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Efficient algorithms for object recognition are crucial for the newly robotics and computer vision applications that demand real-time and on-line methods. Some examples are autonomous systems, navigating robots, autonomous driving. In this work, we focus on efficient semantic segmentation, which is the problem of labeling each pixel of an image with a semantic class.
Our aim is to speed-up all of the parts of the semantic segmentation pipeline. We also aim at delivering a labeling solution on a time budget, that can be decided on-the-fly. For this purpose, we analyze all the components of the semantic segmentation pipeline, and identify the computational bottleneck of each of them. The different components of the pipeline are over-segmenting the image with local regions, extracting features and classify the local regions, and the final inference of the image labeling with semantic classes. We focus on each of these steps.
First, we introduce a new superpixel algorithm to over-segment the image. Our superpixel method runs in real-time and can deliver a solution at any time budget. Then, for feature extraction, we focus on the framework that computes descriptors and encodes them, followed by a pooling step. We see that the encoding step is the bottleneck, for computational efficiency and performance. We present a novel assignment-based encoding formulation, that allows for the design of a new, very efficient, encoding. Finally, the image labeling output is obtained modeling the dependencies with a Conditional Random Field (CRF). In semantic image segmentation, the computational cost of instantiating the potentials is much higher than MAP inference. We introduce Active MAP inference to on-the-fly select a subset of potentials to be instantiated in the energy function, leaving the rest as unknown, and to estimate the MAP labeling from such incomplete energy function.
We perform experiments on all proposed methods for the different parts of the semantic segmentation pipeline. We show that our superpixel extraction achieves higher accuracy than state-of-the-art on standard superpixel benchmark, while it runs in real-time. We test our feature encoding on standard image classification and segmentation benchmarks, and we show that our method achieves competitive results with the state-of-the-art, and requires less time and memory. Finally, results for semantic segmentation benchmark show that Active MAP inference achieves similar levels of accuracy but with major efficiency gains.
When performing transfer learning in Computer Vision, normally a pretrained model (source model) that is trained on a specific task and a large dataset like ImageNet is used. The learned representation of that source model is then used to perform a transfer to a target task. Performing transfer learning in this way had a great impact on Computer Vision, because it worked seamlessly, especially on tasks that are related to each other. Current research topics have investigated the relationship between different tasks and their impact on transfer learning by developing similarity methods. These similarity methods have in common, to do transfer learning without actually doing transfer learning in the first place but rather by predicting transfer learning rankings so that the best possible source model can be selected from a range of different source models. However, these methods have focused only on singlesource transfers and have not paid attention to multi-source transfers. Multi-source transfers promise even better results than single-source transfers as they combine information from multiple source tasks, all of which are useful to the target task. We fill this gap and propose a many-to-one task similarity method called MOTS that predicts both, single-source transfers and multi-source transfers to a specific target task. We do that by using linear regression and the source representations of the source models to predict the target representation. We show that we achieve at least results on par with related state-of-the-art methods when only focusing on singlesource transfers using the Pascal VOC and Taskonomy benchmark. We show that we even outperform all of them when using single and multi-source transfers together (0.9 vs. 0.8) on the Taskonomy benchmark. We additionally investigate the performance of MOTS in conjunction with a multi-task learning architecture. The task-decoder heads of a multi-task learning architecture are used in different variations to do multi-source transfers since it promises efficiency over multiple singletask architectures and incurs less computational cost. Results show that our proposed method accurately predicts transfer learning rankings on the NYUD dataset and even shows the best transfer learning results always being achieved when using more than one source task. Additionally, it is further examined that even just using one task-decoder head from the multi-task learning architecture promises better transfer learning results, than using a single-task architecture for the same task, which is due to the shared information from different tasks in the multi-task learning architecture in previous layers. Since the MOTS rankings for selecting the MTI-Net task-decoder head with the highest transfer learning performance were very accurate for the NYUD but not satisfying for the Pascal VOC dataset, further experiments need to varify the generalizability of MOTS rankings for the selection of the optimal task-decoder head from a multi-task architecture.
