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A clinical benchmark of public self-supervised pathology foundation models
The use of self-supervised learning to train pathology foundation models has increased substantially in the past few years. Notably, several models trained on large quantities of clinical data have been made publicly available in recent months. This will significantly enhance scientific research in computational pathology and help bridge the gap between research and clinical deployment. With the increase in availability of public foundation models of different sizes, trained using different algorithms on different datasets, it becomes important to establish a benchmark to compare the performance of such models on a variety of clinically relevant tasks spanning multiple organs and diseases. In this work, we present a collection of pathology datasets comprising clinical slides associated with clinically relevant endpoints including cancer diagnoses and a variety of biomarkers generated during standard hospital operation from three medical centers. We leverage these datasets to systematically assess the performance of public pathology foundation models and provide insights into best practices for training foundation models and selecting appropriate pretrained models. To enable the community to evaluate their models on our clinical datasets, we make available an automated benchmarking pipeline for external use.
Self-supervised learning (SSL) is increasingly used to train pathology foundation models. Here, the authors introduce a pathology benchmark set generated during standard clinical workflows that includes multiple cancer and disease types; then leverage it to assess the performance of multiple public SSL pathology foundation models and to provide best practices for model training and selection.
Journal Article
Certified Dominance and Symmetry Breaking for Combinatorial Optimisation
Symmetry and dominance breaking can be crucial for solving hard combinatorial search and optimisation problems, but the correctness of these techniques sometimes relies on subtle arguments. For this reason, it is desirable to produce efficient, machine-verifiable certificates that solutions have been computed correctly. Building on the cutting planes proof system, we develop a certification method for optimisation problems in which symmetry and dominance breaking is easily expressible. Our experimental evaluation demonstrates that we can efficiently verify fully general symmetry breaking in Boolean satisfiability (SAT) solving, thus providing, for the first time, a unified method to certify a range of advanced SAT techniques that also includes cardinality and parity (XOR) reasoning. In addition, we apply our method to maximum clique solving and constraint programming as a proof of concept that the approach applies to a wider range of combinatorial problems.
Journal Article
CNN Variants for Computer Vision: History, Architecture, Application, Challenges and Future Scope
Computer vision is becoming an increasingly trendy word in the area of image processing. With the emergence of computer vision applications, there is a significant demand to recognize objects automatically. Deep CNN (convolution neural network) has benefited the computer vision community by producing excellent results in video processing, object recognition, picture classification and segmentation, natural language processing, speech recognition, and many other fields. Furthermore, the introduction of large amounts of data and readily available hardware has opened new avenues for CNN study. Several inspirational concepts for the progress of CNN have been investigated, including alternative activation functions, regularization, parameter optimization, and architectural advances. Furthermore, achieving innovations in architecture results in a tremendous enhancement in the capacity of the deep CNN. Significant emphasis has been given to leveraging channel and spatial information, with a depth of architecture and information processing via multi-path. This survey paper focuses mainly on the primary taxonomy and newly released deep CNN architectures, and it divides numerous recent developments in CNN architectures into eight groups. Spatial exploitation, multi-path, depth, breadth, dimension, channel boosting, feature-map exploitation, and attention-based CNN are the eight categories. The main contribution of this manuscript is in comparing various architectural evolutions in CNN by its architectural change, strengths, and weaknesses. Besides, it also includes an explanation of the CNN’s components, the strengths and weaknesses of various CNN variants, research gap or open challenges, CNN applications, and the future research direction.
Journal Article
Rotational Locomotion in Large-Scale Environments: A Survey and Implications for Evidence-Based Design Practice
Navigation performance in urban and large-scale built-up spaces (e.g. airports, train-stations, hospitals) depends on gradual environmental perception during locomotion, and spatial knowledge acquisition, update/integration at different times along a path. Rotational locomotion is regularly
involved in everyday navigation; this, combined with the fact that people cannot perceive the whole of a large-scale setting at once often leads to incidents of cognitive loading and disorientation. Our research explores the mechanisms involved in rotational locomotion for human navigators,
and the role of familiarity as well as the cost of cognitive load on orientation accuracy and spatial memory. We examine the impact of structural and featural cues on spatial knowledge updating in relation to egorotations from the viewpoint of behaviour-based design practice and evidencebased
design interventions. The results are based on a case study in a train station, experimenting on rotational problems in navigation. Here we present preliminary results emphasizing the role of environmental cues in rotational location, outline possibilities for further study, and discuss implications
for evidence-based design practice and cognitive design assistance technology development.
