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Yoli Shavit, Boyan Yordanov, Sara-Jane Dunn, Christoph M. Wintersteiger, Youssef Hamadi, and Hillel Kugler

A fundamental question in biology is how cells change into specific cell types with unique roles throughout development. This process can be viewed as a program prescribing the system dynamics, governed by a network of genetic interactions. Recent experimental evidence suggests that these networks are not fixed but rather change their topology as cells develop. Currently, there are limited tools for the construction and analysis of such self-modifying biological programs. We introduce Switching Gene...

Publication details
Date: 1 September 2015
Type: Inproceeding
Publisher: Springer
Young-Bum Kim, Karl Stratos, Ruhi Sarikaya, and Minwoo Jeong

In natural language understanding (NLU), a user utterance can be labeled differently depending on the domain or application (e.g., weather vs. calendar). Standard domain adaptation techniques are not directly applicable to take advantage of the existing annotations because they assume that the label set is invariant. We propose a solution based on label embeddings induced from canonical correlation analysis (CCA) that reduces the problem to a standard domain adaptation task and allows use of a number of...

Publication details
Date: 29 August 2015
Type: Proceedings
Publisher: ACL – Association for Computational Linguistics
Young-Bum Kim, Karl Stratos, and Ruhi Sarikaya

In this paper, we apply the concept of pre-training to hidden-unit conditional random
fields (HUCRFs) to enable learning on unlabeled data. We present a simple yet effective pre-training technique that learns to associate words with their clusters, which are obtained in an unsupervised manner. The learned parameters are then used to initialize the supervised learning process. We also propose a word clustering technique based on canonical correlation analysis (CCA) that is sensitive to multiple word...

Publication details
Date: 28 August 2015
Type: Proceedings
Publisher: ACL – Association for Computational Linguistics
Young-Bum Kim, Karl Stratos, Xiaohu Liu, and Ruhi Sarikaya

In this paper, we introduce the task of selecting compact lexicon from large, noisy gazetteers.
This scenario arises often in practice, in particular spoken language understanding (SLU).
We propose a simple and effective solution based on matrix decomposition techniques:
canonical correlation analysis (CCA) and rank-revealing QR (RRQR) factorization. CCA is first used to derive low-dimensional gazetteer embeddings from domain-specific search logs. Then RRQR is used to find a subset of...

Publication details
Date: 27 August 2015
Type: Proceedings
Publisher: ACL – Association for Computational Linguistics
Dan Alistarh and Rati Gelashvili

Population protocols are networks of finite-state agents, interacting randomly, and updating their state using simple rules. Despite their extreme simplicity, these systems have been shown to cooperatively perform complex computational tasks, such as simulating register machines to compute standard arithmetic functions. The election of a unique leader agent is a key requirement in such computational constructions. Yet, the fastest currently known population protocol for electing a leader only...

Publication details
Date: 1 July 2015
Type: Inproceeding
Publisher: Springer
Rasmus Petersen, Matthew R. Lakin, and Andrew Phillips

DNA nanotechnology is a promising approach for engineering computation at the nanoscale, with potential applications in biofabrication and intelligent nanomedicine. DNA strand displacement is a general strategy for implementing a broad range of nanoscale computations, including any computation that can be expressed as a chemical reaction network. Modelling and analysis of DNA strand displacement systems is an important part of the design process, prior to experimental realisation. As experimental...

Publication details
Date: 1 July 2015
Type: Article
Publisher: In press
Jelte Mense, Paul I. Palmer, and Matthew J. Smith

Western Europe has experienced several large riots over the last decade (2005-2015), such as the Paris riots in 2005, the London riots in 2011 and the Stockholm riots in 2013. Such acts of civil violence generally lead to big social and economic costs. Being able to quantitatively describe riots can aid current understanding of the underlying mechanisms, and potentially help to identify and mitigate risks associated with these events. We describe a general agent-based model of riots and demonstrate how...

Publication details
Date: 9 June 2015
Type: Proceedings
Publisher: Springer
Matthew R. Lakin, Darko Stefanovic, and Andrew Phillips

Chemical reaction networks are a powerful means of specifying the intended behaviour of synthetic biochemical systems. A high-level formal specification, expressed as a chemical reaction network, may be compiled into a lower-level encoding, which can be directly implemented in wet chemistry and may itself be expressed as a chemical reaction network. Here we present conditions under which a lower-level encoding correctly emulates the sequential dynamics of a high-level chemical reaction network. We...

Publication details
Date: 1 June 2015
Type: Article
Publisher: In press
Neil Dalchau, Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, and John Reif

Molecular devices made of nucleic acids can perform complex information processing tasks at the nanoscale, with potential applications in biofabrication and smart therapeutics. However, limitations in the speed and scalability of such devices in a well-mixed setting can significantly affect their performance. In this paper, we propose designs for localized circuits involving DNA molecules that are arranged on addressable substrates and interact via hybridization reactions. We propose designs for...

Publication details
Date: 1 June 2015
Type: Article
Publisher: In press
Michael Pedersen, Andrew Phillips, and Gordon D. Plotkin

Rule-based languages such as Kappa excel in their support for handling the combinatorial complexities prevalent in many biological systems, including signalling pathways. But Kappa provides little structure for organising rules, and large models can therefore be hard to read and maintain. This paper introduces a high-level, modular extension of Kappa called LBS-Kappa. We demonstrate the constructs of the language through examples and three case studies: a chemotaxis switch ring, a MAPK cascade, and an...

