Harold Soh

Genomic epidemiology of a dengue virus epidemic in urban Singapore.

ABSTRACT Dengue is one of the most important emerging diseases of humans, with no preventative vaccines or antiviral cures available at present. Although one-third of the worlds population live at risk of infection, little is known about the pattern and dynamics of dengue virus (DENV) within outbreak situations. By exploiting genomic data from an intensively studied major outbreak, we are able to describe the molecular epidemiology of DENV at a uniquely fine-scaled temporal and spatial resolution. Two DENV serotypes (DENV-1 and DENV-3), and multiple component genotypes, spread concurrently and with similar epidemiological and evolutionary profiles during the initial outbreak phase of a major dengue epidemic that took place in Singapore during 2005. Although DENV-1 and DENV-3 differed in viremia and clinical outcome, there was no evidence for adaptive evolution before, during, or after the outbreak, indicating that ecological or immunological rather than virological factors were the key determinants of epidemic dynamics.

Online spatio-temporal Gaussian process experts with application to tactile classification

In this work, we are primarily concerned with robotic systems that learn online and continuously from multi-variate data-streams. Our first contribution is a new recursive kernel, which we have integrated into a sparse Gaussian Process to yield the Spatio-Temporal Online Recursive Kernel Gaussian Process (STORK-GP). This algorithm iteratively learns from time-series, providing both predictions and uncertainty estimates. Experiments on benchmarks demonstrate that our method achieves high accuracies relative to state-of-the-art methods. Second, we contribute an online tactile classifier which uses an array of STORK-GP experts. In contrast to existing work, our classifier is capable of learning new objects as they are presented, improving itself over time. We show that our approach yields results comparable to highly-optimised offline classification methods. Moreover, we conducted experiments with human subjects in a similar online setting with true-label feedback and present the insights gained.

Discovering Unique, Low-Energy Pure Water Isomers: Memetic Exploration, Optimization, and Landscape Analysis

The discovery of low-energy stable and meta-stable molecular structures remains an important and unsolved problem in search and optimization. In this paper, we contribute two stochastic algorithms, the archiving molecular memetic algorithm (AMMA) and the archiving basin hopping algorithm (ABHA) for sampling low-energy isomers on the landscapes of pure water clusters (H2O)n. We applied our methods to two sophisticated empirical water cluster models, TTM2.1-F and OSS2, and generated archives of low-energy water isomers (H2O)n n=3-15. Our algorithms not only reproduced previously-found best minima, but also discovered new global minima candidates for sizes 9-15 on OSS2. Further numerical results show that AMMA and ABHA outperformed a baseline stochastic multistart local search algorithm in terms of convergence and isomer archival. Noting a performance differential between TTM2.1-F and OSS2, we analyzed both model landscapes to reveal that the global and local correlation properties of the empirical models differ significantly. In particular, the OSS2 landscape was less correlated and hence, more difficult to explore and optimize. Guided by our landscape analyses, we proposed and demonstrated the effectiveness of a hybrid local search algorithm, which significantly improved the sampling performance of AMMA on the larger OSS2 landscapes. Although applied to pure water clusters in this paper, AMMA and ABHA can be easily modified for subsequent studies in computational chemistry and biology. Moreover, the landscape analyses conducted in this paper can be replicated for other molecular systems to uncover landscape properties and provide insights to both physical chemists and evolutionary algorithmists.

Multiscale Approach to Explore the Potential Energy Surface of Water Clusters (H2O)nn ≤ 8

We propose a multiscale method to explore the energy landscape of water clusters. An asynchronous genetic algorithm is employed to explore the potential energy surface (PES) of OSS2 and TTM2.1-F models. Local minimum structures are collected on the fly, and the ultrafast shape recognition algorithm was used to remove duplicate structures. These structures are then refined at the B3LYP/6-31+G* level. The number of distinct local minima we found (21, 76, 369, 1443, and 3563 isomers for n = 4-8, respectively) reflects the complexity of the PES of water clusters.

Spatio-Temporal Learning With the Online Finite and Infinite Echo-State Gaussian Processes

Successful biological systems adapt to change. In this paper, we are principally concerned with adaptive systems that operate in environments where data arrives sequentially and is multivariate in nature, for example, sensory streams in robotic systems. We contribute two reservoir inspired methods: 1) the online echostate Gaussian process (OESGP) and 2) its infinite variant, the online infinite echostate Gaussian process (OIESGP) Both algorithms are iterative fixed-budget methods that learn from noisy time series. In particular, the OESGP combines the echo-state network with Bayesian online learning for Gaussian processes. Extending this to infinite reservoirs yields the OIESGP, which uses a novel recursive kernel with automatic relevance determination that enables spatial and temporal feature weighting. When fused with stochastic natural gradient descent, the kernel hyperparameters are iteratively adapted to better model the target system. Furthermore, insights into the underlying system can be gleamed from inspection of the resulting hyperparameters. Experiments on noisy benchmark problems (one-step prediction and system identification) demonstrate that our methods yield high accuracies relative to state-of-the-art methods, and standard kernels with sliding windows, particularly on problems with irrelevant dimensions. In addition, we describe two case studies in robotic learning-by-demonstration involving the Nao humanoid robot and the Assistive Robot Transport for Youngsters (ARTY) smart wheelchair.

