@inproceedings{1839, abstract = {We present MultiGain, a tool to synthesize strategies for Markov decision processes (MDPs) with multiple mean-payoff objectives. Our models are described in PRISM, and our tool uses the existing interface and simulator of PRISM. Our tool extends PRISM by adding novel algorithms for multiple mean-payoff objectives, and also provides features such as (i) generating strategies and exploring them for simulation, and checking them with respect to other properties; and (ii) generating an approximate Pareto curve for two mean-payoff objectives. In addition, we present a new practical algorithm for the analysis of MDPs with multiple mean-payoff objectives under memoryless strategies.}, author = {Brázdil, Tomáš and Chatterjee, Krishnendu and Forejt, Vojtěch and Kučera, Antonín}, location = {London, United Kingdom}, pages = {181 -- 187}, publisher = {Springer}, title = {{Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives}}, doi = {10.1007/978-3-662-46681-0_12}, volume = {9035}, year = {2015}, } @article{1837, abstract = {Transition to turbulence in straight pipes occurs in spite of the linear stability of the laminar Hagen-Poiseuille flow if both the amplitude of flow perturbations and the Reynolds number Re exceed a minimum threshold (subcritical transition). As the pipe curvature increases, centrifugal effects become important, modifying the basic flow as well as the most unstable linear modes. If the curvature (tube-to-coiling diameter d/D) is sufficiently large, a Hopf bifurcation (supercritical instability) is encountered before turbulence can be excited (subcritical instability). We trace the instability thresholds in the Re - d/D parameter space in the range 0.01 ≤ d/D\ ≤ 0.1 by means of laser-Doppler velocimetry and determine the point where the subcritical and supercritical instabilities meet. Two different experimental set-ups are used: a closed system where the pipe forms an axisymmetric torus and an open system employing a helical pipe. Implications for the measurement of friction factors in curved pipes are discussed.}, author = {Kühnen, Jakob and Braunshier, P and Schwegel, M and Kuhlmann, Hendrik and Hof, Björn}, journal = {Journal of Fluid Mechanics}, number = {5}, publisher = {Cambridge University Press}, title = {{Subcritical versus supercritical transition to turbulence in curved pipes}}, doi = {10.1017/jfm.2015.184}, volume = {770}, year = {2015}, } @article{1848, abstract = {The ability to escape apoptosis is a hallmark of cancer-initiating cells and a key factor of resistance to oncolytic therapy. Here, we identify FAM96A as a ubiquitous, evolutionarily conserved apoptosome-activating protein and investigate its potential pro-apoptotic tumor suppressor function in gastrointestinal stromal tumors (GISTs). Interaction between FAM96A and apoptotic peptidase activating factor 1 (APAF1) was identified in yeast two-hybrid screen and further studied by deletion mutants, glutathione-S-transferase pull-down, co-immunoprecipitation and immunofluorescence. Effects of FAM96A overexpression and knock-down on apoptosis sensitivity were examined in cancer cells and zebrafish embryos. Expression of FAM96A in GISTs and histogenetically related cells including interstitial cells of Cajal (ICCs), “fibroblast-like cells” (FLCs) and ICC stem cells (ICC-SCs) was investigated by Northern blotting, reverse transcription—polymerase chain reaction, immunohistochemistry and Western immunoblotting. Tumorigenicity of GIST cells and transformed murine ICC-SCs stably transduced to re-express FAM96A was studied by xeno- and allografting into immunocompromised mice. FAM96A was found to bind APAF1 and to enhance the induction of mitochondrial apoptosis. FAM96A protein or mRNA was dramatically reduced or lost in 106 of 108 GIST samples representing three independent patient cohorts. Whereas ICCs, ICC-SCs and FLCs, the presumed normal counterparts of GIST, were found to robustly express FAM96A protein and mRNA, FAM96A expression was much reduced in tumorigenic ICC-SCs. Re-expression of FAM96A in GIST cells and transformed ICC-SCs increased apoptosis sensitivity and diminished tumorigenicity. Our data suggest FAM96A is a novel pro-apoptotic tumor suppressor that is lost during GIST tumorigenesis.