Fine-Grain Checkpointing with In-Cache-Line Logging

Non-Volatile Memory offers the possibility of implementing high-performance, durable data structures. However, achieving performance comparable to well-designed data structures in non-persistent (transient) memory is difficult, primarily because of the cost of ensuring the order in which memory writes reach NVM. Often, this requires flushing data to NVM and waiting a full memory round-trip time. In this paper, we introduce two new techniques: Fine-Grained Checkpointing, which ensures a consistent, quickly recoverable data structure in NVM after a system failure, and In-Cache-Line Logging, an undo-logging technique that enables recovery of earlier state without requiring cache-line flushes in the normal case. We implemented these techniques in the Masstree data structure, making it persistent and demonstrating the ease of applying them to a highly optimized system and their low (5.9-15.4\%) runtime overhead cost.Comment: In 2019 Architectural Support for Programming Languages and Operating Systems (ASPLOS 19), April 13, 2019, Providence, RI, US

A Toolkit of Engineered Recombinational Balancers in C. elegans

Dejima and colleagues report using CRISPR/Cas9 to generate a new collection of greatly improved balancer chromosomes in the standard laboratory nematode Caenorhabditis elegans, using methods previously reported by the same laboratory, expanding the set of C. elegans balancers to cover nearly 90% of coding genes

Capturing trade-offs between daily scheduling choices

We propose a new modelling approach for daily activity scheduling which integrates the different daily scheduling choice dimensions (activity participation, location, schedule, duration and transportation mode) into a single optimisation problem. The fundamental behavioural principle behind our approach is that individuals schedule their day to maximise their overall derived utility from the activities they complete, according to their individual needs, constraints, and preferences. By combining multiple choices into a single optimisation problem, our framework is able to capture the complex trade-offs between scheduling decisions for multiple activities. These trade-offs could include how spending longer in one activity will reduce the time-availability for other activities or how the order of activities determines the travel-times. The implemented framework takes as input a set of considered activities, with associated locations and travel modes, and uses these to produce empirical distributions of individual schedules from which different daily schedules can be drawn. The model is illustrated using historic trip diary data from the Swiss Mobility and Transport Microcensus. The results demonstrate the ability of the proposed framework to generate complex and realistic distributions of starting time and duration for different activities within the tight time constraints. The generated schedules are then compared to the aggregate distributions from the historical data to demonstrate the feasibility and flexibility of our approach

Assessing the discrepancies between recorded and commonly assumed journey times in London

Transport models for infrastructure investment and operations planning make use of generalised trip cost to predict travel choice decisions. In cities, the most important factors in the generalised cost is trip duration. When calibrating such models to achieve simulation fidelity, observed data such as the choice of destination and means of travel recorded in travel surveys are used in estimating model parameters. Ideally, observed travel durations should also be used in the model estimation. However, in the past it was infeasible to record the actual trip durations to any degree of accuracy in travel surveys. Trip durations derived from a transport network model were commonly assumed to be sufficiently representative. Increasing availability of better recorded trip durations from travel surveys and better modelled trip durations from online mapping present the promise of significant improvements in the fidelity of transport models. As a preamble to adopting such data, we investigate how the best developed recording of actual trip durations from the London Travel Demand Survey compares with the most advanced trip duration modelling from Google Map travel directions API. We find clear discrepancies between the two, with the discrepancies varying systematically for different means and purposes of travel. The magnitude of the discrepancies is greater than can be attributed to randomness or noise. The systematic nature of the discrepancies suggests that transport network modelling even in its advanced form still has a long way to go to represent the observed patterns of behaviour, particularly for non-commuting journeys which account for about 80% of all trips made in cities. Since the discrepancies may create a systematic bias in the model parameters, it is of critical importance to understand them better in future analysis.This research is an update from Tim Hillel’s MRes thesis which was undertaken as part of the Future Infrastructure and Built Environment Centre for Doctoral Training at the University of Cambridge, which is funded by the UK Engineering and Physical Sciences Research Council (EPSRC)

Estimating flexibility preferences to resolve temporal scheduling conflicts in activity-based modelling

This paper presents a novel activity-based demand model that combines an optimisation framework for continuous temporal scheduling decisions (i.e. activity timings and durations) with traditional discrete choice models for non-temporal choice dimensions (i.e. activity participation, number and type of tours, and destinations). The central idea of our approach is that individuals resolve temporal scheduling conflicts that arise from overlapping activities, e.g. needing to work and desiring to shop at the same time, in order to maximise their daily utility. Flexibility parameters capture behavioural preferences that penalise deviations from desired timings. This framework has three advantages over existing activity-based modelling approaches: (i) the time conflicts between different temporal scheduling decisions including the activity sequence are treated jointly; (ii) flexibility parameters follow a utility maximisation approach; and (iii) the framework can be used to estimate and simulate a city-scale case study in reasonable time. We introduce an estimation routine that allows flexibility parameters to be estimated using real-world observations as well as a simulation routine to efficiently resolve temporal conflicts using an optimisation model. The framework is applied to the full-time workers of a synthetic population for the city of Lausanne, Switzerland. We validate the model results against reported schedules. The results demonstrate the capabilities of our approach to reproduce empirical observations in a real-world case study