The archaeological data dealt with in our database solution Antike Fundmünzen in Europa (AFE), which records finds of ancient coins, is entered by humans. Based on the Linked Open Data (LOD) approach, we link our data to Nomisma.org concepts, as well as to other resources like Online Coins of the Roman Empire (OCRE). Since information such as denomination, material, etc. is recorded for each single coin, this information should be identical for coins of the same type. Unfortunately, this is not always the case, mostly due to human errors. Based on rules that we implemented, we were able to make use of this redundant information in order to detect possible errors within AFE, and were even able to correct errors in Nomimsa.org. However, the approach had the weakness that it was necessary to transform the data into an internal data model. In a second step, we therefore developed our rules within the Linked Open Data world. The rules can now be applied to datasets following the Nomisma. org modelling approach, as we demonstrated with data held by Corpus Nummorum Thracorum (CNT). We believe that the use of methods like this to increase the data quality of individual databases, as well as across different data sources and up to the higher levels of OCRE and Nomisma.org, is mandatory in order to increase trust in them.
The Specialized Information Service Biodiversity Research (BIOfid) has been launched to mobilize valuable biological data from printed literature hidden in German libraries for over the past 250 years. In this project, we annotate German texts converted by OCR from historical scientific literature on the biodiversity of plants, birds, moths and butterflies. Our work enables the automatic extraction of biological information previously buried in the mass of papers and volumes. For this purpose, we generated training data for the tasks of Named Entity Recognition (NER) and Taxa Recognition (TR) in biological documents. We use this data to train a number of leading machine learning tools and create a gold standard for TR in biodiversity literature. More specifically, we perform a practical analysis of our newly generated BIOfid dataset through various downstream-task evaluations and establish a new state of the art for TR with 80.23% F-score. In this sense, our paper lays the foundations for future work in the field of information extraction in biology texts.
In dieser Arbeit werden 4,6 Millionen englische Tweets, welche das Keyword „Bitcoin“ enthalten, analysiert und der Zusammenhang zwischen dem Sentiment der Tweets und den Renditen des Bitcoin untersucht. Zur Bestimmung der Sentiment-Klassen werden Text-Klassifizierer mit verschiedenen Ansätzen, darunter auch auf Convolutional Neural Networks und Transformern basierende Modelle, in diesem Kontext evaluiert und optimiert. Es wird außerdem ein Meta-Modell konstruiert, welches beim Problem der Sentiment-Klassifikation von Tweets in drei Klassen {Positiv, Negativ, Neutral} in der betrachteten Domäne besser abschneidet, als die anderen begutachteten Modelle. Bezüglich des Zusammenhangs wird im Speziellen auch der Einfluss von Merkmalen der Tweets und ihrer Verfassern anhand der Distanzkorrelation untersucht.
Jeden Tag werden 2,5 Trillionen Bytes an Daten generiert. Diese enorme Menge an Daten wird beispielsweise durch digitale Bilder, Videos, Beiträge in den sozialen Medien, intelligente Sensoren, Einzelhandels- und Finanztransaktionen und GPS-Signale von Handys erzeugt. Das ist Big Data. Es besteht kein Zweifel daran, dass Big Data und das, was wir damit tun, das Potential hat, ein signifikanter Treiber für Innovationen und Wertschöpfung zu werden.
Multi-view microscopy techniques are used to increase the resolution along the optical axis for 3D imaging. Without this, the resolution is insufficient to resolve subcellular events. In addition, parts of the images of opaque specimens are often highly degraded or masked. Both problems motivate scientists to record the same specimen from multiple directions. The images, then have to be digitally fused into a single high-quality image. Selective-plane illumination microscopy has proven to be a powerful imaging technique due to its unsurpassed acquisition speed and gentle optical sectioning. However, even in the case of multi view imaging techniques that illuminate and image the sample from multiple directions, light scattering inside tissues often severely impairs image contrast.
Here we show that for c-elegans embryos multi view registration can be achieved based on segmented nuclei. However, segmentation of nuclei in high density distribution like c-elegans embryo is challenging. We propose a method which uses 3D Mexican hat filter for preprocessing and 3D Gaussian curvature for the post-processing step to separate nuclei. We used this method successfully on 3 data sets of c-elegans embryos in 3 different views. The result of segmentation outperforms previous methods. Moreover, we provide a simple GUI for manual correction and adjusting the parameters for different data.
We then proposed a method that combines point and voxel registration for an accurate multi view reg- istration of c-elegans embryo, which does not need any special experimental preparation. We demonstrate the performance of our approach on data acquired from fixed embryos of c-elegans worms. This multi step approach is successfully evaluated by comparison to different methods and also by using synthetic data. The proposed method could overcome the typically low resolution along the optical axis and enable stitching to- gether the different parts of the embryo available through the different views. A tool for running the code and analyzing the results is developed.
