Machines Learning - Towards a New Synthetic Autobiographical Memory

Autobiographical memory is the organisation of episodes and contextual information from an individual’s experiences into a coherent narrative, which is key to our sense of self. Formation and recall of autobiographical memories is essential for effective, adaptive behaviour in the world, providing contextual information necessary for planning actions and memory functions such as event reconstruction. A synthetic autobiographical memory system would endow intelligent robotic agents with many essential components of cognition through active compression and storage of historical sensorimotor data in an easily addressable manner. Current approaches neither fulfil these functional requirements, nor build upon recent understanding of predictive coding, deep learning, nor the neurobiology of memory. This position paper highlights desiderata for a modern implementation of synthetic autobiographical memory based on human episodic memory, and proposes that a recently developed model of hippocampal memory could be extended as a generalised model of autobiographical memory. Initial implementation will be targeted at social interaction, where current synthetic autobiographical memory systems have had success

iCub visual memory inspector: Visualising the iCub’s thoughts

This paper describes the integration of multiple sensory recognition models created by a Synthetic Autobiographical Memory into a structured system. This structured system provides high level control of the overall architecture and interfaces with an iCub simulator based in Unity which provides a virtual space for the display of recollected events

Fluctuations in granular gases

A driven granular material, e.g. a vibrated box full of sand, is a stationary system which may be very far from equilibrium. The standard equilibrium statistical mechanics is therefore inadequate to describe fluctuations in such a system. Here we present numerical and analytical results concerning energy and injected power fluctuations. In the first part we explain how the study of the probability density function (pdf) of the fluctuations of total energy is related to the characterization of velocity correlations. Two different regimes are addressed: the gas driven at the boundaries and the homogeneously driven gas. In a granular gas, due to non-Gaussianity of the velocity pdf or lack of homogeneity in hydrodynamics profiles, even in the absence of velocity correlations, the fluctuations of total energy are non-trivial and may lead to erroneous conclusions about the role of correlations. In the second part of the chapter we take into consideration the fluctuations of injected power in driven granular gas models. Recently, real and numerical experiments have been interpreted as evidence that the fluctuations of power injection seem to satisfy the Gallavotti-Cohen Fluctuation Relation. We will discuss an alternative interpretation of such results which invalidates the Gallavotti-Cohen symmetry. Moreover, starting from the Liouville equation and using techniques from large deviation theory, the general validity of a Fluctuation Relation for power injection in driven granular gases is questioned. Finally a functional is defined using the Lebowitz-Spohn approach for Markov processes applied to the linear inelastic Boltzmann equation relevant to describe the motion of a tracer particle. Such a functional results to be different from injected power and to satisfy a Fluctuation Relation.Comment: 40 pages, 18 figure

Preparing medical students for clinical practice: easing the transition

The transition from medical student to junior doctor is a challenge; the UK General Medical Council has issued guidance emphasizing the importance of adequate preparation of medical students for clinical practice. This study aimed to determine whether a junior doctor-led simulation-based course is an effective way of preparing final year medical students for practice as a junior doctor. We piloted a new 'preparation for practice' course for final year medical students prior to beginning as Foundation Year 1 (first year of practice) doctors. The course ran over three days and consisted of four simulated stations: ward round, prescribing, handover, and lessons learnt. Quantitative and qualitative feedback was obtained .A total of 120 students attended (40 on each day) and feedback was collected from 95 of them. Using a scale of 1 (lowest) to 5 (highest), feedback was positive, with 99% and 96% rating 4 or 5 for the overall quality of the program and the relevance of the program content, respectively. A score of 5 was awarded by 67% of students for the ward round station; 58% for the handover station; 71% for the prescribing station, and 35% for the lessons learnt station. Following the prescribing station, students reported increased confidence in their prescribing. Preparation for practice courses and simulation are an effective and enjoyable way of easing the transition from medical student to junior doctor. Together with 'on-the-job' shadowing time, such programs can be used to improve students' confidence, competence, and ultimately patient safety and quality of care

Conservation genomics reveals possible illegal trade routes and admixture across pangolin lineages in Southeast Asia

The use of genome-wide genetic markers is an emerging approach for informing evidence-based management decisions for highly threatened species. Pangolins are the most heavily trafficked mammals across illegal wildlife trade globally, but critically endangered Sunda pangolins (Manis javanica) have not been widely studied in insular Southeast Asia. We used > 12,000 single nucleotide polymorphic markers (SNPs) to assign pangolin seizures from illegal trade of unknown origin to possible geographic sources via genetic clustering with pangolins of known origin. Our SNPs reveal three previously unrecognized genetic lineages of Sunda pangolins, possibly from Borneo, Java and Singapore/Sumatra. The seizure assignments suggest the majority of pangolins were traded from Borneo to Java. Using mitochondrial markers did not provide the same resolution of pangolin lineages, and to explore if admixture might explain these differences, we applied sophisticated tests of introgression using > 2000 SNPs to investigate secondary gene flow between each of the three Sunda pangolin lineages. It is possible the admixture which we discovered is due to human-mediated movements of pangolins. Our findings impact a range of conservation actions, including tracing patterns of trade, repatriation of rescue animals, and conservation breeding. In order to conserve genetic diversity, we suggest that, pending further research, each pangolin lineage should as a precaution be protected and managed as an evolutionarily distinct conservation unit