}, author = {Schwamb, Bettina and Pick, Robert and Fernández, Sara and Völp, Kirsten and Heering, Jan and Dötsch, Volker and Bösser, Susanne and Jung, Jennifer and Beinoravičiute Kellner, Rasa and Wesely, Josephine and Zörnig, Inka and Hammerschmidt, Matthias and Nowak, Matthias and Penzel, Roland and Zatloukal, Kurt and Joos, Stefan and Rieker, Ralf and Agaimy, Abbas and Söder, Stephan and Reid Lombardo, Kmarie and Kendrick, Michael and Bardsley, Michael and Hayashi, Yujiro and Asuzu, David and Syed, Sabriya and Ördög, Tamás and Zörnig, Martin}, journal = {International Journal of Cancer}, number = {6}, pages = {1318 -- 1329}, publisher = {Wiley}, title = {{FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors}}, doi = {10.1002/ijc.29498}, volume = {137}, year = {2015}, } @article{1846, abstract = {Modal transition systems (MTS) is a well-studied specification formalism of reactive systems supporting a step-wise refinement methodology. Despite its many advantages, the formalism as well as its currently known extensions are incapable of expressing some practically needed aspects in the refinement process like exclusive, conditional and persistent choices. We introduce a new model called parametric modal transition systems (PMTS) together with a general modal refinement notion that overcomes many of the limitations. We investigate the computational complexity of modal and thorough refinement checking on PMTS and its subclasses and provide a direct encoding of the modal refinement problem into quantified Boolean formulae, allowing us to employ state-of-the-art QBF solvers for modal refinement checking. The experiments we report on show that the feasibility of refinement checking is more influenced by the degree of nondeterminism rather than by the syntactic restrictions on the types of formulae allowed in the description of the PMTS.}, author = {Beneš, Nikola and Kretinsky, Jan and Larsen, Kim and Möller, Mikael and Sickert, Salomon and Srba, Jiří}, journal = {Acta Informatica}, number = {2-3}, pages = {269 -- 297}, publisher = {Springer}, title = {{Refinement checking on parametric modal transition systems}}, doi = {10.1007/s00236-015-0215-4}, volume = {52}, year = {2015}, } @article{1845, abstract = {Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression. Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression.}, author = {Vandael, David H and Espinoza Martinez, Claudia and Jonas, Peter M}, journal = {Neuron}, number = {6}, pages = {1149 -- 1151}, publisher = {Elsevier}, title = {{Excitement about inhibitory presynaptic terminals}}, doi = {10.1016/j.neuron.2015.03.006}, volume = {85}, year = {2015}, } @article{1840, abstract = {In this paper, we present a method for reducing a regular, discrete-time Markov chain (DTMC) to another DTMC with a given, typically much smaller number of states. The cost of reduction is defined as the Kullback-Leibler divergence rate between a projection of the original process through a partition function and a DTMC on the correspondingly partitioned state space. Finding the reduced model with minimal cost is computationally expensive, as it requires an exhaustive search among all state space partitions, and an exact evaluation of the reduction cost for each candidate partition. Our approach deals with the latter problem by minimizing an upper bound on the reduction cost instead of minimizing the exact cost. The proposed upper bound is easy to compute and it is tight if the original chain is lumpable with respect to the partition. Then, we express the problem in the form of information bottleneck optimization, and propose using the agglomerative information bottleneck algorithm for searching a suboptimal partition greedily, rather than exhaustively. The theory is illustrated with examples and one application scenario in the context of modeling bio-molecular interactions.}, author = {Geiger, Bernhard and Petrov, Tatjana and Kubin, Gernot and Koeppl, Heinz}, issn = {0018-9286}, journal = {IEEE Transactions on Automatic Control}, number = {4}, pages = {1010 -- 1022}, publisher = {IEEE}, title = {{Optimal Kullback-Leibler aggregation via information bottleneck}}, doi = {10.1109/TAC.2014.2364971}, volume = {60}, year = {2015}, } @article{1841, abstract = {We propose a new family of message passing techniques for MAP estimation in graphical models which we call Sequential Reweighted Message Passing (SRMP). Special cases include well-known techniques such as Min-Sum Diffusion (MSD) and a faster Sequential Tree-Reweighted Message Passing (TRW-S). Importantly, our derivation is simpler than the original derivation of TRW-S, and does not involve a decomposition into trees. This allows easy generalizations. The new family of algorithms can be viewed as a generalization of TRW-S from pairwise to higher-order graphical models. We test SRMP on several real-world problems with promising results.