A new non-monotonic infeasible simplex-type algorithm for Linear Programming

This paper presents a new simplex-type algorithm for Linear Programming with the following two main characteristics: (i) the algorithm computes basic solutions which are neither primal or dual feasible, nor monotonically improving and (ii) the sequence of these basic solutions is connected with a sequence of monotonically improving interior points to construct a feasible direction at each iteration. We compare the proposed algorithm with the state-of-the-art commercial CPLEX and Gurobi Primal-Simplex optimizers on a collection of 93 well known benchmarks. The results are promising, showing that the new algorithm competes versus the state-of-the-art solvers in the total number of iterations required to converge

An integrated optimisation platform for sustainable resource and infrastructure planning

It is crucial for sustainable planning to consider broad environmental and social dimensions and systemic implications of new infrastructure to build more resilient societies, reduce poverty, improve human well-being, mitigate climate change and address other global change processes. This article presents resilience.io, 2 a platform to evaluate new infrastructure projects by assessing their design and effectiveness in meeting growing resource demands, simulated using Agent-Based Modelling due to socio-economic population changes. We then use Mixed-Integer Linear Programming to optimise a multi-objective function to find cost-optimal solutions, inclusive of environmental metrics such as greenhouse gas emissions. The solutions in space and time provide planning guidance for conventional and novel technology selection, changes in network topology, system costs, and can incorporate any material, waste, energy, labour or emissions flow. As an application, a use case is provided for the Water, Sanitation and Hygiene (WASH) sector for a four million people city-region in Ghana

A machine learning and directed network optimization approach to uncover TP53 regulatory patterns

TP53, the Guardian of the Genome, is the most frequently mutated gene in human cancers and the functional characterization of its regulation is fundamental. To address this we employ two strategies: machine learning to predict the mutation status of TP53 from transcriptomic data, and directed regulatory networks to reconstruct the effect of mutations on the transcipt levels of TP53 targets. Using data from established databases (Cancer Cell Line Encyclopedia, The Cancer Genome Atlas), machine learning could predict the mutation status, but not resolve different mutations. On the contrary, directed network optimization allowed to infer the TP53 regulatory profile across: (1) mutations, (2) irradiation in lung cancer, and (3) hypoxia in breast cancer, and we could observe differential regulatory profiles dictated by (1) mutation type, (2) deleterious consequences of the mutation, (3) known hotspots, (4) protein changes, (5) stress condition (irradiation/hypoxia). This is an important first step toward using regulatory networks for the characterization of the functional consequences of mutations, and could be extended to other perturbations, with implications for drug design and precision medicine

An integrated optimisation platform for sustainable resource and infrastructure planning

It is crucial for sustainable planning to consider broad environmental and social dimensions and systemic implications of new infrastructure to build more resilient societies, reduce poverty, improve human well-being, mitigate climate change and address other global change processes. This article presents resilience.io, 2 a platform to evaluate new infrastructure projects by assessing their design and effectiveness in meeting growing resource demands, simulated using Agent-Based Modelling due to socio-economic population changes. We then use Mixed-Integer Linear Programming to optimise a multi-objective function to find cost-optimal solutions, inclusive of environmental metrics such as greenhouse gas emissions. The solutions in space and time provide planning guidance for conventional and novel technology selection, changes in network topology, system costs, and can incorporate any material, waste, energy, labour or emissions flow. As an application, a use case is provided for the Water, Sanitation and Hygiene (WASH) sector for a four million people city-region in Ghana