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Network Identifiability from Intrinsic Noise Goncalves, Jorge ; ; in IEEE Transactions on Automatic Control (in press) Detailed reference viewed: 200 (18 UL)Sparse Network Identifiability via Compressed Sensing Goncalves, Jorge ; ; et al in Automatica (in press) Detailed reference viewed: 180 (13 UL)Experimental design trade-offs for gene regulatory network inference: an in silico study of the yeast Saccharomyces cerevisiae cell cycle Markdahl, Johan ; Colombo, Nicolo ; Thunberg, Johan et al in Proceedings of the 56th IEEE Conference on Decision and Control (in press) Time-series of high throughput gene sequencing data intended for gene regulatory network (GRN) inference are often short due to the high costs of sampling cell systems. Moreover, experimentalists lack a ... [more ▼] Time-series of high throughput gene sequencing data intended for gene regulatory network (GRN) inference are often short due to the high costs of sampling cell systems. Moreover, experimentalists lack a set of quantitative guidelines that prescribe the minimal number of samples required to infer a reliable GRN model. We study the temporal resolution of data vs.quality of GRN inference in order to ultimately overcome this deficit. The evolution of a Markovian jump process model for the Ras/cAMP/PKA pathway of proteins and metabolites in the G1 phase of the Saccharomyces cerevisiae cell cycle is sampled at a number of different rates. For each time-series we infer a linear regression model of the GRN using the LASSO method. The inferred network topology is evaluated in terms of the area under the precision-recall curve (AUPR). By plotting the AUPR against the number of samples, we show that the trade-off has a, roughly speaking, sigmoid shape. An optimal number of samples corresponds to values on the ridge of the sigmoid. [less ▲] Detailed reference viewed: 37 (5 UL)A minimal realization technique for the dynamical structure function of a class of LTI systems Goncalves, Jorge ; ; et al in IEEE Transactions on Control of Network Systems (in press) Detailed reference viewed: 104 (3 UL)Bayesian variable selection in linear dynamical systems Aalto, Atte ; Goncalves, Jorge E-print/Working paper (2018) We develop a method for reconstructing regulatory interconnection networks between variables evolving according to a linear dynamical system. The work is motivated by the problem of gene regulatory ... [more ▼] We develop a method for reconstructing regulatory interconnection networks between variables evolving according to a linear dynamical system. The work is motivated by the problem of gene regulatory network inference, that is, finding causal effects between genes from gene expression time series data. In biological applications, the typical problem is that the sampling frequency is low, and consequentially the system identification problem is ill-posed. The low sampling frequency also makes it impossible to estimate derivatives directly from the data. We take a Bayesian approach to the problem, as it offers a natural way to incorporate prior information to deal with the ill-posedness, through the introduction of sparsity promoting prior for the underlying dynamics matrix. It also provides a framework for modelling both the process and measurement noises. We develop Markov Chain Monte Carlo samplers for the discrete-valued zero-structure of the dynamics matrix, and for the continuous-time trajectory of the system. [less ▲] Detailed reference viewed: 31 (2 UL)Almost Global Consensus on the n-Sphere Markdahl, Johan ; Thunberg, Johan ; Goncalves, Jorge in IEEE Transactions on Automatic Control (2018) This paper establishes novel results regarding the global convergence properties of a large class of consensus protocols for multi-agent systems that evolve in continuous time on the n-dimensional unit ... [more ▼] This paper establishes novel results regarding the global convergence properties of a large class of consensus protocols for multi-agent systems that evolve in continuous time on the n-dimensional unit sphere or n-sphere. For any connected, undirected graph and all n 2 N\{1}, each protocol in said class is shown to yield almost global consensus. The feedback laws are negative gradients of Lyapunov functions and one instance generates the canonical intrinsic gradient descent protocol. This convergence result sheds new light on the general problem of consensus on Riemannian manifolds; the n-sphere for n 2 N\{1} differs from the circle and SO(3) where the corresponding protocols fail to generate almost global consensus. Moreover, we derive a novel consensus protocol on SO(3) by combining two almost globally convergent protocols on the n-sphere for n in {1, 