Guides and Shortcuts in Graphs

The geodesic structure of a graphs appears to be a very rich structure. There are many ways to describe this structure, each of which captures only some aspects. Ternary algebras are for this purpose very useful and have a long tradition. We study two instances: signpost systems, and a special case of which, step systems. Signpost systems were already used to characterize graph classes. Here we use these for the study of the geodesic structure of a spanning subgraph F with respect to its host graph G. Such a signpost system is called a guide to (F,G). Our main results are: the characterization of the step system of a cycle, the characterization of guides for spanning trees and hamiltonian cycles

On properties of a graph that depend on its distance function

summary:If $G$ is a connected graph with distance function $d$, then by a step in $G$ is meant an ordered triple $(u, x, v)$ of vertices of $G$ such that $d(u, x) = 1$ and $d(u, v) = d(x, v) + 1$. A characterization of the set of all steps in a connected graph was published by the present author in 1997. In Section 1 of this paper, a new and shorter proof of that characterization is presented. A stronger result for a certain type of connected graphs is proved in Section 2

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is highly motivated by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should therefore be as reliable and versatile as possible. In this context, we examined five aspects of the organization and mining of malaria genomic and post-genomic data: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Progresses toward a grid-enabled chemogenomic knowledge space are discussed.Comment: 43 pages, 4 figures, to appear in Malaria Journa

Factor Machine: Mixed-signal Architecture for Fine-Grained Graph-Based Computing

This paper proposes the design and implementation strategy of a novel computing architecture, the Factor Machine. The work is a step towards a general-purpose parallel system operating in a non-sequential manner, exploiting processing/memory co-integration and replacing the traditional Turing/von Neumann model of a computer system with a framework based on "factorised computation". This architecture is inspired by neural information processing principles and aims to progress the development of brain-like machine intelligence systems, through providing a computing substrate designed from the ground up to enable efficient implementations of algorithms based on relational networks. The paper provides a rationale for such machine, in the context of the history of computing, and more recent developments in neuromorphic hardware, reviews its general features, and proposes a mixed-signal hardware implementation, based on using analogue circuits to carry out computation and localised and sparse communication between the compute units.Comment: An essay in contribution to the Festschrift for Professor Steve Furber, Manchester, 12 January 202

Employing patient-reported outcome (PRO) measures to support newly diagnosed patients with melanoma: feasibility and acceptability of a holistic needs assessment intervention

Purpose: Living with a melanoma diagnosis can be challenging. We aimed to assess the feasibility, acceptability, and perceived value of a nurse-led intervention that utilised patient-reported outcome (PRO) measures to identify and address the supportive care needs of newly diagnosed patients with Stage I/II melanoma over the first 4 months post-diagnosis. Methods: We conducted an exploratory, repeated-measures, single-arm, feasibility trial. One baseline (4 weeks post-diagnosis; T1) and one follow-up intervention session (4 weeks after wide local excision; T3) took place, two months apart. Patient survey data were collected monthly, at four assessment points (T1-T4), followed by exit interviews. Results: A recruitment rate of 55% (10/18) was achieved. The skin cancer nurse specialist (CNS) performed 19 in-clinic patient assessments within 6 months. One patient missed their follow-up intervention session (90% retention rate). Three participants (30%) were lost to follow-up at T4. Patients endorsed the standardised use of easy-to-use PRO measures as a means to help them shortlist, report and prioritise their needs. The CNS viewed the intervention as a highly structured activity that allowed tailoring support priority needs. A sizeable reduction in information needs was found from T1 to T4 (Standardised Response Mean [SRM] change = −0.99; p < 0.05). From T1 to T2, significant reductions in psychological (SRM change = −1.18; p < 0.001), practical (SRM change = −0.67; p < 0.05) and sexuality needs (SRM change = −0.78; p < 0.05) were observed. Conclusions: The intervention appears to be feasible in clinical practice and acceptable to both patients with newly diagnosed melanoma and clinicians. Future research is warranted to test its effectiveness against standard care