Publication details
Date: 1 June 2015
Type: Article
Publisher: In press
Young-Bum Kim, Minwoo Jeong, Karl Stratos, and Ruhi Sarikaya

In this paper, we apply a weakly-supervised learning approach for slot tagging using conditional random fields by exploiting web search click logs. We extend the constrained lattice training of Tackstrom et al. (2013) to ¨ non-linear conditional random fields in which latent variables mediate between observations and labels. When combined with a novel initialization scheme that leverages unlabeled data, we show that our method gives significant improvement over strong supervised and weakly-supervised...

Publication details
Date: 1 June 2015
Type: Proceedings
Publisher: ACL – Association for Computational Linguistics
Íñigo Goiri, Thu D. Nguyen, and Ricardo Bianchini
Publication details
Date: 1 March 2015
Type: Inproceeding
Publication details
Date: 1 March 2015
Type: Article
Sonia Kéfi, Eric L Berlow, Evie A Wieters, Lucas N Joppa, Spencer A Wood, Ulrich Brose, and Sergio A Navarrete
Publication details
Date: 1 March 2015
Type: Article
Publisher: Ecological Society of America
Number: 1
Publication details
Date: 1 March 2015
Type: Article
Number: 3
Piero Visconti, Michel Bakkenes, Daniele Baisero, Thomas Brooks, Stuart HM Butchart, Lucas Joppa, Rob Alkemade, Moreno Di Marco, Luca Santini, Michael Hoffmann, and others
Publication details
Date: 1 March 2015
Type: Article
Sebastián Martinuzzi, Volker C Radeloff, Lucas N Joppa, Christopher M Hamilton, David P Helmers, Andrew J Plantinga, and David J Lewis
Publication details
Date: 1 March 2015
Type: Article
Publisher: Elsevier
Sadia E Ahmed, Greg McInerny, Kenton O'Hara, Richard Harper, Lara Salido, Stephen Emmott, and Lucas N Joppa
Publication details
Date: 1 February 2015
Type: Article
Stuart HM Butchart, Martin Clarke, Robert J Smith, Rachel E Sykes, Jörn PW Scharlemann, Mike Harfoot, Graeme M Buchanan, Ariadne Angulo, Andrew Balmford, Bastian Bertzky, others, and lucas joppa
Publication details
Date: 1 February 2015
Type: Article
sadia ahmed, Greg McInerny, Kenton O'Hara, Richard Harper, Lara Salido, Stephen Emmott, and Lucas Joppa

Aim: Software use is ubiquitous in the species distribution modelling (SDM) domain; nearly every scientist working on SDM either uses or develops specialist SDM software; however, little is formally known about the prevalence or preference of one software over another. We seek to provide, for the first time, a ‘snapshot’ of SDM users, the methods they use and the questions they answer.

Location: Global.

Methods: We conducted a survey of over 300 SDM scientists to capture a snapshot of...

Publication details
Date: 1 January 2015
Type: Article
Publisher: Wiley
Camille Guilbaud, Neil Dalchau, Drew Purves, and Lindsay Turnbull
  • Flowering time in annual plants has large fitness consequences and has been the focus of theoretical and empirical study. Previous theory has concluded that flowering time has evolved over evolutionary time to maximize fitness over a particular season length.
  • We introduce a new model where flowering is cued by a growth-rate rule (peak nitrogen (N)). Flowering is therefore sensitive to physiological parameters and to current environmental conditions, including N availability and the...
Publication details
Date: 1 January 2015
Type: Article
Publisher: New Phytologist Trust
Number: 2
Oleksandra Hararuk and Matthew J. Smith

Soil is the largest terrestrial pool of carbon (C), storing 1395-2293 Pg C. Under changing climate a large portion of soil C could potentially transfer back to the atmosphere as CO₂, pushing the earth system into a positive feedback loop between increasing soil CO₂ emissions and rising temperatures. We rely on models to estimate soil responses to climate change; however recent global carbon cycle model intercomparisons have shown poor model performance in capturing C cycle processes in the soil. To gain...

Publication details
Date: 15 December 2014
Type: Proceedings
Matthew J. Smith, Stephen Emmott, Drew W. Purves, Lucas N. Joppa, and Vassily Lyutsarev

In scientific research and development, emphasis is placed on research over development. A significant cost is that the two-way interaction between scientific insights and societal needs does not function effectively to lead to impacts in the wider world. We simply must embrace new software and hardware approaches if we are to provide timely predictive information to address global problems, support businesses and inform governments and citizens. The Microsoft Research Computational Science Lab has been...

Publication details
Date: 15 December 2014
Type: Proceedings
Katherine E Todd-Brown, Yiqi Luo, James Tremper Randerson, Stephen D. Allison, and Matthew J. Smith

Soil carbon stocks have the potential to be a strong source or sink for carbon dioxide over the next century, playing a critical role in climate change. These stocks are the result of small differences between much larger primary carbon fluxes: gross primary production, litter fall, autotrophic respiration and heterotrophic respiration. There was little agreement on predicted soil carbon stocks between Earth system models (ESMs) in the most recent Climate Model Intercomparison Project. Predicted...

Publication details
Date: 15 December 2014
Type: Proceedings
Silvia Caldararu, Drew W. Purves, and Matthew J. Smith

Simple mechanistic models of vegetation processes are essential both to our understanding of plant behaviour and to our ability to predict future changes in vegetation. One concept that can take us closer to such models is that of plant optimality, the hypothesis that plants aim to achieve an optimal state. Conceptually, plant optimality can be either structural or functional optimality. A structural constraint would mean that plants aim to achieve a certain structural characteristic such as an...

Publication details
Date: 15 December 2014
Type: Proceedings
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