2}. Theoretical and simulation results suggest that the combined protocol yields almost global consensus on SO(3). [less ▲] Detailed reference viewed: 23 (3 UL)PaCER - A fully automated method for electrode trajectory and contact reconstruction in deep brain stimulation Husch, Andreas ; ; et al in NeuroImage: Clinical (2018), 17 Abstract Deep brain stimulation (DBS) is a neurosurgical intervention where electrodes are permanently implanted into the brain in order to modulate pathologic neural activity. The post-operative ... [more ▼] Abstract Deep brain stimulation (DBS) is a neurosurgical intervention where electrodes are permanently implanted into the brain in order to modulate pathologic neural activity. The post-operative reconstruction of the DBS electrodes is important for an efficient stimulation parameter tuning. A major limitation of existing approaches for electrode reconstruction from post-operative imaging that prevents the clinical routine use is that they are manual or semi-automatic, and thus both time-consuming and subjective. Moreover, the existing methods rely on a simplified model of a straight line electrode trajectory, rather than the more realistic curved trajectory. The main contribution of this paper is that for the first time we present a highly accurate and fully automated method for electrode reconstruction that considers curved trajectories. The robustness of our proposed method is demonstrated using a multi-center clinical dataset consisting of N=44 electrodes. In all cases the electrode trajectories were successfully identified and reconstructed. In addition, the accuracy is demonstrated quantitatively using a high-accuracy phantom with known ground truth. In the phantom experiment, the method could detect individual electrode contacts with high accuracy and the trajectory reconstruction reached an error level below 100 μm (0.046 ± 0.025 mm). An implementation of the method is made publicly available such that it can directly be used by researchers or clinicians. This constitutes an important step towards future integration of lead reconstruction into standard clinical care. [less ▲] Detailed reference viewed: 73 (23 UL)Post-operative deep brain stimulation assessment: Automatic data integration and report generation Husch, Andreas ; ; et al in Brain Stimulation (2018) Background The gold standard for post-operative deep brain stimulation (DBS) parameter tuning is a monopolar review of all stimulation contacts, a strategy being challenged by recent developments of more ... [more ▼] Background The gold standard for post-operative deep brain stimulation (DBS) parameter tuning is a monopolar review of all stimulation contacts, a strategy being challenged by recent developments of more complex electrode leads. Objective Providing a method to guide clinicians on DBS assessment and parameter tuning by automatically integrating patient individual data. Methods We present a fully automatic method for visualization of individual deep brain structures in relation to a DBS lead by combining precise electrode recovery from post-operative imaging with individual estimates of deep brain morphology utilizing a 7T-MRI deep brain atlas. Results The method was evaluated on 20 STN DBS cases. It demonstrated robust automatic creation of 3D-enabled PDF reports visualizing electrode to brain structure relations and proved valuable in detecting miss placed electrodes. Discussion Automatic DBS assessment is feasible and can conveniently provide clinicians with relevant information on DBS contact positions in relation to important anatomical structures. [less ▲] Detailed reference viewed: 29 (2 UL)On definition and inference of nonlinear Boolean dynamic networks Yue, Zuogong ; Thunberg, Johan ; et al in On definition and inference of nonlinear Boolean dynamic networks (2017, December) Network reconstruction has become particularly important in systems biology, and is now expected to deliver information on causality. Systems in nature are inherently nonlinear. However, for nonlinear ... [more ▼] Network reconstruction has become particularly important in systems biology, and is now expected to deliver information on causality. Systems in nature are inherently nonlinear. However, for nonlinear dynamical systems with hidden states, how to give a useful definition of dynamic networks is still an open question. This paper presents a useful definition of Boolean dynamic networks for a large class of nonlinear systems. Moreover, a robust inference method is provided. The well-known Millar-10 model in systems biology is used as a numerical example, which provides the ground truth of causal networks for key mRNAs involved in eukaryotic circadian clocks. In addition, as second contribution