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Institute
We present dimensionality reduction methods like autoencoders and t-SNE for visualization of high-dimensional data into a two-dimensional map. In this thesis, we initially implement basic and deep autoencoders using breast cancer and mushroom datasets. Next, we build another dimensionality reduction method t-SNE using the same datasets. The obtained visualization results of the datasets using the dimensionality reduction methods are documented in the experiments section of the thesis. The evaluation of classification and clustering for the dimensionality reduction techniques is also performed. The visualization and evaluation results of t-SNE are significantly better than the other dimensionality reduction techniques.
Glycans play an important role in the intracellular interactions of pathogenic bacteria. Pathogenic bacteria possess binding proteins capable of recognizing certain sugar motifs on other cells, which are found in glycan structures. Artificial carbohydrate synthesis allows scientists to recreate those sugar motifs in a rational, precise, and pure form. However, due to the high specificity of sugar-binding proteins, known as lectins, to glycan structures, methods for identifying suitable binding agents need to be developed. To tackle this hurdle, the Fraunhofer Institute for Cell Therapy and Immunology (Fraunhofer IZI) and the Max-Planck Institute of Colloids and Interfaces (MPIKG) developed a binding assay for the high throughput testing of sugar motifs that are presented on modular scaffolds formed by the assembly of four DNA strands into simple, branched DNA nanostructures. The first generation of this assay was used in combination with bacteria that express a fluorescent protein as a proof-of-concept. Here, the assay was optimized to be used with bacteria not possessing a marker gene for a fluorescent protein by staining their genomic DNA with SYBR® Green. For the binding assay, DNA nanostructures were combined with artificially synthesized mannose polymers, typical targets for many lectins on the surface of bacteria, presenting them in a defined constellation to bind bacteria strongly due to multivalent cooperativity. The testing of multiple mannose polymers identified monomeric mannose with a 5’-carbon linker and 1,2-linked dimeric mannose with linker as the best binding candidates for E. coli, presumably due to binding with the FimH protein on the surface. Despite similarities between the FimH proteins of E. coli and K. pneumoniae, binding was only observed between E. coli and the different sugar molecules on DNA structures. Furthermore, the degree of free movement seemed to affect the binding of mannose polymers to targeted proteins, since when utilizing a more flexible DNA nanostructure, an increase in binding could be observed. An alternative to the simple DNA nanostructures described above is the use of larger, more complex DNA origami structures consisting of several hundred strands. DNA origami structures are capable of carrying dozens of modifications at the same time. The results for the DNA origami structure showed a successful functionalization with up to 71 1,2-linked dimeric mannose with linker molecules. These results point towards a solution for the high-throughput analysis of potential binding agents for pathogenic bacteria e.g. as an alternative treatment for antibiotic-resistant.
Drought is one of the most common and dangerous threats plants have to face, costing the global agricultural sector billions of dollars every year and leading to the loss of tons of harvest. Until people drastically reduce their consumption of animal products or cellular agriculture comes of age, more and more crops will need to be produced to sustain the ever growing human population. Even then, as more areas on earth are becoming prone to drought due to climate change, we may still have to find or breed plant varieties more suitable to grow and prosper in these changing environments.
Plants respond to drought stress with a complex interplay of hormones, transcription factors, and many other functional or regulatory proteins and mapping out this web of agents is no trivial task. In the last two to three decades or so, machine learning has become immensely popular and is increasingly used to find patterns in situations that are too complex for the human mind to overlook. Even though much of the hype is focused on the latest developments in deep learning, relatively simple methods often yield superior results, especially when data is limited and expensive to gather.
This Master Thesis, conducted at the IPK in Gatersleben, develops an approach for shedding light on the phenotypic and transcriptomic processes that occur when a plant is subjected to stress. It centers around a random forest feature selection algorithm and although it is used here to illuminate drought stress response in Arabidopsis thaliana, it can be applied to all kinds of stresses in all kinds of plants.
Genetic sequence variations at the level of gene promoters influence the binding of transcription factors. In plants, this often leads to differential gene expression across natural accessions and crop cultivars. Some of these differences are propagated through molecular networks and lead to macroscopic phenotypes. However, the link between promoter sequence variation and the variation of its activity is not yet well understood. In this project, we use the power of deep learning in 728 genotypes of Arabidopsis thaliana to shed light on some aspects of that link. Convolutional neural networks were successfully implemented to predict the likelihood of a gene being expressed from its promoter sequence. These networks were also capable of highlighting known and putative new sequence motifs causal for the expression of genes. We tested our algorithms in various scenarios, including single and multiple point mutations, as well as indels on synthetic and real promoter sequences and the respective performance characteristics of the algorithm have been estimated. Finally, we showed that the decision boundary to classify genes as expressed and non-expressed depends on the sensitivity of the transcriptome profiling assay and changing it has an impact on the algorithm’s performance.
