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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.
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.
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.
Co-design of a trustworthy AI system in healthcare: deep learning based skin lesion classifier
(2021)
This paper documents how an ethically aligned co-design methodology ensures trustworthiness in the early design phase of an artificial intelligence (AI) system component for healthcare. The system explains decisions made by deep learning networks analyzing images of skin lesions. The co-design of trustworthy AI developed here used a holistic approach rather than a static ethical checklist and required a multidisciplinary team of experts working with the AI designers and their managers. Ethical, legal, and technical issues potentially arising from the future use of the AI system were investigated. This paper is a first report on co-designing in the early design phase. Our results can also serve as guidance for other early-phase AI-similar tool developments.
Point-based geometry representations have become widely used in numerous contexts, ranging from particle-based simulations, over stereo image matching, to depth sensing via light detection and ranging. Our application focus is on the reconstruction of curved line structures in noisy 3D point cloud data. Respective algorithms operating on such point clouds often rely on the notion of a local neighborhood. Regarding the latter, our approach employs multi-scale neighborhoods, for which weighted covariance measures of local points are determined. Curved line structures are reconstructed via vector field tracing, using a bidirectional piecewise streamline integration. We also introduce an automatic selection of optimal starting points via multi-scale geometric measures. The pipeline development and choice of parameters was driven by an extensive, automated initial analysis process on over a million prototype test cases. The behavior of our approach is controlled by several parameters — the majority being set automatically, leaving only three to be controlled by a user. In an extensive, automated final evaluation, we cover over one hundred thousand parameter sets, including 3D test geometries with varying curvature, sharp corners, intersections, data holes, and systematically applied varying types of noise. Further, we analyzed different choices for the point of reference in the co-variance computation; using a weighted mean performed best in most cases. In addition, we compared our method to current, publicly available line reconstruction frameworks. Up to thirty times faster execution times were achieved in some cases, at comparable error measures. Finally, we also demonstrate an exemplary application on four real-world 3D light detection and ranging datasets, extracting power line cables.
In this talk we presented a novel technique, based on Deep Learning, to determine the impact parameter of nuclear collisions at the CBM experiment. PointNet based Deep Learning models are trained on UrQMD followed by CBMRoot simulations of Au+Au collisions at 10 AGeV to reconstruct the impact parameter of collisions from raw experimental data such as hits of the particles in the detector planes, tracks reconstructed from the hits or their combinations. The PointNet models can perform fast, accurate, event-by-event impact parameter determination in heavy ion collision experiments. They are shown to outperform a simple model which maps the track multiplicity to the impact parameter. While conventional methods for centrality classification merely provide an expected impact parameter distribution for a given centrality class, the PointNet models predict the impact parameter from 2–14 fm on an event-by-event basis with a mean error of −0.33 to 0.22 fm.
The ongoing digitalization of educational resources and the use of the internet lead to a steady increase of potentially available learning media. However, many of the media which are used for educational purposes have not been designed specifically for teaching and learning. Usually, linguistic criteria of readability and comprehensibility as well as content-related criteria are used independently to assess and compare the quality of educational media. This also holds true for educational media used in economics. This article aims to improve the analysis of textual learning media used in economic education by drawing on threshold concepts. Threshold concepts are key terms in knowledge acquisition within a domain. From a linguistic perspective, however, threshold concepts are instances of specialized vocabularies, exhibiting particular linguistic features. In three kinds of (German) resources, namely in textbooks, in newspapers, and on Wikipedia, we investigate the distributive profiles of 63 threshold concepts identified in economics education (which have been collected from threshold concept research). We looked at the threshold concepts' frequency distribution, their compound distribution, and their network structure within the three kinds of resources. The two main findings of our analysis show that firstly, the three kinds of resources can indeed be distinguished in terms of their threshold concepts' profiles. Secondly, Wikipedia definitely shows stronger associative connections between economic threshold concepts than the other sources. We discuss the findings in relation to adequate media use for teaching and learning—not only in economic education.