of this paper, we suggest definitions of linear network identifiability, which helps to unify the available work on network identifiability. [less ▲] Detailed reference viewed: 37 (0 UL)Distributed synchronization of euclidean transformations with guaranteed convergence Thunberg, Johan ; Goncalves, Jorge ; in 56th IEEE Conference on Decision and Control (2017, December) This paper addresses synchronization of Euclidean transformations over graphs. Synchronization in this context, unlike rendezvous or consensus, means that composite transformations over loops in the graph ... [more ▼] This paper addresses synchronization of Euclidean transformations over graphs. Synchronization in this context, unlike rendezvous or consensus, means that composite transformations over loops in the graph are equal to the identity. Given a set of non-synchronized transformations, the problem at hand is to find a set of synchronized transformations approximating well the non-synchronized transformations. This is formulated as a nonlinear least-squares optimization problem. We present a distributed synchronization algorithm that converges to the optimal solution to an approximation of the optimization problem. This approximation stems from a spectral relaxation of the rotational part on the one hand and from a separation between the rotations and the translations on the other. The method can be used to distributively improve the measurements obtained in sensor networks such as networks of cameras where pairwise relative transformations are measured. The convergence of the method is verified in numerical simulations. [less ▲] Detailed reference viewed: 19 (0 UL)Distributed methods for synchronization of orthogonal matrices over graphs Thunberg, Johan ; Bernard, Florian ; Goncalves, Jorge in Automatica (2017), 80 This paper addresses the problem of synchronizing orthogonal matrices over directed graphs. For synchronized transformations (or matrices), composite transformations over loops equal the identity. We ... [more ▼] This paper addresses the problem of synchronizing orthogonal matrices over directed graphs. For synchronized transformations (or matrices), composite transformations over loops equal the identity. We formulate the synchronization problem as a least-squares optimization problem with nonlinear constraints. The synchronization problem appears as one of the key components in applications ranging from 3D-localization to image registration. The main contributions of this work can be summarized as the introduction of two novel algorithms; one for symmetric graphs and one for graphs that are possibly asymmetric. Under general conditions, the former has guaranteed convergence to the solution of a spectral relaxation to the synchronization problem. The latter is stable for small step sizes when the graph is quasi-strongly connected. The proposed methods are verified in numerical simulations. [less ▲] Detailed reference viewed: 47 (3 UL)Shape-aware surface reconstruction from sparse 3D point-clouds Bernard, Florian ; Salamanca Mino, Luis ; Thunberg, Johan et al in Medical Image Analysis (2017), 38 The reconstruction of an object’s shape or surface from a set of 3D points plays an important role in medical image analysis, e.g. in anatomy reconstruction from tomographic measurements or in the process ... [more ▼] The reconstruction of an object’s shape or surface from a set of 3D points plays an important role in medical image analysis, e.g. in anatomy reconstruction from tomographic measurements or in the process of aligning intra-operative navigation and preoperative planning data. In such scenarios, one usually has to deal with sparse data, which significantly aggravates the problem of reconstruction. However, medical applications often provide contextual information about the 3D point data that allow to incorporate prior knowledge about the shape that is to be reconstructed. To this end, we propose the use of a statistical shape model (SSM) as a prior for surface reconstruction. The SSM is represented by a point distribution model (PDM), which is associated with a surface mesh. Using the shape distribution that is modelled by the PDM, we formulate the problem of surface reconstruction from a probabilistic perspective based on a Gaussian Mixture Model (GMM). In order to do so, the given points are interpreted as samples of the GMM. By using mixture components with anisotropic covariances that are “oriented” according to the surface normals at the PDM points, a surface-based fitting is accomplished. Estimating the parameters of the GMM in a maximum a posteriori manner yields the reconstruction of the surface from the given data points. We compare our method to the extensively used Iterative Closest