Localized Spectral Graph Filter Frames: A Unifying Framework, Survey of Design Considerations, and Numerical Comparison

A major line of work in graph signal processing [2] during the past 10 years has been to design new transform methods that account for the underlying graph structure to identify and exploit structure in data residing on a connected, weighted, undirected graph. The most common approach is to construct a dictionary of atoms (building block signals) and represent the graph signal of interest as a linear combination of these atoms. Such representations enable visual analysis of data, statistical analysis of data, and data compression, and they can also be leveraged as regularizers in machine learning and ill-posed inverse problems, such as inpainting, denoising, and classification.

Rate allocation and optimized decoding in inter-session network coding

Eirina Bourtsoulatze

Recent advances in data processing and communication systems have led to a continuous increase in the amount of data communicated over today’s networks. These large volumes of data pose new challenges on the current networking infrastructure that only offers a best effort mechanism for data delivery. The emergence of new distributed network architectures, such as peer-to-peer networks and wireless mesh networks, and the need for efficient data delivery mechanisms have motivated researchers to reconsider the way that information is communicated and processed in the networks. This has given rise to a new research field called network coding. The network coding paradigm departs from the traditional routing principle where information is simply relayed by the network nodes towards the destination, and introduces some intelligence in the network through coding at the intermediate nodes. This in-network data processing has been proved to substantially improve the performance of data delivery systems in terms of throughput and error resilience in networks with high path diversity. Motivated by the promising results in the network coding research, we focus in this thesis on the design of network coding algorithms for simultaneous transmission of multiple data sources in overlay networks. We investigate several problems that arise in the context of inter-session network coding, namely (i) decoding delay minimization in inter-session network coding, (ii) distributed rate allocation for inter-session network coding and (iii) correlation-aware decoding of incomplete network coded data. We start by proposing a novel framework for data delivery from multiple sources to multiple clients in an overlay wireline network, where intermediate nodes employ randomized inter-session network coding. We consider networks with high resource diversity, which creates network coding opportunities with possibly large gains in terms of throughput, delay and error robustness. However, the coding operations in the intermediate nodes must be carefully designed in order to enable efficient data delivery. We look at the problem from the decoding delay perspective and design solutions that lead to a small decoding delay at clients through proper coding and rate allocation. We cast the optimization problem as a rate allocation problem, which seeks for the coding operations that minimize the average decoding delay in the client population. We demonstrate the validity of our algorithm through simulations in representative network topologies. The results show that an effective combination of intra- and inter-session network coding based on randomized linear coding permits to reach small decoding delays and to better exploit the available network resources even in challenging network settings. Next, we design a distributed rate allocation algorithm where the users decide locally how many intra- and inter-session network coded packets should be requested from the parent nodes in order to get minimal decoding delay. The capability to take coding decisions locally with only a partial knowledge of the network statistics is of crucial importance for applications where users are organized in dynamic overlay networks. We propose a receiver-driven communication protocol that operates in two rounds. First, the users request and obtain information regarding the network conditions and packet availability in their local neighborhood. Then, every user independently optimizes the rate allocation among different possible intra- and inter-session packet combinations to be requested from its parents. We also introduce the novel concept of equivalent flows, which permits to efficiently estimate the expected number of packets that are necessary for decoding and hence to simplify the rate allocation process. Experimental results indicate that our algorithm is capable of eliminating the bottlenecks and reducing the decoding delay of users with limited resources. We further investigate the application of the proposed distributed rate allocation algorithm to the transmission of video sequences and validate the performance of our system using the NS-3 simulator. The simulation results show that the proposed rate allocation algorithm is successful in improving the quality of the delivered video compared to intra-session network coding based solutions. Finally, we investigate the problem of decoding the source information from an incomplete set of network coded data with the help of source priors in a finite algebraic field. The inability to form a complete decoding system can be often caused by transmission losses or timing constraints imposed by the application. In this case, exact reconstruction of the source data by conventional algorithms such as Gaussian elimination is not feasible; however, partial recovery of the source data may still be possible, which can be useful in applications where approximate reconstruction is informative. We use the statistical characteristics of the source data in order to perform approximate decoding. We first analyze the performance of a hypothetical maximum a posteriori decoder, which recovers the source data from an incomplete set of network coded data given the joint statistics of the sources. We derive an upper bound on the probability of erroneous source sequence decoding as a function of the system parameters. We then propose a constructive solution to the approximate decoding problem and design an iterative decoding algorithm based on message passing, which jointly considers the network coding and the correlation constraints. We illustrate the performance of our decoding algorithm through extensive simulations on synthetic and real data sets. The results demonstrate that, even by using a simple correlation model expressed as a correlation noise between pairs of sources, the original source data can be partially decoded in practice from an incomplete set of network coded symbols. Overall, this thesis addresses several important issues related to the design of efficient data delivery methods with inter-session network coding. Our novel framework for decoding delay minimization can impact the development of practical inter-session network coding algorithms that are appropriate for applications with low delay requirements. Our rate allocation algorithms are able to exploit the high resource diversity of modern networking systems and represent an effective alternative in the development of distributed communication systems. Finally, our algorithm for data recovery from incomplete network coded data using correlation priors can contribute significantly to the improvement of the delivered data quality and provide new insights towards the design of joint source and network coding algorithms.