Correctness of program transformations and translations in concurrent programming is the focus of our research. In this case study the relation of the synchronous pi-calculus and a core language of Concurrent Haskell (CH) with asynchronous communication is investigated. We show that CH embraces the synchronous pi-calculus. The formal foundations are contextual semantics in both languages, where may- as well as should-convergence are observed. We succeed in defining and proving smart properties of a particular translation mapping the synchronous pi-calculus into CH. This implies that pi-processes are error-free if and only if their translation is an error-free CH-program Our result shows that the chosen semantics is not only powerful, but can also be applied in concrete and technically complex situations. The developed translation uses private names. We also automatically check potentially correct translations that use global names instead of private names. As a complexity parameter we use the number of MVars introduced by the transformation, where MVars are synchronized 1-place buffers. The automated refutation of incorrect translations leads to a classification of potentially correct translations, and to the conjecture that one global MVar is insufficient.
Correctness of program transformations and translations in concurrent programming is the focus of our research. In this case study the relation of the synchronous pi-calculus and a core language of Concurrent Haskell (CH) with asynchronous communication is investigated. We show that CH embraces the synchronous pi-calculus. The formal foundations are contextual semantics in both languages, where may- as well as should-convergence are observed. We succeed in defining and proving smart properties of a particular translation mapping the synchronous pi-calculus into CH. This implies that pi-processes are error-free if and only if their translation is an error-free CH-program Our result shows that the chosen semantics is not only powerful, but can also be applied in concrete and technically complex situations. The developed translation uses private names. We also automatically check potentially correct translations that use global names instead of private names. As a complexity parameter we use the number of MVars introduced by the transformation, where MVars are synchronized 1-place buffers. The automated refutation of incorrect translations leads to a classification of potentially correct translations, and to the conjecture that one global MVar is insufficient.
Correctness of program transformations and translations in concurrent programming is the focus of our research. In this case study the relation of the synchronous pi-calculus and a core language of Concurrent Haskell (CH) with asynchronous communication is investigated. We show that CH embraces the synchronous pi-calculus. The formal foundations are contextual semantics in both languages, where may- as well as should-convergence are observed. We succeed in defining and proving smart properties of a particular translation mapping the synchronous pi-calculus into CH. This implies that pi-processes are error-free if and only if their translation is an error-free CH-program Our result shows that the chosen semantics is not only powerful, but can also be applied in concrete and technically complex situations. The developed translation uses private names. We also automatically check potentially correct translations that use global names instead of private names. As a complexity parameter we use the number of MVars introduced by the transformation, where MVars are synchronized 1-place buffers. The automated refutation of incorrect translations leads to a classification of potentially correct translations, and to the conjecture that one global MVar is insufficient.
We investigate translations from the synchronous pi-calculus
into a core language of Concurrent Haskell (CH). Synchronous messagepassing of the pi-calculus is encoded as sending messages and adding synchronization using Concurrent Haskell’s mutable shared-memory locations (MVars). Our correctness criterion for translations is invariance of may- and should-convergence. This embraces that all executions of a process are error-free if and only if this also holds for the translated program. We exhibit a particular correct translation that uses a fresh, private MVar per communication interaction and that is in addition adequate, and which is also fully abstract on closed expressions. A metaresult is that CH has the expressive power and the concurrency capabilities of the synchronous pi-calculus.
We also automatically check variants of translations of synchronous communication into an asynchronous calculus where only an a priori fixed number of MVars per channel (and not per communication interaction!) is available. We obtain non-correctness results for classes of small translations, and exemplary argue for the correctness (and adequacy) for two translations with a higher number of MVars. We introduce a classification of the potentially correct translations.
We consider matching, rewriting, critical pairs and the Knuth-Bendix confluence test on rewrite rules in a nominal setting extended by atom-variables. Computing critical pairs is done using nominal unification, and rewriting using nominal matching. We utilise atom-variables to formulate rewrite rules, which is an improvement over previous approaches, using usual nominal unification, nominal matching and nominal equivalence of expressions coupled with a freshness constraint. We determine the complexity of several problems in a quantified freshness logic. In particular we show that nominal matching is Πp2-complete. We prove that the adapted Knuth-Bendix confluence test is applicable to a nominal rewrite system with atom-variabes and thus, that there is a decidable test whether confluence of the ground instance of the abstract rewrite system holds. We apply the nominal Knuth Bendix confluence criterion to the theory of monads, and compute a convergent nominal rewrite system modulo alpha-equivalence.