}, author = {Kolmogorov, Vladimir}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, number = {5}, pages = {919 -- 930}, publisher = {IEEE}, title = {{A new look at reweighted message passing}}, doi = {10.1109/TPAMI.2014.2363465}, volume = {37}, year = {2015}, } @article{1849, abstract = {Cell polarity is a fundamental property of pro- and eukaryotic cells. It is necessary for coordination of cell division, cell morphogenesis and signaling processes. How polarity is generated and maintained is a complex issue governed by interconnected feed-back regulations between small GTPase signaling and membrane tension-based signaling that controls membrane trafficking, and cytoskeleton organization and dynamics. Here, we will review the potential role for calcium as a crucial signal that connects and coordinates the respective processes during polarization processes in plants. This article is part of a Special Issue entitled: 13th European Symposium on Calcium.}, author = {Himschoot, Ellie and Beeckman, Tom and Friml, Jiřĺ and Vanneste, Steffen}, journal = {Biochimica et Biophysica Acta - Molecular Cell Research}, number = {9}, pages = {2168 -- 2172}, publisher = {Elsevier}, title = {{Calcium is an organizer of cell polarity in plants}}, doi = {10.1016/j.bbamcr.2015.02.017}, volume = {1853}, year = {2015}, } @article{1847, author = {Grones, Peter and Friml, Jiřĺ}, journal = {Molecular Plant}, number = {3}, pages = {356 -- 358}, publisher = {Elsevier}, title = {{ABP1: Finally docking}}, doi = {10.1016/j.molp.2014.12.013}, volume = {8}, year = {2015}, } @article{1850, abstract = {Entomopathogenic fungi are potent biocontrol agents that are widely used against insect pests, many of which are social insects. Nevertheless, theoretical investigations of their particular life history are scarce. We develop a model that takes into account the main distinguishing features between traditionally studied diseases and obligate killing pathogens, like the (biocontrol-relevant) insect-pathogenic fungi Metarhizium and Beauveria. First, obligate killing entomopathogenic fungi produce new infectious particles (conidiospores) only after host death and not yet on the living host. Second, the killing rates of entomopathogenic fungi depend strongly on the initial exposure dosage, thus we explicitly consider the pathogen load of individual hosts. Further, we make the model applicable not only to solitary host species, but also to group living species by incorporating social interactions between hosts, like the collective disease defences of insect societies. Our results identify the optimal killing rate for the pathogen that minimises its invasion threshold. Furthermore, we find that the rate of contact between hosts has an ambivalent effect: dense interaction networks between individuals are considered to facilitate disease outbreaks because of increased pathogen transmission. In social insects, this is compensated by their collective disease defences, i.e., social immunity. For the type of pathogens considered here, we show that even without social immunity, high contact rates between live individuals dilute the pathogen in the host colony and hence can reduce individual pathogen loads below disease-causing levels.}, author = {Novak, Sebastian and Cremer, Sylvia}, journal = {Journal of Theoretical Biology}, number = {5}, pages = {54 -- 64}, publisher = {Elsevier}, title = {{Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates}}, doi = {10.1016/j.jtbi.2015.02.018}, volume = {372}, year = {2015}, } @article{1851, abstract = {We consider mating strategies for females who search for males sequentially during a season of limited length. We show that the best strategy rejects a given male type if encountered before a time-threshold but accepts him after. For frequency-independent benefits, we obtain the optimal time-thresholds explicitly for both discrete and continuous distributions of males, and allow for mistakes being made in assessing the correct male type. When the benefits are indirect (genes for the offspring) and the population is under frequency-dependent ecological selection, the benefits depend on the mating strategy of other females as well. This case is particularly relevant to speciation models that seek to explore the stability of reproductive isolation by assortative mating under frequency-dependent ecological selection. We show that the indirect benefits are to be quantified by the reproductive values of couples, and describe how the evolutionarily stable time-thresholds can be found. We conclude with an example based on the Levene model, in which we analyze the evolutionarily stable assortative mating strategies and the strength of reproductive isolation provided by them.