There is an abundance of complex dynamic systems that are critical to our daily lives and our society but that are hardly understood, and even with today's possibilities to sense and collect large amounts of experimental data, they are so complex and continuously evolving that it is unlikely that their dynamics will ever be understood in full detail. Nevertheless, through computational tools we can try to make the best possible use of the current technologies and available data. We believe that the most useful models will have to take into account the imbalance between system complexity and available data in the context of limited knowledge or multiple hypotheses. The complex system of biological cells is a prime example of such a system that is studied in systems biology and has motivated the methods presented in this paper. They were developed as part of the DARPA Rapid Threat Assessment (RTA) program, which is concerned with understanding of the mechanism of action (MoA) of toxins or drugs affecting human cells. Using a combination of Gaussian processes and abstract network modeling, we present three fundamentally different machine-learning-based approaches to learn causal relations and synthesize causal networks from high-dimensional time series data. While other types of data are available and have been analyzed and integrated in our RTA work, we focus on transcriptomics (that is gene expression) data obtained from high-throughput microarray experiments in this paper to illustrate capabilities and limitations of our algorithms. Our algorithms make different but overall relatively few biological assumptions, so that they are applicable to other types of biological data and potentially even to other complex systems that exhibit high dimensionality but are not of biological nature.
The particular artificial neural networks we use for causality detection in our primary method fall into the general class of Siamese neural networks, which are composed using two subnetworks with shared weights, each responsible for processing one of the inputs. While originally proposed for signature verification (a type of similarity detection) in @cite_13 @cite_16 , they have recently attracted renewed interest @cite_32 @cite_29 @cite_17 @cite_5 @cite_11 @cite_28 @cite_30 @cite_14 , with many applications ranging from image recognition to audio search. The key abstract feature of Siamese networks that is important for us is their capability to directly encode structural properties of a logical relation (in our case causality) and hence to enable efficient learning tailored to the domain. Although we use relatively low-complexity 1D convolutional Siamese networks suitable for time series processing, we had to resort to curriculum training to obtain a stable learning algorithm. While conventional Siamese networks are suitable for similarity relations that exhibit a structural symmetry, we also use a variation of Siamese networks to detect causality which directly encode the structural antisymmetry of this relation (when viewed as a function) in terms of the network structure.
@cite_30 @cite_11 @cite_14 @cite_28 @cite_29 @cite_32 @cite_5 @cite_16 @cite_13 @cite_17
2275111880 2219193941 2751947065 2345229200
We consider the statistical problem of learning common source of variability in data which are synchronously captured by multiple sensors, and demonstrate that Siamese neural networks can be naturally applied to this problem. This approach is useful in particular in exploratory, data-driven applications, where neither a model nor label information is available. In recent years, many researchers have successfully applied Siamese neural networks to obtain an embedding of data which corresponds to a "semantic similarity". We present an interpretation of this "semantic similarity" as learning of equivalence classes. We discuss properties of the embedding obtained by Siamese networks and provide empirical results that demonstrate the ability of Siamese networks to learn common variability. Recent innovations in training deep convolutional neural network (ConvNet) models have motivated the design of new methods to automatically learn local image descriptors. The latest deep ConvNets proposed for this task consist of a siamese network that is trained by penalising misclassification of pairs of local image patches. Current results from machine learning show that replacing this siamese by a triplet network can improve the classification accuracy in several problems, but this has yet to be demonstrated for local image descriptor learning. Moreover, current siamese and triplet networks have been trained with stochastic gradient descent that computes the gradient from individual pairs or triplets of local image patches, which can make them prone to overfitting. In this paper, we first propose the use of triplet networks for the problem of local image descriptor learning. Furthermore, we also propose the use of a global loss that minimises the overall classification error in the training set, which can improve the generalisation capability of the model. Using the UBC benchmark dataset for comparing local image descriptors, we show that the triplet network produces a more accurate embedding than the siamese network in terms of the UBC dataset errors. Moreover, we also demonstrate that a combination of the triplet and global losses produces the best embedding in the field, using this triplet network. Finally, we also show that the use of the central-surround siamese network trained with the global loss produces the best result of the field on the UBC dataset. Pre-trained models are available online at this https URL Abstract We consider the statistical problem of learning a common source of variability in data which are synchronously captured by multiple sensors, and demonstrate that Siamese neural networks can be naturally applied to this problem. This approach is useful in particular in exploratory, data-driven applications, where neither a model nor label information is available. In recent years, many researchers have successfully applied Siamese neural networks to obtain an embedding of data which corresponds to a “semantic similarity”. We present an interpretation of this “semantic similarity” as learning of equivalence classes. We demonstrate the ability of Siamese networks to learn common variability in a range of experiments on synthetic and real-world data, and demonstrate the potential of Siamese networks to provide new leads for data-driven research through unsupervised learning in cancer data. This paper introduces a novel approach to the task of data association within the context of pedestrian tracking, by introducing a two-stage learning scheme to match pairs of detections. First, a Siamese convolutional neural network (CNN) is trained to learn descriptors encoding local spatio-temporal structures between the two input image patches, aggregating pixel values and optical flow information. Second, a set of contextual features derived from the position and size of the compared input patches are combined with the CNN output by means of a gradient boosting classifier to generate the final matching probability. This learning approach is validated by using a linear programming based multi-person tracker showing that even a simple and efficient tracker may outperform much more complex models when fed with our learned matching probabilities. Results on publicly available sequences show that our method meets state-of-the-art standards in multiple people tracking.