Assisted specification of discrete choice models

Determining appropriate utility specifications for discrete choice models is time-consuming and prone to errors. With the availability of larger and larger datasets, as the number of possible specifications exponentially grows with the number of variables under consideration, the analysts need to spend increasing amounts of time on searching for good models through trial-and-error, while expert knowledge is required to ensure these models are sound. This paper proposes an algorithm that aims at assisting modelers in their search. Our approach translates the task into a multi-objective combinatorial optimization problem and makes use of a variant of the variable neighborhood search algorithm to generate sets of promising model specifications. We apply the algorithm both to semi-synthetic data and to real mode choice datasets as a proof of concept. The results demonstrate its ability to provide relevant insights in reasonable amounts of time so as to effectively assist the modeler in developing interpretable and powerful models

Functional Neural Correlates of Attentional Deficits in Amnestic Mild Cognitive Impairment

Although amnestic mild cognitive impairment (aMCI; often considered a prodromal phase of Alzheimer’s disease, AD) is most recognized by its implications for decline in memory function, research suggests that deficits in attention are present early in aMCI and may be predictive of progression to AD. The present study used functional magnetic resonance imaging to examine differences in the brain during the attention network test between 8 individuals with aMCI and 8 neurologically healthy, demographically matched controls. While there were no significant behavioral differences between groups for the alerting and orienting functions, patients with aMCI showed more activity in neural regions typically associated with the networks subserving these functions (e.g., temporoparietal junction and posterior parietal regions, respectively). More importantly, there were both behavioral (i.e., greater conflict effect) and corresponding neural deficits in executive control (e.g., less activation in the prefrontal and anterior cingulate cortices). Although based on a small number of patients, our findings suggest that deficits of attention, especially the executive control of attention, may significantly contribute to the behavioral and cognitive deficits of aMCI

Distributed Edge Connectivity in Sublinear Time

We present the first sublinear-time algorithm for a distributed message-passing network sto compute its edge connectivity $\lambda$ exactly in the CONGEST model, as long as there are no parallel edges. Our algorithm takes $\tilde O(n^{1-1/353}D^{1/353}+n^{1-1/706})$ time to compute $\lambda$ and a cut of cardinality $\lambda$ with high probability, where $n$ and $D$ are the number of nodes and the diameter of the network, respectively, and $\tilde O$ hides polylogarithmic factors. This running time is sublinear in $n$ (i.e. $\tilde O(n^{1-\epsilon})$) whenever $D$ is. Previous sublinear-time distributed algorithms can solve this problem either (i) exactly only when $\lambda=O(n^{1/8-\epsilon})$ [Thurimella PODC'95; Pritchard, Thurimella, ACM Trans. Algorithms'11; Nanongkai, Su, DISC'14] or (ii) approximately [Ghaffari, Kuhn, DISC'13; Nanongkai, Su, DISC'14]. To achieve this we develop and combine several new techniques. First, we design the first distributed algorithm that can compute a $k$-edge connectivity certificate for any $k=O(n^{1-\epsilon})$ in time $\tilde O(\sqrt{nk}+D)$. Second, we show that by combining the recent distributed expander decomposition technique of [Chang, Pettie, Zhang, SODA'19] with techniques from the sequential deterministic edge connectivity algorithm of [Kawarabayashi, Thorup, STOC'15], we can decompose the network into a sublinear number of clusters with small average diameter and without any mincut separating a cluster (except the `trivial' ones). Finally, by extending the tree packing technique from [Karger STOC'96], we can find the minimum cut in time proportional to the number of components. As a byproduct of this technique, we obtain an $\tilde O(n)$-time algorithm for computing exact minimum cut for weighted graphs.Comment: Accepted at 51st ACM Symposium on Theory of Computing (STOC 2019

Transgene-Free Genome Editing in Caenorhabditis elegans Using CRISPR-Cas

CRISPR-Cas is an efficient method for genome editing in organisms from bacteria to human cells. We describe a transgene-free method for CRISPR-Cas-mediated cleavage in nematodes, enabling RNA-homology-targeted deletions that cause loss of gene function; analysis of whole-genome sequencing indicates that the nuclease activity is highly specific