Live tracking of moving samples in confocal microscopy for vertically grown rootsRobert Hauschild
Current minimal version of TipTracker
Algorithmic advances in program analysis and their applicationsAndreas Pavlogiannis
This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the static analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms. Our contributions can be broadly grouped into five categories. Our first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of...
The lac operon in the wildFabienne Jesse
The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown. In...
Synthetic tools for optogenetic and chemogenetic inhibition of cellular signalsStephanie Kainrath
Proteins and their complex dynamic interactions regulate cellular mechanisms from sensing and transducing extracellular signals, to mediating genetic responses, and sustaining or changing cell morphology. To manipulate these protein-protein interactions (PPIs) that govern the behavior and fate of cells, synthetically constructed, genetically encoded tools provide the means to precisely target proteins of interest (POIs), and control their subcellular localization and activity in vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e....
On the average-case hardness of total search problemsChethan Kamath
A search problem lies in the complexity class FNP if a solution to the given instance of the problem can be verified efficiently. The complexity class TFNP consists of all search problems in FNP that are total in the sense that a solution is guaranteed to exist. TFNP contains a host of interesting problems from fields such as algorithmic game theory, computational topology, number theory and combinatorics. Since TFNP is a semantic class, it is...
Reconfiguration problemsZuzana Masarova
This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a...
MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'Martin Lukačišin
MATLAB code and processed datasets available for reproducing the results in: Lukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast. *equal contributions.
A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPsKrishnendu Chatterjee, Martin Chmelik & Jessica Davies
POMDPs are standard models for probabilistic planning problems, where an agent interacts with an uncertain environment. We study the problem of almost-sure reachability, where given a set of target states, the question is to decide whether there is a policy to ensure that the target set is reached with probability 1 (almost-surely). While in general the problem is EXPTIME-complete, in many practical cases policies with a small amount of memory suffice. Moreover, the existing solution...
Bounded rationality in concurrent parity gamesKrishnendu Chatterjee
We consider 2-player games played on a finite state space for an infinite number of rounds. The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine the successor state. We study concurrent games with ω-regular winning conditions specified as parity objectives. We consider the qualitative analysis problems: the computation of the almost-sure and limit-sure winning set...
Strong amplifiers of natural selectionAndreas Pavlogiannis, Josef Tkadlec, Krishnendu Chatterjee & Martin Nowak
Games with a weak adversaryKrishnendu Chatterjee & Laurent Doyen
We consider multi-player graph games with partial-observation and parity objective. While the decision problem for three-player games with a coalition of the first and second players against the third player is undecidable, we present a decidability result for partial-observation games where the first and third player are in a coalition against the second player, thus where the second player is adversarial but weaker due to partial-observation. We establish tight complexity bounds in the case where...
Supplementary Files for \"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W\"Christelle Fraisse
The de novo genome assemblies generated for this study, and the associated metadata.
Graph matching problems for annotating C. ElegansDagmar Kainmueller, Florian Jug, Carsten Rother & Gene Meyers
Graph matching problems as described in "Active Graph Matching for Automatic Joint Segmentation and Annotation of C. Elegans." by Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Myers, Gene, MICCAI 2014. Problems are in OpenGM2 hdf5 format (see http://hciweb2.iwr.uni-heidelberg.de/opengm/) and a custom text format used by the feature matching solver described in "Feature Correspondence via Graph Matching: Models and Global Optimization." by Lorenzo Torresani, Vladimir Kolmogorov and Carsten Rother, ECCV 2008, code at http://pub.ist.ac.at/~vnk/software/GraphMatching-v1.02.src.zip.
Onset of turbulence in plane Poiseuille flowChaitanya Paranjape
Qualitative analysis of concurrent mean-payoff gamesKrishnendu Chatterjee & Rasmus Ibsen-Jensen
We consider concurrent games played by two-players on a finite state graph, where in every round the players simultaneously choose a move, and the current state along with the joint moves determine the successor state. We study the most fundamental objective for concurrent games, namely, mean-payoff or limit-average objective, where a reward is associated to every transition, and the goal of player 1 is to maximize the long-run average of the rewards, and the objective...
Multi-electrode array recording from salamander retinal ganglion cellsOlivier Marre, Gasper Tkacik, Dario Amodei, Elad Schneidman, William Bialek & Michael J Berry
This data was collected as part of the study . It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with...
Data for \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\".Beatriz Vicoso
This folder contains all the data used in each of the main figures of "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology" (Kelemen, R., Vicoso, B.), as well as in the supplementary figures.
Combinatorial width parameters for 3-dimensional manifoldsKristóf Huszár
Algorithms in computational 3-manifold topology typically take a triangulation as an input and return topological information about the underlying 3-manifold. However, extracting the desired information from a triangulation (e.g., evaluating an invariant) is often computationally very expensive. In recent years this complexity barrier has been successfully tackled in some cases by importing ideas from the theory of parameterized algorithms into the realm of 3-manifolds. Various computationally hard problems were shown to be efficiently solvable for...
Springer Austrian Publications 2013-2016Márton Villanyi
Data on Austrian open access publication output at Springer from 2013-2016 including data analysis.
IOP Austrian Publications 2012-2015Márton Villanyi
Data on Austrian open access publication output at IOP from 2012-2015 including data analysis.
Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistabilityRan Zhang
Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical quantities, with the help of numerical and combinatorial algorithms, they can assist...
Bulk actin dynamics drive phase segregation in zebrafish oocytesShayan Shamipour
Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at...
Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"Daniele De Martino & Gasper Tkacik
Inferring recent demography from spatial genetic structureHarald Ringbauer
This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be...