dataset for performance benchmarking in the domain of computer vision, it also enabled a variety of other research efforts. Adversarial machine learning is one such research effort, employing deceptive inputs to fool models in making wrong predictions. To evaluate attacks and defenses in the field of adversarial machine learning, ImageNet remains one of the most frequently used datasets. However, a topic that is yet to be investigated is the nature of the classes into which adversarial examples are misclassified. In this paper, we perform a detailed analysis of these misclassification classes, leveraging the ImageNet class hierarchy and measuring the relative positions of the aforementioned type of classes in the unperturbed origins of the adversarial examples. We find that $71\%$ of the adversarial examples that achieve model-to-model adversarial transferability are misclassified into one of the top-5 classes predicted for the underlying source images. We also find that a large subset of untargeted misclassifications are, in fact, misclassifications into semantically similar classes. Based on these findings, we discuss the need to take into account the ImageNet class hierarchy when evaluating untargeted adversarial successes. Furthermore, we advocate for future research efforts to incorporate categorical information.

Selection of Source Images Heavily Influences the Effectiveness of Adversarial Attacks

Although the adoption rate of deep neural networks (DNNs) has tremendously increased in recent years, a solution for their vulnerability against adversarial examples has not yet been found. As a result, substantial research efforts are dedicated to fix this weakness, with many studies typically using a subset of source images to generate adversarial examples, treating every image in this subset as equal. We demonstrate that, in fact, not every source image is equally suited for this kind of assessment. To do so, we devise a large-scale model-to-model transferability scenario for which we meticulously analyze the properties of adversarial examples, generated from every suitable source image in ImageNet by making use of two of the most frequently deployed attacks. In this transferability scenario, which involves seven distinct DNN models, including the recently proposed vision transformers, we reveal that it is possible to have a difference of up to $12.5\%$ in model-to-model transferability success, $1.01$ in average $L_2$ perturbation, and $0.03$ ($8/225$) in average $L_{\infty}$ perturbation when $1,000$ source images are sampled randomly among all suitable candidates. We then take one of the first steps in evaluating the robustness of images used to create adversarial examples, proposing a number of simple but effective methods to identify unsuitable source images, thus making it possible to mitigate extreme cases in experimentation and support high-quality benchmarking.