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Scalable and Loosely-Coupled Multimodal Deep Learning for Breast Cancer Subtyping

Amer, Mohammed, Suliman, Mohamed A., Bui, Tu, Garcia, Nuria, Georgescu, Serban

arXiv.org Artificial Intelligence

Healthcare applications are inherently multimodal, benefiting greatly from the integration of diverse data sources. However, the modalities available in clinical settings can vary across different locations and patients. A key area that stands to gain from multimodal integration is breast cancer molecular subtyping, an important clinical task that can facilitate personalized treatment and improve patient prognosis. In this work, we propose a scalable and loosely-coupled multimodal framework that seamlessly integrates data from various modalities, including copy number variation (CNV), clinical records, and histopathology images, to enhance breast cancer subtyping. While our primary focus is on breast cancer, our framework is designed to easily accommodate additional modalities, offering the flexibility to scale up or down with minimal overhead without requiring re-training of existing modalities, making it applicable to other types of cancers as well. We introduce a dual-based representation for whole slide images (WSIs), combining traditional image-based and graph-based WSI representations. This novel dual approach results in significant performance improvements. Moreover, we present a new multimodal fusion strategy, demonstrating its ability to enhance performance across a range of multimodal conditions. Our comprehensive results show that integrating our dual-based WSI representation with CNV and clinical health records, along with our pipeline and fusion strategy, outperforms state-of-the-art methods in breast cancer subtyping.


A Semantic Social Network Analysis Tool for Sensitivity Analysis and What-If Scenario Testing in Alcohol Consumption Studies

Benítez-Andrades, José Alberto, Rodríguez-González, Alejandro, Benavides, Carmen, Sánchez-Valdeón, Leticia, García, Isaías

arXiv.org Artificial Intelligence

Social Network Analysis (SNA) is a set of techniques developed in the field of social and behavioral sciences research, in order to characterize and study the social relationships that are established among a set of individuals. When building a social network for performing an SNA analysis, an initial process of data gathering is achieved in order to extract the characteristics of the individuals and their relationships. This is usually done by completing a questionnaire containing different types of questions that will be later used to obtain the SNA measures needed to perform the study. There are, then, a great number of different possible network generating questions and also many possibilities for mapping the responses to the corresponding characteristics and relationships. Many variations may be introduced into these questions (the way they are posed, the weights given to each of the responses, etc.) that may have an effect on the resulting networks. All these different variations are difficult to achieve manually, because the process is time-consuming and error prone. The tool described in this paper uses semantic knowledge representation techniques in order to facilitate this kind of sensitivity studies. The base of the tool is a conceptual structure, called "ontology" that is able to represent the different concepts and their definitions. The tool is compared to other similar ones, and the advantages of the approach are highlighted, giving some particular examples from an ongoing SNA study about alcohol consumption habits in adolescents.


Comparing the Digital Annealer with Classical Evolutionary Algorithm

Ayodele, Mayowa

arXiv.org Artificial Intelligence

In more recent years, there has been increasing research interest in exploiting the use of application specific hardware for solving optimisation problems. Examples of solvers that use specialised hardware are IBM's Quantum System One and D-wave's Quantum Annealer (QA) and Fujitsu's Digital Annealer (DA). These solvers have been developed to optimise problems faster than traditional meta-heuristics implemented on general purpose machines. Previous research has shown that these solvers (can optimise many problems much quicker than exact solvers such as GUROBI and CPLEX. Such conclusions have not been made when comparing hardware solvers with classical evolutionary algorithms. Making a fair comparison between traditional evolutionary algorithms, such as Genetic Algorithm (GA), and the DA (or other similar solvers) is challenging because the later benefits from the use of application specific hardware while evolutionary algorithms are often implemented on general-purpose machines. Moreover, quantum or quantum-inspired solvers are limited to solving problems in a specific format. A common formulation used is Quadratic Unconstrained Binary Optimisation (QUBO). Many optimisation problems are however constrained and have natural representations that are non-binary. Converting such problems to QUBO can lead to more problem difficulty and/or larger search space. The question addressed in this paper is whether quantum or quantum-inspired solvers can optimise QUBO transformations of combinatorial optimisation problems faster than classical evolutionary algorithms applied to the same problems in their natural representations. We show that the DA often present better average objective function values than GA on Travelling Salesman, Quadratic Assignment and Multi-dimensional Knapsack Problem instances.


Chemistry42: An AI-based platform for de novo molecular design

Ivanenkov, Yan A., Zhebrak, Alex, Bezrukov, Dmitry, Zagribelnyy, Bogdan, Aladinskiy, Vladimir, Polykovskiy, Daniil, Putin, Evgeny, Kamya, Petrina, Aliper, Alexander, Zhavoronkov, Alex

arXiv.org Artificial Intelligence

Abstract: Chemistry42 is a software platform for de novo small molecule design that integrates Artificial Intelligence (AI) techniques with computational and medicinal chemistry methods. Chemistry42 is unique in its ability to generate novel molecular structures with predefined properties validated through in vitro and in vivo studies. Keywords: generative chemistry, target identification, deep learning, reinforcement learning, drug discovery, de novo drug design Introduction Deep Learning (DL) has proven to be very effective in speech and image recognition. This is because DL-based architectures are uniquely suited for the automatic identification of patterns within complex, nonlinear data sets without the need for manual feature engineering. DL methods have successfully overcome limitations inherent in the standard techniques used for small molecule design (Chen et al. 2018; Vanhaelen, Lin, and Zhavoronkov 2020; Yang et al. 2019) which offers exciting possibilities for the development of new methods that efficiently explore uncharted chemical space.


The prospects of quantum computing in computational molecular biology

Outeiral, Carlos, Strahm, Martin, Shi, Jiye, Morris, Garrett M., Benjamin, Simon C., Deane, Charlotte M.

arXiv.org Machine Learning

Quantum computers can in principle solve certain problems exponentially more quickly than their classical counterparts. We have not yet reached the advent of useful quantum computation, but when we do, it will affect nearly all scientific disciplines. In this review, we examine how current quantum algorithms could revolutionize computational biology and bioinformatics. There are potential benefits across the entire field, from the ability to process vast amounts of information and run machine learning algorithms far more efficiently, to algorithms for quantum simulation that are poised to improve computational calculations in drug discovery, to quantum algorithms for optimization that may advance fields from protein structure prediction to network analysis. However, these exciting prospects are susceptible to "hype", and it is also important to recognize the caveats and challenges in this new technology. Our aim is to introduce the promise and limitations of emerging quantum computing technologies in the areas of computational molecular biology and bioinformatics.


Arvato and Blue Prism Partner to Bring Robotic Process Automation to Local Government

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SLOUGH, England--(BUSINESS WIRE)--Global business outsourcing provider Arvato has entered a strategic partnership with Blue Prism to offer Robotic Process Automation (RPA) to help councils deliver back-office transformation. The partnership will see Arvato use the cutting-edge automation software to provide local authorities with an end-to-end solution of identifying, designing, building and monitoring automated processes, providing RPA-as-a-service and consultancy and training. Arvato will use the innovative technology to help current and future clients in local government automate transactional back office functions, such as revenues and benefits, HR, payroll and finance, increasing process speed and efficiency while freeing up employees to deliver front-line services. RPA uses software to create an agile, virtual workforce which mimics human processing of repetitive labour-intensive tasks. It follows rule-based business processes and interacts with systems in the same way that people do.