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A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
This paper shows the machine learning system which performs instance segmentation of cytological images in veterinary medicine. Eleven cell types were used directly and indirectly in the experiments, including damaged and unrecognized…
In the cancer diagnosis pipeline, digital pathology plays an instrumental role in the identification, staging, and grading of malignant areas on biopsy tissue specimens. High resolution histology images are subject to high variance in…
Spatial proteomics technologies have transformed our understanding of complex tissue architecture in cancer but present unique challenges for computational analysis. Each study uses a different marker panel and protocol, and most methods…
Machine learning and computer vision techniques have grown rapidly in recent years due to their automation, suitability, and ability to generate astounding results. Hence, in this paper, we survey the key studies that are published between…
There is a widening recognition that cancer cells are products of complex developmental processes. Carcinogenesis and metastasis formation are increasingly described as systems-level, network phenomena. Here we propose that malignant…
In this review we make the statement that hybrid models in oncology are required as a mean for enhanced data integration. In the context of systems oncology, experimental and clinical data need to be at the heart of the models developments…
Although a standard in natural science, reproducibility has been only episodically applied in experimental computer science. Scientific papers often present a large number of tables, plots and pictures that summarize the obtained results,…
Spatial agent-based models are increasingly used to investigate the evolution of solid tumours subject to localised cell-cell interactions and microenvironmental heterogeneity. Here we present a non-technical step by step guide to…
We summarize recent progress on the theory and applications of structural identifiability of compartmental models. On the applications side, we review identifiability analyses undertaken recently for models arising in epidemiology,…
Motivation: Gene selection has become a common task in most gene expression studies. The objective of such research is often to identify the smallest possible set of genes that can still achieve good predictive performance. The problem of…
Despite advances in methods to interrogate tumor biology, the observational and population-based approach of classical cancer research and clinical oncology does not enable anticipation of tumor outcomes to hasten the discovery of cancer…
The concept of personalised medicine in cancer therapy is becoming increasingly important. There already exist drugs administered specifically for patients with tumours presenting well-defined mutations. However, the field is still in its…
We propose an extension of a standard stochastic individual-based model in population dynamics which broadens the range of biological applications. Our primary motivation is modelling of immunotherapy of malignant tumours. In this context…
We consider a one--spatial dimensional tumour growth model [2, 3, 4] that consists of three dependent variables of space and time: volume fraction of tumour cells, velocity of tumour cells, and nutrient concentration. The model variables…
This article is a public deliverable of the EU project "Memory technologies with multi-scale time constants for neuromorphic architectures" (MeMScales, https://memscales.eu, Call ICT-06-2019 Unconventional Nanoelectronics, project number…
The objectives of this "perspective" paper are to review some recent advances in sparse feature selection for regression and classification, as well as compressed sensing, and to discuss how these might be used to develop tools to advance…
Chimeric Antigen Receptor (CAR) T-cell therapy is an immunotherapy that has recently become highly instrumental in the fight against life-threatening diseases. A variety of modeling and computational simulation efforts have addressed…
Software now lies at the heart of scholarly research. Here we argue that as well as being important from a methodological perspective, software should, in many instances, be recognised as an output of research, equivalent to an academic…
We study a tumor growth model in two space dimensions, where proliferation of the tumor cells leads to expansion of the tumor domain and migration of surrounding normal tissues into the exterior vacuum. The model features two moving…