}, author = {Priklopil, Tadeas and Kisdi, Eva and Gyllenberg, Mats}, issn = {1558-5646}, journal = {Evolution}, number = {4}, pages = {1015 -- 1026}, publisher = {Wiley}, title = {{Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating}}, doi = {10.1111/evo.12618}, volume = {69}, year = {2015}, } @inproceedings{1859, abstract = {Structural support vector machines (SSVMs) are amongst the best performing models for structured computer vision tasks, such as semantic image segmentation or human pose estimation. Training SSVMs, however, is computationally costly, because it requires repeated calls to a structured prediction subroutine (called \emph{max-oracle}), which has to solve an optimization problem itself, e.g. a graph cut. In this work, we introduce a new algorithm for SSVM training that is more efficient than earlier techniques when the max-oracle is computationally expensive, as it is frequently the case in computer vision tasks. The main idea is to (i) combine the recent stochastic Block-Coordinate Frank-Wolfe algorithm with efficient hyperplane caching, and (ii) use an automatic selection rule for deciding whether to call the exact max-oracle or to rely on an approximate one based on the cached hyperplanes. We show experimentally that this strategy leads to faster convergence to the optimum with respect to the number of requires oracle calls, and that this translates into faster convergence with respect to the total runtime when the max-oracle is slow compared to the other steps of the algorithm. }, author = {Shah, Neel and Kolmogorov, Vladimir and Lampert, Christoph}, location = {Boston, MA, USA}, pages = {2737 -- 2745}, publisher = {IEEE}, title = {{A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle}}, doi = {10.1109/CVPR.2015.7298890}, year = {2015}, } @inproceedings{1860, abstract = {Classifiers for object categorization are usually evaluated by their accuracy on a set of i.i.d. test examples. This provides us with an estimate of the expected error when applying the classifiers to a single new image. In real application, however, classifiers are rarely only used for a single image and then discarded. Instead, they are applied sequentially to many images, and these are typically not i.i.d. samples from a fixed data distribution, but they carry dependencies and their class distribution varies over time. In this work, we argue that the phenomenon of correlated data at prediction time is not a nuisance, but a blessing in disguise. We describe a probabilistic method for adapting classifiers at prediction time without having to retrain them. We also introduce a framework for creating realistically distributed image sequences, which offers a way to benchmark classifier adaptation methods, such as the one we propose. Experiments on the ILSVRC2010 and ILSVRC2012 datasets show that adapting object classification systems at prediction time can significantly reduce their error rate, even with no additional human feedback.}, author = {Royer, Amélie and Lampert, Christoph}, location = {Boston, MA, United States}, pages = {1401 -- 1409}, publisher = {IEEE}, title = {{Classifier adaptation at prediction time}}, doi = {10.1109/CVPR.2015.7298746}, year = {2015}, } @inproceedings{1858, abstract = {We study the problem of predicting the future, though only in the probabilistic sense of estimating a future state of a time-varying probability distribution. This is not only an interesting academic problem, but solving this extrapolation problem also has many practical application, e.g. for training classifiers that have to operate under time-varying conditions. Our main contribution is a method for predicting the next step of the time-varying distribution from a given sequence of sample sets from earlier time steps. For this we rely on two recent machine learning techniques: embedding probability distributions into a reproducing kernel Hilbert space, and learning operators by vector-valued regression. We illustrate the working principles and the practical usefulness of our method by experiments on synthetic and real data. We also highlight an exemplary application: training a classifier in a domain adaptation setting without having access to examples from the test time distribution at training time.