Iterative temporal learning and prediction with the sparse online echo state gaussian process

In this work, we contribute the online echo state gaussian process (OESGP), a novel Bayesian-based online method that is capable of iteratively learning complex temporal dynamics and producing predictive distributions (instead of point predictions). Our method can be seen as a combination of the echo state network with a sparse approximation of Gaussian processes (GPs). Extensive experiments on the one-step prediction task on well-known benchmark problems show that OESGP produced statistically superior results to current online ESNs and state-of-the-art regression methods. In addition, we characterise the benefits (and drawbacks) associated with the considered online methods, specifically with regards to the trade-off between computational cost and accuracy. For a high-dimensional action recognition task, we demonstrate that OESGP produces high accuracies comparable to a recently published graphical model, while being fast enough for real-time interactive scenarios.

Incrementally Learning Objects by Touch: Online Discriminative and Generative Models for Tactile-Based Recognition

Human beings not only possess the remarkable ability to distinguish objects through tactile feedback but are further able to improve upon recognition competence through experience. In this work, we explore tactile-based object recognition with learners capable of incremental learning. Using the sparse online infinite Echo-State Gaussian process (OIESGP), we propose and compare two novel discriminative and generative tactile learners that produce probability distributions over objects during object grasping/ palpation. To enable iterative improvement, our online methods incorporate training samples as they become available. We also describe incremental unsupervised learning mechanisms, based on novelty scores and extreme value theory, when teacher labels are not available. We present experimental results for both supervised and unsupervised learning tasks using the iCub humanoid, with tactile sensors on its five-fingered anthropomorphic hand, and 10 different object classes. Our classifiers perform comparably to state-of-the-art methods (C4.5 and SVM classifiers) and findings indicate that tactile signals are highly relevant for making accurate object classifications. We also show that accurate “early” classifications are possible using only 20-30 percent of the grasp sequence. For unsupervised learning, our methods generate high quality clusterings relative to the widely-used sequential k-means and self-organising map (SOM), and we present analyses into the differences between the approaches.

Microsimulation of Demand and Supply of Autonomous Mobility On Demand

Agent-based models have gained wide acceptance in transportation planning because with increasing computational power, large-scale people-centric mobility simulations are possible. Several modeling efforts have been reported in the literature on the demand side (with sophisticated activity-based models that focus on an individual’s day activity patterns) and on the supply side (with detailed representation of network dynamics through simulation-based dynamic traffic assignment models). This paper proposes an extension to a state-of-the-art integrated agent-based demand and supply model—SimMobility—for the design and evaluation of autonomous vehicle systems. SimMobility integrates various mobility-sensitive behavioral models in a multiple time-scale structure comprising three simulation levels: (a) a long-term level that captures land use and economic activity, with special emphasis on accessibility; (b) a midterm level that handles agents’ activities and travel patterns; and (c) a short-term level that simulates movement of agents, operational systems, and decisions at a microscopic granularity. In that context, this paper proposes several extensions at the short-term and midterm levels to model and simulate autonomous vehicle systems and their effects on travel behavior. To showcase these features, the first-cut results of a hypothetical on-demand service with autonomous vehicles in a car-restricted zone of Singapore are presented. SimMobility was successfully used in an integrated manner to test and assess the performance of different autonomous vehicle fleet sizes and parking station configurations and to uncover changes in individual mobility patterns, specifically in regard to modal shares, routes, and destinations.

Evolving policies for multi-reward partially observable markov decision processes (MR-POMDPs)

Plans and decisions in many real-world scenarios are made under uncertainty and to satisfy multiple, possibly conflicting, objectives. In this work, we contribute the multi-reward partially-observable Markov decision process (MR-POMDP) as a general modelling framework. To solve MR-POMDPs, we present two hybrid (memetic) multi-objective evolutionary algorithms that generate non-dominated sets of policies (in the form of stochastic finite state controllers). Performance comparisons between the methods on multi-objective problems in robotics (with 2, 3 and 5 objectives), web-advertising (with 3, 4 and 5 objectives) and infectious disease control (with 3 objectives), revealed that memetic variants outperformed their original counterparts. We anticipate that the MR-POMDP along with multi-objective evolutionary solvers will prove useful in a variety of theoretical and real-world applications.

Robustness of scale-free networks under rewiring operations

Scale-free networks have strong tolerance against random failures yet are fragile under intentional attacks. Existing results show that the network robustness can also be affected by its correlation profile. Specifically, scale-free networks with larger assortativity coefficients generally tend to be more robust against intentional attack. In this letter, we reveal some interesting different observations. By proposing a simple rewiring method which does not change any nodal degree, we show that network robustness can be steadily enhanced at a slightly decreased assortativity coefficient. The tolerance against random failures meanwhile remains largely unaffected. Such observations demonstrate the more complicated relationship between network robustness and its assortativity level, as well as some new possibilities of network enhancement and protection.