We discuss the applicability of large quantum annealers for the purpose of processing Remote Sensing images. We show an application of currently existing quantum annealers for the purpose of post-processing segmentation of a hyperspectral image. We show that in principle there might exist useful applications of large scale quantum annealers for the purpose of Remote Sensing data processing.

Supervised machine learning techniques are widely used for hyper-spectral images segmentation. A typical simple scheme of classification of such images probabilistically assigns a label to each individual pixel omitting information about pixel surroundings. In order to achieve better classification results for real world images one has to agree the local label obtained from the classifier with the classes of pixel neighborhood. A popular way to do it is through a probabilistic graphical model, where label distributions for individual pixels are mapped into a graph of neighborhood relations. One way to realize this approach is to use Ising models, where class probability is mapped to spin energy and class-class interaction is mapped to the spins coupling. By finding low energy states of such an Ising model we can perform post-processing of segmented images. In this work we present how this postprocessing can be implemented using a quantum annealer.

This article describes a practical Earth Observation use case that would benefit from quantum computing. We analyze three quantum neural network algorithms. We implemented one of the algorithms on the EuroSAT dataset. We compare the algorithms with respect to complexity and degree of quantization. We believe that the algorithms we propose would be useful for the remote sensing community when quantum computing technologies become widely available.1

Quantum computers consisting of hundreds of noisy qubits are already available and can run specific quantum algorithms although a large-scale fully error-corrected quantum computer is decades away. It is important to study their application to real-life computational problems. One such problem is Land Use and Land Cover classification of Earth Observation data set collected from the earth observation satellite mission using quantum machine learning methods. In this work, we compare the performance of the classical neural network on the re-labeled dataset of the Copernicus Sentinel-2 mission, when the model has access to Projected Quantum Kernel features. We show that classical neural net-work training accuracy increases drastically when the model has access to Projected Quantum Kernel features. This study shows the potential for quantum machine learning methods to Earth Observation data and provides key evidence for further investigation.

The first version of this article listed one of its authors as Jan Hausenauer rather than Jan Hasenauer. This has now been corrected. The authors regret the error.

Processing Earth observation images to obtain land cover classification is an important task allowing to track changes on the Earth's surface resulting from natural processes, human activity, and climate change. The amount of data acquired from Earth observation satellites is very large and their processing takes large amount of computational resources. We investigate application of quantum circuit based neural network classifiers for multi-spectral data classification aimed at obtaining the land cover information. We show a proof-of-concept of our approach.

The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network layouts and hinders their reuse and extension. In this paper, we present a high-level overview of the layout formats in systems biology, focusing on their commonalities and differences, review their support in existing software tools, libraries and repositories and finally introduce a new conversion module within the MINERVA platform. The module is available via a REST API and offers, besides the ability to convert between layout-aware systems biology formats, the possibility to export layouts into several graphical formats. The module enables conversion of very large networks with thousands of elements, such as disease maps or metabolic reconstructions, rendering it widely applicable in systems biology.

The Disease Maps Project builds on a network of scientific and clinical groups that exchange best practices, share information and develop systems biomedicine tools. The project aims for an integrated, highly curated and user-friendly platform for disease-related knowledge. The primary focus of disease maps is on interconnected signaling, metabolic and gene regulatory network pathways represented in standard formats. The involvement of domain experts ensures that the key disease hallmarks are covered and relevant, up-to-date knowledge is adequately represented. Expert-curated and computer readable, disease maps may serve as a compendium of knowledge, allow for data-supported hypothesis generation or serve as a scaffold for the generation of predictive mathematical models. This article summarizes the 2nd Disease Maps Community meeting, highlighting its important topics and outcomes. We outline milestones on the roadmap for the future development of disease maps, including creating and maintaining standardized disease maps; sharing parts of maps that encode common human disease mechanisms; providing technical solutions for complexity management of maps; and Web tools for in-depth exploration of such maps. A dedicated discussion was focused on mathematical modeling approaches, as one of the main goals of disease map development is the generation of mathematically interpretable representations to predict disease comorbidity or drug response and to suggest drug repositioning, altogether supporting clinical decisions.

SUMMARY: The complexity of molecular networks makes them difficult to navigate and interpret, creating a need for specialized software. MINERVA is a web platform for visualization, exploration and management of molecular networks. Here, we introduce an extension to MINERVA architecture that greatly facilitates the access and use of the stored molecular network data. It allows to incorporate such data in analytical pipelines via a programmatic access interface, and to extend the platform's visual exploration and analytics functionality via plugin architecture. This is possible for any molecular network hosted by the MINERVA platform encoded in well-recognized systems biology formats. To showcase the possibilities of the plugin architecture, we have developed several plugins extending the MINERVA core functionalities. In the article, we demonstrate the plugins for interactive tree traversal of molecular networks, for enrichment analysis and for mapping and visualization of known disease variants or known adverse drug reactions to molecules in the network. AVAILABILITY AND IMPLEMENTATION: Plugins developed and maintained by the MINERVA team are available under the AGPL v3 license at https://git-r3lab.uni.lu/minerva/plugins/. The MINERVA API and plugin documentation is available at https://minerva-web.lcsb.uni.lu.

Summary: MolArt fills the gap between sequence and structure visualization by providing a light-weight, interactive environment enabling exploration of sequence annotations in the context of available experimental or predicted protein structures. Provided a UniProt ID, MolArt downloads and displays sequence annotations, sequence-structure mapping and relevant structures. The sequence and structure views are interlinked, enabling sequence annotations being color overlaid over the mapped structures, thus providing an enhanced understanding and interpretation of the available molecular data. Availability and implementation: MolArt is released under the Apache 2 license and is available at https://github.com/davidhoksza/MolArt. The project web page https://davidhoksza.github.io/MolArt/ features examples and applications of the tool.

Motivation: A genome-scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualize its content integrated with omics data and simulation results. Results: We manually drew a comprehensive map, ReconMap 2.0, that is consistent with the content of Recon 2. We present it within a web interface that allows content query, visualization of custom datasets and submission of feedback to manual curators. Availability and Implementation: ReconMap can be accessed via http://vmh.uni.lu , with network export in a Systems Biology Graphical Notation compliant format released under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. A Constraint-Based Reconstruction and Analysis (COBRA) Toolbox extension to interact with ReconMap is available via https://github.com/opencobra/cobratoolbox . Contact: [email protected].