}, author = {Lampert, Christoph}, location = {Boston, MA, United States}, pages = {942 -- 950}, publisher = {IEEE}, title = {{Predicting the future behavior of a time-varying probability distribution}}, doi = {10.1109/CVPR.2015.7298696}, year = {2015}, } @inproceedings{1857, abstract = {Sharing information between multiple tasks enables algorithms to achieve good generalization performance even from small amounts of training data. However, in a realistic scenario of multi-task learning not all tasks are equally related to each other, hence it could be advantageous to transfer information only between the most related tasks. In this work we propose an approach that processes multiple tasks in a sequence with sharing between subsequent tasks instead of solving all tasks jointly. Subsequently, we address the question of curriculum learning of tasks, i.e. finding the best order of tasks to be learned. Our approach is based on a generalization bound criterion for choosing the task order that optimizes the average expected classification performance over all tasks. Our experimental results show that learning multiple related tasks sequentially can be more effective than learning them jointly, the order in which tasks are being solved affects the overall performance, and that our model is able to automatically discover the favourable order of tasks. }, author = {Pentina, Anastasia and Sharmanska, Viktoriia and Lampert, Christoph}, location = {Boston, MA, United States}, pages = {5492 -- 5500}, publisher = {IEEE}, title = {{Curriculum learning of multiple tasks}}, doi = {10.1109/CVPR.2015.7299188}, year = {2015}, } @article{1867, abstract = {Cultured mammalian cells essential are model systems in basic biology research, production platforms of proteins for medical use, and testbeds in synthetic biology. Flavin cofactors, in particular flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), are critical for cellular redox reactions and sense light in naturally occurring photoreceptors and optogenetic tools. Here, we quantified flavin contents of commonly used mammalian cell lines. We first compared three procedures for extraction of free and noncovalently protein-bound flavins and verified extraction using fluorescence spectroscopy. For separation, two CE methods with different BGEs were established, and detection was performed by LED-induced fluorescence with limit of detections (LODs 0.5-3.8 nM). We found that riboflavin (RF), FMN, and FAD contents varied significantly between cell lines. RF (3.1-14 amol/cell) and FAD (2.2-17.0 amol/cell) were the predominant flavins, while FMN (0.46-3.4 amol/cell) was found at markedly lower levels. Observed flavin contents agree with those previously extracted from mammalian tissues, yet reduced forms of RF were detected that were not described previously. Quantification of flavins in mammalian cell lines will allow a better understanding of cellular redox reactions and optogenetic tools.}, author = {Hühner, Jens and Inglés Prieto, Álvaro and Neusüß, Christian and Lämmerhofer, Michael and Janovjak, Harald L}, journal = {Electrophoresis}, number = {4}, pages = {518 -- 525}, publisher = {Wiley}, title = {{Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection}}, doi = {10.1002/elps.201400451}, volume = {36}, year = {2015}, } @article{1865, abstract = {The plant hormone auxin and its directional transport are known to play a crucial role in defining the embryonic axis and subsequent development of the body plan. Although the role of PIN auxin efflux transporters has been clearly assigned during embryonic shoot and root specification, the role of the auxin influx carriers AUX1 and LIKE-AUX1 (LAX) proteins is not well established. Here, we used chemical and genetic tools on Brassica napus microspore-derived embryos and Arabidopsis thaliana zygotic embryos, and demonstrate that AUX1, LAX1 and LAX2 are required for both shoot and root pole formation, in concert with PIN efflux carriers. Furthermore, we uncovered a positive-feedback loop betweenMONOPTEROS(ARF5)-dependent auxin signalling and auxin transport. ThisMONOPTEROSdependent transcriptional regulation of auxin influx (AUX1, LAX1 and LAX2) and auxin efflux (PIN1 and PIN4) carriers by MONOPTEROS helps to maintain proper auxin transport to the root tip. These results indicate that auxin-dependent cell specification during embryo development requires balanced auxin transport involving both influx and efflux mechanisms, and that this transport is maintained by a positive transcriptional feedback on auxin signalling.