Synthetic Gene Circuits: Design with Directed Evolution

Synthetic circuits offer great promise for generating insights into nature's underlying design principles or forward engineering novel biotechnology applications. However, construction of these circuits is not straightforward. Synthetic circuits generally consist of components optimized to function in their natural context, not in the context of the synthetic circuit. Combining mathematical modeling with directed evolution offers one promising means for addressing this problem. Modeling identifies mutational targets and limits the evolutionary search space for directed evolution, which alters circuit performance without the need for detailed biophysical information. This review examines strategies for integrating modeling and directed evolution and discusses the utility and limitations of available methods

Towards End-to-End Acoustic Localization using Deep Learning: from Audio Signal to Source Position Coordinates

This paper presents a novel approach for indoor acoustic source localization using microphone arrays and based on a Convolutional Neural Network (CNN). The proposed solution is, to the best of our knowledge, the first published work in which the CNN is designed to directly estimate the three dimensional position of an acoustic source, using the raw audio signal as the input information avoiding the use of hand crafted audio features. Given the limited amount of available localization data, we propose in this paper a training strategy based on two steps. We first train our network using semi-synthetic data, generated from close talk speech recordings, and where we simulate the time delays and distortion suffered in the signal that propagates from the source to the array of microphones. We then fine tune this network using a small amount of real data. Our experimental results show that this strategy is able to produce networks that significantly improve existing localization methods based on \textit{SRP-PHAT} strategies. In addition, our experiments show that our CNN method exhibits better resistance against varying gender of the speaker and different window sizes compared with the other methods.Comment: 18 pages, 3 figures, 8 table

Multiresolution vector quantization

Multiresolution source codes are data compression algorithms yielding embedded source descriptions. The decoder of a multiresolution code can build a source reproduction by decoding the embedded bit stream in part or in whole. All decoding procedures start at the beginning of the binary source description and decode some fraction of that string. Decoding a small portion of the binary string gives a low-resolution reproduction; decoding more yields a higher resolution reproduction; and so on. Multiresolution vector quantizers are block multiresolution source codes. This paper introduces algorithms for designing fixed- and variable-rate multiresolution vector quantizers. Experiments on synthetic data demonstrate performance close to the theoretical performance limit. Experiments on natural images demonstrate performance improvements of up to 8 dB over tree-structured vector quantizers. Some of the lessons learned through multiresolution vector quantizer design lend insight into the design of more sophisticated multiresolution codes

Convolutional neural networks: a magic bullet for gravitational-wave detection?

In the last few years, machine learning techniques, in particular convolutional neural networks, have been investigated as a method to replace or complement traditional matched filtering techniques that are used to detect the gravitational-wave signature of merging black holes. However, to date, these methods have not yet been successfully applied to the analysis of long stretches of data recorded by the Advanced LIGO and Virgo gravitational-wave observatories. In this work, we critically examine the use of convolutional neural networks as a tool to search for merging black holes. We identify the strengths and limitations of this approach, highlight some common pitfalls in translating between machine learning and gravitational-wave astronomy, and discuss the interdisciplinary challenges. In particular, we explain in detail why convolutional neural networks alone cannot be used to claim a statistically significant gravitational-wave detection. However, we demonstrate how they can still be used to rapidly flag the times of potential signals in the data for a more detailed follow-up. Our convolutional neural network architecture as well as the proposed performance metrics are better suited for this task than a standard binary classifications scheme. A detailed evaluation of our approach on Advanced LIGO data demonstrates the potential of such systems as trigger generators. Finally, we sound a note of caution by constructing adversarial examples, which showcase interesting "failure modes" of our model, where inputs with no visible resemblance to real gravitational-wave signals are identified as such by the network with high confidence.Comment: First two authors contributed equally; appeared at Phys. Rev.

