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Cancer diagnosis and prognosis primarily depend on clinical parameters such as age and tumor grade, and are increasingly complemented by molecular data, such as gene expression, from tumor sequencing. However, sequencing is costly and delays oncology workflows. Recent advances in Deep Learning allow to predict molecular information from morphological features within Whole Slide Images (WSIs), offering a cost-effective proxy of the molecular markers. While promising, current methods lack the robustness to fully replace direct sequencing. Here we aim to improve existing methods by introducing a model-agnostic framework that allows to inject prior knowledge on gene-gene interactions into Deep Learning architectures, thereby increasing accuracy and robustness. We design the framework to be generic and flexibly adaptable to a wide range of architectures. In a case study on breast cancer, our strategy leads to an average increase of 983 significant genes (out of 25,761) across all 18 experiments, with 14 generalizing to an increase on an independent dataset. Our findings reveal a high potential for injection of prior knowledge to increase gene expression prediction performance from WSIs across a wide range of architectures.

Multispectral point cloud (MPC) captures 3D spatial-spectral information from the observed scene, which can be used for scene understanding and has a wide range of applications. However, most of the existing classification methods were extensively tested on indoor datasets, and when applied to outdoor datasets they still face problems including sparse labeled targets, differences in land-covers scales, and long-tailed distributions. To address the above issues, an enhanced classification method based on adaptive multi-scale fusion for MPCs with long-tailed distributions is proposed. In the training set generation stage, a grid-balanced sampling strategy is designed to reliably generate training samples from sparse labeled datasets. In the feature learning stage, a multi-scale feature fusion module is proposed to fuse shallow features of land-covers at different scales, addressing the issue of losing fine features due to scale variations in land-covers. In the classification stage, an adaptive hybrid loss module is devised to utilize multi-classification heads with adaptive weights to balance the learning ability of different classes, improving the classification performance of small classes due to various-scales and long-tailed distributions in land-covers. Experimental results on three MPC datasets demonstrate the effectiveness of the proposed method compared with the state-of-the-art methods., Comment: 16 pages, 9 figures, 5 tables

Deep subspace clustering methods are now prominent in clustering, typically using fully connected networks and a self-representation loss function. However, these methods often struggle with overfitting and lack interpretability. In this paper, we explore an alternative clustering approach based on deep unfolding. By unfolding iterative optimization methods into neural networks, this approach offers enhanced interpretability and reliability compared to data-driven deep learning methods, and greater adaptability and generalization than model-based approaches. Hence, unfolding has become widely used in inverse imaging problems, such as image restoration, reconstruction, and super-resolution, but has not been sufficiently explored yet in the context of clustering. In this work, we introduce an innovative clustering architecture for hyperspectral images (HSI) by unfolding an iterative solver based on the Alternating Direction Method of Multipliers (ADMM) for sparse subspace clustering. To our knowledge, this is the first attempt to apply unfolding ADMM for computing the self-representation matrix in subspace clustering. Moreover, our approach captures well the structural characteristics of HSI data by employing the K nearest neighbors algorithm as part of a structure preservation module. Experimental evaluation of three established HSI datasets shows clearly the potential of the unfolding approach in HSI clustering and even demonstrates superior performance compared to state-of-the-art techniques.

Automated mark localization in scatter images, greatly helpful for discovering knowledge and understanding enormous document images and reasoning in visual question answering AI systems, is a highly challenging problem because of the ubiquity of overlapping marks. Locating overlapping marks faces many difficulties such as no texture, less contextual information, hallow shape and tiny size. Here, we formulate it as a combinatorial optimization problem on clustering-based re-visualization from a non-training generative perspective, to locate scatter marks by finding the status of multi-variables when an objective function reaches a minimum. The objective function is constructed on difference between binarized scatter images and corresponding generated re-visualization based on their clustering. Fundamentally, re-visualization tries to generate a new scatter graph only taking a rasterized scatter image as an input, and clustering is employed to provide the information for such re-visualization. This method could stably locate severely-overlapping, variable-size and variable-shape marks in scatter images without dependence of any training dataset or reference. Meanwhile, we propose an adaptive variant of simulated annealing which can works on various connected regions. In addition, we especially built a dataset named SML2023 containing hundreds of scatter images with different markers and various levels of overlapping severity, and tested the proposed method and compared it to existing methods. The results show that it can accurately locate most marks in scatter images with different overlapping severity and marker types, with about 0.3 absolute increase on an assignment-cost-based metric in comparison with state-of-the-art methods. This work is of value to data mining on massive web pages and literatures, and shedding new light on image measurement such as bubble counting., Comment: 22pages

Drug-target interaction (DTI) prediction is a challenging, albeit essential task in drug repurposing. Learning on graph models have drawn special attention as they can significantly reduce drug repurposing costs and time commitment. However, many current approaches require high-demanding additional information besides DTIs that complicates their evaluation process and usability. Additionally, structural differences in the learning architecture of current models hinder their fair benchmarking. In this work, we first perform an in-depth evaluation of current DTI datasets and prediction models through a robust benchmarking process, and show that DTI prediction methods based on transductive models lack generalization and lead to inflated performance when evaluated as previously done in the literature, hence not being suited for drug repurposing approaches. We then propose a novel biologically-driven strategy for negative edge subsampling and show through in vitro validation that newly discovered interactions are indeed true. We envision this work as the underpinning for future fair benchmarking and robust model design. All generated resources and tools are publicly available as a python package.