Journal Article
Fake News Detection Using Machine Learning Ensemble Methods
The advent of the World Wide Web and the rapid adoption of social media platforms (such as Facebook and Twitter) paved the way for information dissemination that has never been witnessed in the human history before. With the current usage of social media platforms, consumers are creating and sharing more information than ever before, some of which are misleading with no relevance to reality. Automated classification of a text article as misinformation or disinformation is a challenging task. Even an expert in a particular domain has to explore multiple aspects before giving a verdict on the truthfulness of an article. In this work, we propose to use machine learning ensemble approach for automated classification of news articles. Our study explores different textual properties that can be used to distinguish fake contents from real. By using those properties, we train a combination of different machine learning algorithms using various ensemble methods and evaluate their performance on 4 real world datasets. Experimental evaluation confirms the superior performance of our proposed ensemble learner approach in comparison to individual learners.
Journal Article
Smelling Nano Aerial Vehicle for Gas Source Localization and Mapping
This paper describes the development and validation of the currently smallest aerial platform with olfaction capabilities. The developed Smelling Nano Aerial Vehicle (SNAV) is based on a lightweight commercial nano-quadcopter (27 g) equipped with a custom gas sensing board that can host up to two in situ metal oxide semiconductor (MOX) gas sensors. Due to its small form-factor, the SNAV is not a hazard for humans, enabling its use in public areas or inside buildings. It can autonomously carry out gas sensing missions of hazardous environments inaccessible to terrestrial robots and bigger drones, for example searching for victims and hazardous gas leaks inside pockets that form within the wreckage of collapsed buildings in the aftermath of an earthquake or explosion. The first contribution of this work is assessing the impact of the nano-propellers on the MOX sensor signals at different distances to a gas source. A second contribution is adapting the ‘bout’ detection algorithm, proposed by Schmuker et al. (2016) to extract specific features from the derivative of the MOX sensor response, for real-time operation. The third and main contribution is the experimental validation of the SNAV for gas source localization (GSL) and mapping in a large indoor environment (160 m2) with a gas source placed in challenging positions for the drone, for example hidden in the ceiling of the room or inside a power outlet box. Two GSL strategies are compared, one based on the instantaneous gas sensor response and the other one based on the bout frequency. From the measurements collected (in motion) along a predefined sweeping path we built (in less than 3 min) a 3D map of the gas distribution and identified the most likely source location. Using the bout frequency yielded on average a higher localization accuracy than using the instantaneous gas sensor response (1.38 m versus 2.05 m error), however accurate tuning of an additional parameter (the noise threshold) is required in the former case. The main conclusion of this paper is that a nano-drone has the potential to perform gas sensing tasks in complex environments.
Journal Article
Geometric deep learning and equivariant neural networks
We survey the mathematical foundations of geometric deep learning, focusing on group equivariant and gauge equivariant neural networks. We develop gauge equivariant convolutional neural networks on arbitrary manifolds M using principal bundles with structure group K and equivariant maps between sections of associated vector bundles. We also discuss group equivariant neural networks for homogeneous spaces M=G/K, which are instead equivariant with respect to the global symmetry G on M. Group equivariant layers can be interpreted as intertwiners between induced representations of G, and we show their relation to gauge equivariant convolutional layers. We analyze several applications of this formalism, including semantic segmentation and object detection networks. We also discuss the case of spherical networks in great detail, corresponding to the case M=S2=SO(3)/SO(2). Here we emphasize the use of Fourier analysis involving Wigner matrices, spherical harmonics and Clebsch–Gordan coefficients for G=SO(3), illustrating the power of representation theory for deep learning.
Journal Article
Mycobiome diversity: high-throughput sequencing and identification of fungi
Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous — and largely uncharted — taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
Journal Article
Domain generalization through meta-learning: a survey
Deep neural networks (DNNs) have revolutionized artificial intelligence but often lack performance when faced with out-of-distribution data, a common scenario due to the inevitable domain shifts in real-world applications. This limitation stems from the common assumption that training and testing data share the same distribution-an assumption frequently violated in practice. Despite their effectiveness with large amounts of data and computational power, DNNs struggle with distributional shifts and limited labeled data, leading to overfitting and poor generalization across various tasks and domains. Meta-learning presents a promising approach by employing algorithms that acquire transferable knowledge across various tasks for fast adaptation, eliminating the need to learn each task from scratch. This survey paper delves into the realm of meta-learning with a focus on its contribution to domain generalization. We first clarify the concept of meta-learning for domain generalization and introduce a novel taxonomy based on the feature extraction strategy and the classifier learning methodology, offering a granular view of methodologies. Additionally, we present a decision graph to assist readers in navigating the taxonomy based on data availability and domain shifts, enabling them to select and develop a proper model tailored to their specific problem requirements. Through an exhaustive review of existing methods and underlying theories, we map out the fundamentals of the field. Our survey provides practical insights and an informed discussion on promising research directions.
Journal Article