}, author = {Robert, Hélène and Grunewald, Wim and Sauer, Michael and Cannoot, Bernard and Soriano, Mercedes and Swarup, Ranjan and Weijers, Dolf and Bennett, Malcolm and Boutilier, Kim and Friml, Jirí}, journal = {Development}, number = {4}, pages = {702 -- 711}, publisher = {Company of Biologists}, title = {{Plant embryogenesis requires AUX/LAX-mediated auxin influx}}, doi = {10.1242/dev.115832}, volume = {142}, year = {2015}, } @article{1868, abstract = {We investigate high-dimensional nonlinear dynamical systems exhibiting multiple resonances under adiabatic parameter variations. Our motivations come from experimental considerations where time-dependent sweeping of parameters is a practical approach to probing and characterizing the bifurcations of the system. The question is whether bifurcations so detected are faithful representations of the bifurcations intrinsic to the original stationary system. Utilizing a harmonically forced, closed fluid flow system that possesses multiple resonances and solving the Navier-Stokes equation under proper boundary conditions, we uncover the phenomenon of the early effect. Specifically, as a control parameter, e.g., the driving frequency, is adiabatically increased from an initial value, resonances emerge at frequency values that are lower than those in the corresponding stationary system. The phenomenon is established by numerical characterization of physical quantities through the resonances, which include the kinetic energy and the vorticity field, and a heuristic analysis based on the concept of instantaneous frequency. A simple formula is obtained which relates the resonance points in the time-dependent and time-independent systems. Our findings suggest that, in general, any true bifurcation of a nonlinear dynamical system can be unequivocally uncovered through adiabatic parameter sweeping, in spite of a shift in the bifurcation point, which is of value to experimental studies of nonlinear dynamical systems.}, author = {Park, Youngyong and Do, Younghae and Altmeyer, Sebastian and Lai, Yingcheng and Lee, Gyuwon}, issn = {1539-3755}, journal = {Physical Review E}, number = {2}, publisher = {American Physical Society}, title = {{Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances}}, doi = {10.1103/PhysRevE.91.022906}, volume = {91}, year = {2015}, } @article{1864, abstract = {The Altshuler–Shklovskii formulas (Altshuler and Shklovskii, BZh Eksp Teor Fiz 91:200, 1986) predict, for any disordered quantum system in the diffusive regime, a universal power law behaviour for the correlation functions of the mesoscopic eigenvalue density. In this paper and its companion (Erdős and Knowles, The Altshuler–Shklovskii formulas for random band matrices I: the unimodular case, 2013), we prove these formulas for random band matrices. In (Erdős and Knowles, The Altshuler–Shklovskii formulas for random band matrices I: the unimodular case, 2013) we introduced a diagrammatic approach and presented robust estimates on general diagrams under certain simplifying assumptions. In this paper, we remove these assumptions by giving a general estimate of the subleading diagrams. We also give a precise analysis of the leading diagrams which give rise to the Altschuler–Shklovskii power laws. Moreover, we introduce a family of general random band matrices which interpolates between real symmetric (β = 1) and complex Hermitian (β = 2) models, and track the transition for the mesoscopic density–density correlation. Finally, we address the higher-order correlation functions by proving that they behave asymptotically according to a Gaussian process whose covariance is given by the Altshuler–Shklovskii formulas. }, author = {Erdös, László and Knowles, Antti}, journal = {Annales Henri Poincare}, number = {3}, pages = {709 -- 799}, publisher = {Springer}, title = {{The Altshuler–Shklovskii formulas for random band matrices II: The general case}}, doi = {10.1007/s00023-014-0333-5}, volume = {16}, year = {2015}, } @article{1861, abstract = {Continuous-time Markov chains are commonly used in practice for modeling biochemical reaction networks in which the inherent randomness of themolecular interactions cannot be ignored. This has motivated recent research effort into methods for parameter inference and experiment design for such models. The major difficulty is that such methods usually require one to iteratively solve the chemical master equation that governs the time evolution of the probability distribution of the system. This, however, is rarely possible, and even approximation techniques remain limited to relatively small and simple systems. An alternative explored in this article is to base methods on only some low-order moments of the entire probability distribution. We summarize the theory behind such moment-based methods for parameter inference and experiment design and provide new case studies where we investigate their performance.}, author = {Ruess, Jakob and Lygeros, John}, journal = {ACM Transactions on Modeling and Computer Simulation}, number = {2}, publisher = {ACM}, title = {{Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks}}, doi = {10.1145/2688906}, volume = {25}, year = {2015}, }