A sound and complete algorithm for nominal unification of higher-order expressions with a recursive let is described, and shown to run in non-deterministic polynomial time. We also explore specializations like nominal letrec-matching for expressions, for DAGs, and for garbage-free expressions and determine their complexity. As extension a nominal unification algorithm for higher-order expressions with recursive let and atom-variables is constructed, where we show that it also runs in non-deterministic polynomial time.
In the last two decades, our understanding of human gene regulation has improved tremendously. There are plentiful computational methods which focus on integrative data analysis of humans, and model organisms, like mouse and drosophila. However, these tools are not directly employable by researchers working on non-model organisms to answer fundamental biological, and evolutionary questions. We aimed to develop new tools, and adapt existing software for the analysis of transcriptomic and epigenomic data of one such non-model organism, Paramecium tetraurelia, an unicellular eukaryote. Paramecium contains two diploid (2n) germline micronuclei (MIC) and a polyploid (800n) somatic macronuclei (MAC). The transcriptomic and epigenomic regulatory landscape of the MAC genome, which has 80% protein-coding genes and short intergenic regions, is poorly understood.
We developed a generic automated eukaryotic short interfering RNA (siRNA) analysis tool, called RAPID. Our tool captures diverse siRNA characteristics from small RNA sequencing data and provides easily navigable visualisations. We also introduced a normalisation technique to facilitate comparison of multiple siRNA-based gene knockdown studies. Further, we developed a pipeline to characterise novel genome-wide endogenous short interfering RNAs (endo-siRNAs). In contrary to many organisms, we found that the endo-siRNAs are not acting in cis, to silence their parent mRNA. We also predicted phasing of siRNAs, which are regulated by the RNA interference (RNAi) pathway.
Further, using RAPID, we investigated the aberrations of endo-siRNAs, and their respective transcriptomic alterations caused by an RNAi pathway triggered by feeding small RNAs against a target gene. We find that the small RNA transcriptome is altered, even if a gene unrelated to RNAi pathway is targeted. This is important in the context of investigations of genetically modified organisms (GMOs). We suggest that future studies need to distinguish transcriptomic changes caused by RNAi inducing techniques and actual regulatory changes.
Subsequently, we adapted existing epigenomics analysis tools to conduct the first comprehensive epigenomic characterisation of nucleosome positioning and histone modifications of the Paramecium MAC. We identified well positioned nucleosomes shifted downstream of the transcription start site. GC content seems to dictate, in cis, the positioning of nucleosomes, histone marks (H3K4me3, H3K9ac, and H3K27me3), and Pol II in the AT-rich Paramecium genome. We employed a chromatin state segmentation approach, on nucleosomes and histone marks, which revealed genes with active, repressive, and bivalent chromatin states. Further, we constructed a regulatory association network of all the aforementioned data, using the sparse partial correlation network technique. Our analysis revealed subsets of genes, whose expression is positively associated with H3K27me3, different to the otherwise reported negative association with gene expression in many other organisms.
Further, we developed a Random Forests classifier to predict gene expression using genic (gene length, intron frequency, etc.) and epigenetic features. Our model has a test performance (PR-AUC) of 0.83. Upon evaluating different feature sets, we found that genic features are as predictive, of gene expression, as the epigenetic features. We used Shapley local feature explanation values, to suggest that high H3K4me3, high intron frequency, low gene length, high sRNA, and high GC content are the most important elements for determining gene expression status.
In this thesis, we developed novel tools, and employed several bioinformatics and machine learning methods to characterise the regulatory landscape of the Paramecium’s (epi)genome.
We empirically investigate algorithms for solving Connected Components in the external memory model. In particular, we study whether the randomized O(Sort(E)) algorithm by Karger, Klein, and Tarjan can be implemented to compete with practically promising and simpler algorithms having only slightly worse theoretical cost, namely Borůvka’s algorithm and the algorithm by Sibeyn and collaborators. For all algorithms, we develop and test a number of tuning options. Our experiments are executed on a large set of different graph classes including random graphs, grids, geometric graphs, and hyperbolic graphs. Among our findings are: The Sibeyn algorithm is a very strong contender due to its simplicity and due to an added degree of freedom in its internal workings when used in the Connected Components setting. With the right tunings, the Karger-Klein-Tarjan algorithm can be implemented to be competitive in many cases. Higher graph density seems to benefit Karger-Klein-Tarjan relative to Sibeyn. Borůvka’s algorithm is not competitive with the two others.