Structural basis for the RING catalyzed synthesis of K63 linked ubiquitin chains

This work was supported by grants from Cancer Research UK (C434/A13067), the Wellcome Trust (098391/Z/12/Z) and Biotechnology and Biological Sciences Research Council (BB/J016004/1).The RING E3 ligase catalysed formation of lysine 63 linked ubiquitin chains by the Ube2V2–Ubc13 E2 complex is required for many important biological processes. Here we report the structure of the RING domain dimer of rat RNF4 in complex with a human Ubc13~Ub conjugate and Ube2V2. The structure has captured Ube2V2 bound to the acceptor (priming) ubiquitin with Lys63 in a position that could lead to attack on the linkage between the donor (second) ubiquitin and Ubc13 that is held in the active “folded back” conformation by the RING domain of RNF4. The interfaces identified in the structure were verified by in vitro ubiquitination assays of site directed mutants. This represents the first view of the synthesis of Lys63 linked ubiquitin chains in which both substrate ubiquitin and ubiquitin-loaded E2 are juxtaposed to allow E3 ligase mediated catalysis.PostprintPeer reviewe

VeSV- Value at the end of the Sanitation Value Chain: Final Report

Bangladesh is no stranger to composting projects using both green waste and faecal sludge (FS). There have been many initiatives over the years with varying degrees of success. Similarly there have been hundreds, if not thousands of projects to improve access to latrines, latrine use and latrine management. Again there has been a great deal of success, especially in increasing the number of latrines being built. However, a key gap regarding the safe collection and processing of the waste from the pit still remains. In cases where projects have attempted addressing this, the solution has rarely been viable on a large scale. That is where this project—VeSV—is different. The aim of this project is to provide scientific evidence to support the commercial viability of collecting and composting faecal sludge for use in agriculture and horticulture. The gap between a good idea and commercial success is bridged on this project by producing primary scientific data based on qualitative and quantitative research methods and by engaging a number of stakeholders across sectors. A rigorous research was conducted to characterize raw faecal sludge material from single pit latrines in rural Bangladesh, as the starting point to develop value across the sanitation chain from processing FS material, through adding value by recovering nutrient and finally by assessing the potential commercialization of the final product in the fertilizer market. Crucially academics, NGOs, business groups and existing fertilizer, composting and latrine management companies were involved as part of our Reference Group, which helped to develop practical engineering solutions in harmony with the right and relevant context in rural Bangladesh. Our research outcomes include the development of safe methodologies for pit emptying; the assessment of people's intentions to change current operation and maintenance practices of pit latrines at household level and their willingness to participate in commercially viable and sustainable methods for FS management; the assessment of optimised engineering process for FS stabilisation and the production of a safe, high quality fertilizer that is desirable to farmers; and the identification of potential hurdles that may obstruct the widespread adoption of business models for FS fertiliser

The biological origin of linguistic diversity

In contrast with animal communication systems, diversity is characteristic of almost every aspect of human language. Languages variously employ tones, clicks, or manual signs to signal differences in meaning; some languages lack the noun-verb distinction (e.g., Straits Salish), whereas others have a proliferation of fine-grained syntactic categories (e.g., Tzeltal); and some languages do without morphology (e.g., Mandarin), while others pack a whole sentence into a single word (e.g., Cayuga). A challenge for evolutionary biology is to reconcile the diversity of languages with the high degree of biological uniformity of their speakers. Here, we model processes of language change and geographical dispersion and find a consistent pressure for flexible learning, irrespective of the language being spoken. This pressure arises because flexible learners can best cope with the observed high rates of linguistic change associated with divergent cultural evolution following human migration. Thus, rather than genetic adaptations for specific aspects of language, such as recursion, the coevolution of genes and fast-changing linguistic structure provides the biological basis for linguistic diversity. Only biological adaptations for flexible learning combined with cultural evolution can explain how each child has the potential to learn any human language

Longitudinal evaluation of quality of life in 288 patients with Neurofibromatosis 2

Advances in molecular biology have resulted in novel therapy for neurofibromatosis 2-related (NF2) tumours, highlighting the need for robust outcome measures. The disease-focused NF2 impact on quality of life (NFTI-QOL) patient questionnaire was assessed as an outcome measure for treatment in a multi-centre study. NFTI-QOL was related to clinician-rated severity (ClinSev) and genetic severity (GenSev) over repeated visits. Data were evaluated for 288 NF2 patients (n = 464 visits) attending the English national NF2 clinics from 2010 to 2012. The male-to-female ratio was equal and the mean age was 42.2 (SD 17.8) years. The analysis included NFTI-QOL eight-item score, ClinSev graded as mild, moderate, or severe, and GenSev as a rank order of the number of NF2 mutations (graded as mild, moderate, severe). The mean (SD) 8.7 (5.4) score for NFTI-QOL for either a first visit or all visits 9.2 (5.4) was similar to the published norm of 9.4 (5.5), with no significant relationships with age or gender. NFTI-QOL internal reliability was good, with a Cronbach’s alpha score of 0.85 and test re-test reliability r = 0.84. NFTI related to ClinSev (r = 0.41, p < 0.001; r = 0.46 for all visits), but weakly to GenSev (r = 0.16, p < 0.05; r = 0.15 for all visits). ClinSev related to GenSev (r = 0.41, p < 0.001; r = 0.42 for all visits). NFTI-QOL showed a good reliability and ability to detect significant longitudinal changes in the QOL of individuals. The moderate relationships of NFTI-QOL with clinician- and genetic-rated severity suggest that NFTI-QOL taps into NF2 patient experiences that are not encompassed by ClinSev rating or genotype