EPFL2013

Machine Learning for Uncertainty Reduction in Biochemical Kinetic Models

Vassily Hatzimanikatis, Ljubisa Miskovic, Michaël Roger Germain Moret

The primary goal of kinetic models is to capture the systemic properties of the metabolic networks, and we need large-scale kinetic models for reliable in silico analyses of the complex dynamic behavior of metabolism. However, parameter uncertainty hinders the development of kinetic models and uncertainty levels increase with the model size. Current methods for building kinetic models within constraint-based modeling frameworks address uncertainty indirectly by integrating data from different biological origins. We recently proposed iSCHRUNK, a computational approach which combines Monte Carlo sampling methods and machine learning techniques to characterize the uncertainties and to reveal complex relationships between the kinetic parameters and the responses of the metabolic networks. Monte Carlo sampling methods allow us to exploit synergies between different data sources and generate a population of kinetic models that are consistent with the available data and physicochemical laws. The machine learning allows us to data-mine the a priori generated kinetic parameters together with the integrated datasets and derive values of kinetic parameters consistent with the observed physiology. In this work, we modified iSCHRUNK to address a design question: can we identify the kinetic parameters and their values that give rise to a desired metabolic behavior? Such information is important for a wide variety of studies ranging from biotechnology to medicine. As an illustration, we used the proposed methodology to find parameters that ensure a rate improvement of the xylose uptake (XTR) in a glucose-xylose co-utilizing S. cerevisiae strain. Our results indicate that only three kinetic parameters need to be accurately characterized to describe the studied physiology, and ultimately to design and control the desired responses of the metabolism. This framework paves the way for a new generation of methods that will systematically integrate the wealth of omics data and extract the information necessary for metabolic engineering and synthetic biology decisions.

2018

Graph-based image representation learning

Renata Khasanova

Though deep learning (DL) algorithms are very powerful for image processing tasks, they generally require a lot of data to reach their full potential. Furthermore, there is no straightforward way to impose various properties, given by the prior knowledge about the target task, on the features extracted by a DL model. Therefore, in this thesis we propose several techniques that rely on the power of graph representations to embed prior knowledge inside the learning process. This allows to reduce the solution space and leads to faster optimization convergence and higher accuracy in the representation learning. In our first work, inspired by the ability of a human to correctly classify rotated, shifted or flipped objects, we propose an algorithm that permits to inherently encode invariance to isometric transformations of objects in an image. Our DL architecture is based on graph representations and consists of three novel layers, which we refer to as graph convolutional, dynamic pooling and statistical layers. Our experiments on the image classification tasks show that our network correctly recognizes isometrically transformed objects even though such types of transformation are not seen by the network at training time. Standard DL techniques are typically not able to succeed in solving such a problem without extensive data augmentation. Then, we propose to exploit the properties of graph-based approaches to efficiently process images with various types of projective geometry. In particular, we are interested in increasingly popular omnidirectional cameras, which have a 360 degree field of view. Despite their effectiveness, such cameras create images with specific geometric properties, which require special techniques for efficient processing. We propose an efficient way of adjusting the weights of the graph edges to adapt the filter responses to the geometric image properties introduced by omnidirectional cameras. Our experiments prove that using the proposed graph with properly adjusted edge weights permits to reach better performance as compared to using regular grid graph with equal weights. Finally, the approach described above relies on the isotropic filters, which work well within our transformation invariant architecture for image classification. However, for other problems (e.g. image compression) or even when used without dynamic pooling and statistical layers that are defined within the proposed architecture, these filters are unable to efficiently encode the information about the object. Thus, we introduce a different technique based on anisotropic filters that adapt their shape and size according to the omnidirectional image geometry. The main advantage of this approach compared to the previous one is the ability to encode the orientation of an image pattern, which is important for various tasks such as image compression. Our experiments show that our approach adapts to different image projective geometries and achieves state-of-the-art performance on image classification and compression tasks. Overall we propose several methods, which combine the power of DL and graph signal processing towards incorporating prior information about the target task inside the optimization procedure. We hope that the research efforts presented in this thesis will help the development of efficient DL algorithms that can use various types of prior knowledge to make them efficient even when the available training data is scarce.

EPFL2019