Dieser Arbeit war zum Ziel gesetzt, Methoden zur Simulation von neuronalen Prozessen zu entwickeln, zu implementieren, einzusetzen und zu vergleichen. Ein besonderes Augenmerk lag dabei auf der Frage, wo eine volle räumliche Auflösung der Modelle benötigt wird und wo darauf zugunsten von vereinfachenden niederdimensionalen Modellen, die wesentlich weniger Ressourcen und mathematischen Sachverstand erfordern, verzichtet werden kann. Außerdem wurde speziell bei der Beschreibung der verschiedenen Modelle für die Elektrik der Nervenzellen das Anliegen verfolgt, deren Zusammenhänge und die Natur vereinfachender Annahmen herauszuarbeiten, um deutlich zu machen, an welchen Stellen Probleme bei der Benutzung der weniger komplexen Modelle auftreten können.
In etlichen Beispielen wurde daraufhin untersucht, inwieweit die Vereinfachung auf ein eindimensionales Kabelmodell sowie der Verzicht auf die Betrachtung einzelner Ionensorten die realistische Darstellung der zellulären Elektrik beeinträchtigen können. Dabei stellte sich heraus, dass alle betrachteten Modelle für das rein elektrische Verhalten der Neuronen im Wesentlichen dieselben Ergebnisse liefern, weshalb zu dessen Simulation in den allermeisten Fällen ein 1D-Kabelmodell völlig ausreichend und angezeigt sein dürfte.
Nur wenn Größen von Interesse sind, die in diesem Modell nicht erfasst werden, etwa das Außenraumpotential oder die Ionenkonzentrationen, muss auf genauere Modelle zurückgegriffen werden. Außerdem ist in einer Konvergenzstudie exemplarisch vorgeführt worden, dass bereits eine recht grobe Darstellung der zugrundeliegenden Rechengitter genügt, um korrekte Ergebnisse bei der Simulation der rein elektrischen Signale sicherzustellen.
In scharfem Kontrast steht hierzu die Simulation von einzelnen Ionen-Dynamiken. Bereits in der Untersuchung des Poisson-Nernst-Planck-Modells für das Membranpotential erwies sich, dass für eine korrekte Simulation der diffusiven Anteile der Ionenbewegung wesentlich feinere Gitter benötigt werden.
Noch viel deutlicher wurde dies in Simulationen von Calcium-Wellen in Dendriten, wo -- neben anderen Einsichten -- aufgezeigt werden konnte, dass nicht nur eine feine axiale
(und Zeit-) Auflösung der Dendritengeometrie zur Sicherstellung exakter Ergebnisse notwendig ist, sondern auch die räumliche Auflösung in die übrigen Dimensionen wichtig ist, weswegen eine eindimensionale Kabeldarstellung der Calcium-Dynamik erheblich fehlerbehaftet und
(jedenfalls im Zusammenhang mit Ryanodin-Rezeptorkanälen) von deren Nutzung dringend abzuraten ist. Auch die Darstellung von Kanälen als eine kontinuierliche Dichte in der Membran kann, wie darüber hinaus vorgeführt wurde, problematisch sein.
Ihre exaktere Modellierung, etwa durch Einbettung auch probabilistischer Einzelkanaldarstellungen in das räumliche Modell sollte in zukünftigen Arbeiten noch mehr thematisiert werden.
Mit Blick auf die Wiederverwendbarkeit bereits implementierter Funktionalität innerhalb dieser Arbeiten wurden spezielle Teile dieser Funktionalität hier in einem gesonderten
Kapitel genauer beschrieben. Als komplexes Beispiel für das, was simulationstechnisch bereits im Bereich des Machbaren
liegt, und gleichsam für eine Anwendung, die zeigt, wie möglichst viele der im Rahmen dieser Arbeit entwickelten Methoden miteinander kombiniert werden können, wurde die
Calcium-Dynamik eines kompletten Dendriten innerhalb eines großen aktiven neuronalen Netzwerks simuliert.