Points method on several different anatomical datasets/SSMs (brain, femur, tibia, hip, liver) and demonstrate superior accuracy and robustness on sparse data. [less ▲] Detailed reference viewed: 91 (20 UL)Local Lyapunov Functions for Consensus in Switching Nonlinear Systems Thunberg, Johan ; Goncalves, Jorge ; in IEEE Transactions on Automatic Control (2017) This note presents two theorems on asymptotic state consensus of continuous time nonlinear multi-agent systems. The agents reside in Rm and have switching interconnection topologies. Both the first ... [more ▼] This note presents two theorems on asymptotic state consensus of continuous time nonlinear multi-agent systems. The agents reside in Rm and have switching interconnection topologies. Both the first theorem, formulated in terms of the states of individual agents, and the second theorem, formulated in terms of the pairwise states for pairs of agents, can be interpreted as variants of Lyapunov’s second method. The two theorems complement each other; the second provides stronger convergence results under weaker graph topology assumptions, whereas the first often can be applied in a wider context in terms of the structure of the right-hand sides of the systems. The second theorem also sheds some new light on well-known results for consensus of nonlinear systems where the right-hand sides of the agents’ dynamics are convex combinations of directions to neighboring agents. For such systems, instead of proving consensus by using the theory of contracting convex sets, a local quadratic Lyapunov function can be used. [less ▲] Detailed reference viewed: 89 (4 UL)Global converegence properties of a consensus protocol on the n-sphere Markdahl, Johan ; Goncalves, Jorge Scientific Conference (2016, December 13) This paper provides a novel analysis of the global convergence properties of a well-known consensus protocol for multi-agent systems that evolve in continuous time on the n-sphere. The feedback is ... [more ▼] This paper provides a novel analysis of the global convergence properties of a well-known consensus protocol for multi-agent systems that evolve in continuous time on the n-sphere. The feedback is intrinsic to the n-sphere, i.e., it does not rely on the use of local coordinates obtained through a parametrization. It is shown that, for any connected undirected graph topology and all n>1, the consensus protocol yields convergence that is akin to almost global consensus in a weak sense. Simulation results suggest that actual almost global consensus holds. This result is of interest in the context of consensus on Riemannian manifolds since it differs from what is known with regard to the 1-sphere and SO(3) where more advanced intrinsic consensus protocols are required in order to generate equivalent results. [less ▲] Detailed reference viewed: 82 (12 UL)Linear identification of nonlinear systems: A lifting technique based on the Koopman operator Mauroy, Alexandre ; Goncalves, Jorge in Proceedings of the 55th IEEE Conference on Decision and Control (2016, December) We exploit the key idea that nonlinear system identification is equivalent to linear identification of the socalled Koopman operator. Instead of considering nonlinear system identification in the state ... [more ▼] We exploit the key idea that nonlinear system identification is equivalent to linear identification of the socalled Koopman operator. Instead of considering nonlinear system identification in the state space, we obtain a novel linear identification technique by recasting the problem in the infinite-dimensional space of observables. This technique can be described in two main steps. In the first step, similar to a component of the Extended Dynamic Mode Decomposition algorithm, the data are lifted to the infinite-dimensional space and used for linear identification of the Koopman operator. In the second step, the obtained Koopman operator is “projected back” to the finite-dimensional state space, and identified to the nonlinear vector field through a linear least squares problem. The proposed technique is efficient to recover (polynomial) vector fields of different classes of systems, including unstable, chaotic, and open systems. In addition, it is robust to noise, well-suited to model low sampling rate datasets, and able to infer network topology and dynamics. [less ▲] Detailed reference viewed: 74 (8 UL)Optimising time-series experimental design for modelling of circadian rhythms: the value of transient data Mombaerts, Laurent ; Mauroy, Alexandre ; Goncalves, Jorge in IFAC-PapersOnLine (2016, October) Circadian clocks consist of complex networks that coordinate the daily cycle of most organisms. In light/dark cycles, the clock is synchronized (or entrained) by