Anomaly Detection is a very acute technical problem among various business enterprises. In this thesis a combination of the Growing Neural Gas and the Generalized Matrix Learning Vector Quantization is presented as a solution based on collected theoretical and practical knowledge. The whole network is described and implemented along with references and experimental results. The proposed model is carefully documented and all the further open researching questions are stated for future investigations.
Data streams change their statistical behaviour over the time. These changes can occur gradually or abruptly with unforeseen reasons, which may effect the expected outcome. Thus it is important to detect concept drift as soon as it occurs. In this thesis we chose distance based methodology to detect presence of concept drift in the data streams. We used generalized learning vector quantization(GLVQ) and generalized matrix learning vector quantization( GMLVQ) classifiers for distance calculation between prototypes and data points. Chi-square and Kolmogorov–Smirnov tests are used to compare the distance distributions of test and train data sets to indicate the drift presence.
Convolutional Neural network (CNN) has been one of most powerful and popular preprocessing techniques employed for image classification problems. Here, we use other signal processing techniques like Fourier transform and wavelet transform to preprocess the images in conjunction with different classifiers like MLP, LVQ, GLVQ and GMLVQ and compare its performance with CNN.
In response to prevailing environmental conditions, Arabidopsis thaliana plants must increase their photosynthetic capacity to acclimate to potential harmful environmental high light stress. In order to measure these changes in acclimation capacity, different high throughput imaging-based methods can be used. In this master thesis we studied different Arabidopsis thaliana knockout mutants-and accessions in their capacity to acclimate to potential harmful environmental high light and cold temperature conditions using a high throughput phenotyping system with an integrated chlorophyll fluorescence measurement system. In order to determine the acclimation capacity, Arabidopsis thaliana knockout mutants of previously not high light assigned genes as well as accessions of two different haplotype groups with a reference and alternative allele from different countries of origin were grown under switching high light and temperature environmental conditions. Photosynthetic analysis showed that knockout mutant plants did differ in their Photosystem II operating efficiency during an increased light irradiance switch but did not significantly differ a week later under the same circumstances from the wildtype. High throughput phenotyping of haplotype accessions revealed significant better acclimation capacity in non-photochemical quenching and steady-state photosynthetic efficiency in Russian domiciled accessions with an altered SPPA gene during high light and cold stress.
Mathematics Behind the Zcash
(2020)
Among all the new developed cryptocurrencies from Bitcoin, Zcash comes out to be the strongest cryptocurrency providing both transparency and anonymity to the transactions and its users by deploying the strong mathematics of zk-SNARKs.
We discussed the zero knowledge proofs which is a basic building block for providing the functionality to zk-SNARKs. It offers schnorr and sigma protocols with interactive and noninteractive versions. Non-interactive proofs are further used in Zcash transactions where the validation of sent transaction is proved by cryptographic proof.
Further, we deploy zk-SNARKs proofs following common reference string as public parameter when transaction is made. The proof allows sender to prove that she knows a secret for an instance such that the proof is succinct, can be verified very efficiently and does not leak the
secret. Non-malleability, small proofs and very effective verification make zk-SNARKs a classic tool in Zcash. Since we deal with NP problems therefore we have considered the elliptic curve cryptography to provide the same security like RSA but with smaller parameter size.
Lastly, we explain Zcash transaction process after minting the coin, the corresponding transaction completely hides the sender, receiver and amount of transaction using zero knowledge proof.
As future considerations, we talk about the improvements that can be done in term of decentralization, efficiency by comparing with top ranked cryptocurrencies namely Ethereum and Monero, privacy preserving against the thread of quantum computers and enhancements in shielded transactions.
Robust soft learning vector quantization (RSLVQ) is a probabilistic approach of Learning vector quantization (LVQ) algorithm. Basically, the RSLVQ approach describes its functionality with respect to Gaussian mixture model and its cost function is defined in terms of likelihood ratio. Our thesis work involves an approach of modifying standard RSLVQ with non-Gaussian density functions like logistic, lognormal, and Cauchy (referred as PLVQ). In this approach, we derive new update rules for prototypes using gradient of cost function with respect to non-Gaussian density functions. We also derive new learning rules for the model parameters like s and s, by differentiating the cost function with respect to parameters. The main goal of the thesis is to compare the performance results of PLVQ model with Gaussian-RSLVQ model. Therefore, the performance of these classification models have been tested on the Iris and Seeds dataset. To visualize the results of the classification models in an adequate way, the Principal component analysis (PCA) technique has been used.