One of the largest problems in medical image processing is the lack of annotated data. Labeling medical images often requires highly trained experts and can be a time-consuming process. In this paper, we evaluate a method of reducing the need for labeled data in medical image object detection by using self-supervised neural network pretraining. We use a dataset of chest X-ray images with bounding box labels for 13 different classes of anomalies. The networks are pretrained on a percentage of the dataset without labels and then fine-tuned on the rest of the dataset. We show that it is possible to achieve similar performance to a fully supervised model in terms of mean average precision and accuracy with only 60\% of the labeled data. We also show that it is possible to increase the maximum performance of a fully-supervised model by adding a self-supervised pretraining step, and this effect can be observed with even a small amount of unlabeled data for pretraining., Comment: Accepted by 30th European Signal Processing Conference, EUSIPCO 2022

Conditional Variational Auto Encoders (VAE) are gathering significant attention as an Explainable Artificial Intelligence (XAI) tool. The codes in the latent space provide a theoretically sound way to produce counterfactuals, i.e. alterations resulting from an intervention on a targeted semantic feature. To be applied on real images more complex models are needed, such as Hierarchical CVAE. This comes with a challenge as the naive conditioning is no longer effective. In this paper we show how relaxing the effect of the posterior leads to successful counterfactuals and we introduce VAEX an Hierarchical VAE designed for this approach that can visually audit a classifier in applications., Comment: 5 pages, 3 figures

We address the problem of scene classification from optical remote sensing (RS) images based on the paradigm of hierarchical metric learning. Ideally, supervised metric learning strategies learn a projection from a set of training data points so as to minimize intra-class variance while maximizing inter-class separability to the class label space. However, standard metric learning techniques do not incorporate the class interaction information in learning the transformation matrix, which is often considered to be a bottleneck while dealing with fine-grained visual categories. As a remedy, we propose to organize the classes in a hierarchical fashion by exploring their visual similarities and subsequently learn separate distance metric transformations for the classes present at the non-leaf nodes of the tree. We employ an iterative max-margin clustering strategy to obtain the hierarchical organization of the classes. Experiment results obtained on the large-scale NWPU-RESISC45 and the popular UC-Merced datasets demonstrate the efficacy of the proposed hierarchical metric learning based RS scene recognition strategy in comparison to the standard approaches., Comment: Undergoing revision in GRSL

The third edition of the "international - Traveling Workshop on Interactions between Sparse models and Technology" (iTWIST) took place in Aalborg, the 4th largest city in Denmark situated beautifully in the northern part of the country, from the 24th to 26th of August 2016. The workshop venue was at the Aalborg University campus. One implicit objective of this biennial workshop is to foster collaboration between international scientific teams by disseminating ideas through both specific oral/poster presentations and free discussions. For this third edition, iTWIST'16 gathered about 50 international participants and features 8 invited talks, 12 oral presentations, and 12 posters on the following themes, all related to the theory, application and generalization of the "sparsity paradigm": Sparsity-driven data sensing and processing (e.g., optics, computer vision, genomics, biomedical, digital communication, channel estimation, astronomy); Application of sparse models in non-convex/non-linear inverse problems (e.g., phase retrieval, blind deconvolution, self calibration); Approximate probabilistic inference for sparse problems; Sparse machine learning and inference; "Blind" inverse problems and dictionary learning; Optimization for sparse modelling; Information theory, geometry and randomness; Sparsity? What's next? (Discrete-valued signals; Union of low-dimensional spaces, Cosparsity, mixed/group norm, model-based, low-complexity models, ...); Matrix/manifold sensing/processing (graph, low-rank approximation, ...); Complexity/accuracy tradeoffs in numerical methods/optimization; Electronic/optical compressive sensors (hardware)., Comment: 69 pages, 22 extended abstracts, iTWIST'16 website: http://www.itwist16.es.aau.dk

The implicit objective of the biennial "international - Traveling Workshop on Interactions between Sparse models and Technology" (iTWIST) is to foster collaboration between international scientific teams by disseminating ideas through both specific oral/poster presentations and free discussions. For its second edition, the iTWIST workshop took place in the medieval and picturesque town of Namur in Belgium, from Wednesday August 27th till Friday August 29th, 2014. The workshop was conveniently located in "The Arsenal" building within walking distance of both hotels and town center. iTWIST'14 has gathered about 70 international participants and has featured 9 invited talks, 10 oral presentations, and 14 posters on the following themes, all related to the theory, application and generalization of the "sparsity paradigm": Sparsity-driven data sensing and processing; Union of low dimensional subspaces; Beyond linear and convex inverse problem; Matrix/manifold/graph sensing/processing; Blind inverse problems and dictionary learning; Sparsity and computational neuroscience; Information theory, geometry and randomness; Complexity/accuracy tradeoffs in numerical methods; Sparsity? What's next?; Sparse machine learning and inference., Comment: 69 pages, 24 extended abstracts, iTWIST'14 website: http://sites.google.com/site/itwist14

This paper presents a convenient graphical tool for encoding visual patterns (such as image patches and image atoms) as point constellations in a space spanned by perceptual features and with a clear geometrical interpretation. General theory and a practical pattern encoding scheme are presented, inspired by encoding polarization states of a light wave on the Poincare sphere. This new pattern encoding scheme can be useful for many applications in image processing and computer vision. Here, three possible applications are illustrated, in clustering perceptually similar patterns, visualizing properties of learned dictionaries of image atoms and generating new dictionaries of image atoms from spherical codes., Comment: 26 pages, 23 figures