the environment, which corresponds to a ... [more ▼] Circadian clocks consist of complex networks that coordinate the daily cycle of most organisms. In light/dark cycles, the clock is synchronized (or entrained) by the environment, which corresponds to a constant rephasing of the oscillations and leads to a steady state regime. Some circadian clocks are endogenous oscillators with rhythms of about 24-hours that persist in constant light or constant darkness. This operating mechanism with and without entrainment provides flexibility and robustness to the clock against perturbations. Most of the clock-oriented experiments are performed under constant photoperiodic regime, overlooking the transitory regime that takes place between light/dark cycles and constant light or darkness. This paper provides a comparative analysis of the informative potential of the transient time-series data with the other regimes for clock modelling. Realistic data were simulated from 2 experimentally validated plant circadian clock models and sliced into several time windows. These windows represent the different regimes that take place before, meanwhile and after the switch to constant light. Then, a network inference tool was used over each window and its capability of retrieving the ground-truth of the network was compared for each window. The results suggest that including the transient data to the network inference technique significally improves its performance. [less ▲] Detailed reference viewed: 72 (8 UL)Shaping Pulses to Control Bistable Monotone Systems Using Koopman Operator ; Mauroy, Alexandre ; Goncalves, Jorge in 10th IFAC Symposium on Nonlinear Control Systems (2016, August) In this paper, we further develop a recently proposed control method to switch a bistable system between its steady states using temporal pulses. The motivation for using pulses comes from biomedical and ... [more ▼] In this paper, we further develop a recently proposed control method to switch a bistable system between its steady states using temporal pulses. The motivation for using pulses comes from biomedical and biological applications (e.g. synthetic biology), where it is generally di cult to build feedback control systems due to technical limitations in sensing and actuation. The original framework was derived for monotone systems and all the extensions relied on monotone systems theory. In contrast, we introduce the concept of switching function which is related to eigenfunctions of the so-called Koopman operator subject to a xed control pulse. Using the level sets of the switching function we can (i) compute the set of all pulses that drive the system toward the steady state in a synchronous way and (ii) estimate the time needed by the ow to reach an epsilon neighborhood of the target steady state. Additionally, we show that for monotone systems the switching function is also monotone in some sense, a property that can yield e cient algorithms to compute it. This observation recovers and further extends the results of the original framework, which we illustrate on numerical examples inspired by biological applications. [less ▲] Detailed reference viewed: 38 (1 UL)Global and Invariant Aspects of Consensus on the n-Sphere Markdahl, Johan ; ; et al in Proceedings of the 22nd International Symposium on Mathematical Theory of Networks and Systems (2016, July) This paper concerns two aspects of the multi- agent consensus problem on the n-sphere. Firstly, it proves that a standard consensus protocol, in a certain sense, yields asymptotical stability on a global ... [more ▼] This paper concerns two aspects of the multi- agent consensus problem on the n-sphere. Firstly, it proves that a standard consensus protocol, in a certain sense, yields asymptotical stability on a global level for a nontrivial class of graph topologies. Secondly, it provides a novel consensus protocol that leaves the centroid of agent states in Rn+1 projected back to the sphere invariant. It hence becomes possible to determine the consensus point as a function of the initial states. Much of the stability analysis has an intuitive geometric appeal since it is based on the symmetries of the n-sphere rather than generic Lyapunov theory. [less ▲] Detailed reference viewed: 65 (7 UL)Fast Correspondences for Statistical Shape Models of Brain Structures Bernard, Florian ; Vlassis, Nikos ; et al in SPIE Medical Imaging (2016, March) Detailed reference viewed: 92 (17 UL)Robust stability analysis of active voltage control for high-power IGBT switching by Kharitonov's theorem Goncalves, Jorge ; ; et al in IEEE Transactions on Power Electronics (2016), 31(3), 2584-2595 Detailed reference viewed: 66 (7 UL) |
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