Gait learning for soft microrobots controlled by light fields

Soft microrobots based on photoresponsive materials and controlled by light fields can generate a variety of different gaits. This inherent flexibility can be exploited to maximize their locomotion performance in a given environment and used to adapt them to changing conditions. Albeit, because of the lack of accurate locomotion models, and given the intrinsic variability among microrobots, analytical control design is not possible. Common data-driven approaches, on the other hand, require running prohibitive numbers of experiments and lead to very sample-specific results. Here we propose a probabilistic learning approach for light-controlled soft microrobots based on Bayesian Optimization (BO) and Gaussian Processes (GPs). The proposed approach results in a learning scheme that is data-efficient, enabling gait optimization with a limited experimental budget, and robust against differences among microrobot samples. These features are obtained by designing the learning scheme through the comparison of different GP priors and BO settings on a semi-synthetic data set. The developed learning scheme is validated in microrobot experiments, resulting in a 115% improvement in a microrobot's locomotion performance with an experimental budget of only 20 tests. These encouraging results lead the way toward self-adaptive microrobotic systems based on light-controlled soft microrobots and probabilistic learning control.Comment: 8 pages, 7 figures, to appear in the proceedings of the IEEE/RSJ International Conference on Intelligent Robots and Systems 201

Regulatory motif discovery using a population clustering evolutionary algorithm

This paper describes a novel evolutionary algorithm for regulatory motif discovery in DNA promoter sequences. The algorithm uses data clustering to logically distribute the evolving population across the search space. Mating then takes place within local regions of the population, promoting overall solution diversity and encouraging discovery of multiple solutions. Experiments using synthetic data sets have demonstrated the algorithm's capacity to find position frequency matrix models of known regulatory motifs in relatively long promoter sequences. These experiments have also shown the algorithm's ability to maintain diversity during search and discover multiple motifs within a single population. The utility of the algorithm for discovering motifs in real biological data is demonstrated by its ability to find meaningful motifs within muscle-specific regulatory sequences

Bayesian Symbol Detection in Wireless Relay Networks via Likelihood-Free Inference

This paper presents a general stochastic model developed for a class of cooperative wireless relay networks, in which imperfect knowledge of the channel state information at the destination node is assumed. The framework incorporates multiple relay nodes operating under general known non-linear processing functions. When a non-linear relay function is considered, the likelihood function is generally intractable resulting in the maximum likelihood and the maximum a posteriori detectors not admitting closed form solutions. We illustrate our methodology to overcome this intractability under the example of a popular optimal non-linear relay function choice and demonstrate how our algorithms are capable of solving the previously intractable detection problem. Overcoming this intractability involves development of specialised Bayesian models. We develop three novel algorithms to perform detection for this Bayesian model, these include a Markov chain Monte Carlo Approximate Bayesian Computation (MCMC-ABC) approach; an Auxiliary Variable MCMC (MCMC-AV) approach; and a Suboptimal Exhaustive Search Zero Forcing (SES-ZF) approach. Finally, numerical examples comparing the symbol error rate (SER) performance versus signal to noise ratio (SNR) of the three detection algorithms are studied in simulated examples

Direct exoplanet detection and characterization using the ANDROMEDA method: Performance on VLT/NaCo data

Context. The direct detection of exoplanets with high-contrast imaging requires advanced data processing methods to disentangle potential planetary signals from bright quasi-static speckles. Among them, angular differential imaging (ADI) permits potential planetary signals with a known rotation rate to be separated from instrumental speckles that are either statics or slowly variable. The method presented in this paper, called ANDROMEDA for ANgular Differential OptiMal Exoplanet Detection Algorithm is based on a maximum likelihood approach to ADI and is used to estimate the position and the flux of any point source present in the field of view. Aims. In order to optimize and experimentally validate this previously proposed method, we applied ANDROMEDA to real VLT/NaCo data. In addition to its pure detection capability, we investigated the possibility of defining simple and efficient criteria for automatic point source extraction able to support the processing of large surveys. Methods. To assess the performance of the method, we applied ANDROMEDA on VLT/NaCo data of TYC-8979-1683-1 which is surrounded by numerous bright stars and on which we added synthetic planets of known position and flux in the field. In order to accommodate the real data properties, it was necessary to develop additional pre-processing and post-processing steps to the initially proposed algorithm. We then investigated its skill in the challenging case of a well-known target, $\beta$ Pictoris, whose companion is close to the detection limit and we compared our results to those obtained by another method based on principal component analysis (PCA). Results. Application on VLT/NaCo data demonstrates the ability of ANDROMEDA to automatically detect and characterize point sources present in the image field. We end up with a robust method bringing consistent results with a sensitivity similar to the recently published algorithms, with only two parameters to be fine tuned. Moreover, the companion flux estimates are not biased by the algorithm parameters and do not require a posteriori corrections. Conclusions. ANDROMEDA is an attractive alternative to current standard image processing methods that can be readily applied to on-sky data