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Modern biological analysis techniques supply scientists with various forms of data. One category of such data are the so called "expression data". These data indicate the quantities of biochemical compounds present in tissue samples. Recently, expression data can be generated at a high speed. This leads in turn to amounts of data no longer analysable by classical statistical techniques. Systems biology is the new field that focuses on the modelling of this information. At present, various methods are used for this purpose. One superordinate class of these methods is machine learning. Methods of this kind had, until recently, predominantly been used for classification and prediction tasks. This neglected a powerful secondary benefit: the ability to induce interpretable models. Obtaining such models from data has become a key issue within Systems biology. Numerous approaches have been proposed and intensively discussed. This thesis focuses on the examination and exploitation of one basic technique: decision trees. The concept of comparing sets of decision trees is developed. This method offers the possibility of identifying significant thresholds in continuous or discrete valued attributes through their corresponding set of decision trees. Finding significant thresholds in attributes is a means of identifying states in living organisms. Knowing about states is an invaluable clue to the understanding of dynamic processes in organisms. Applied to metabolite concentration data, the proposed method was able to identify states which were not found with conventional techniques for threshold extraction. A second approach exploits the structure of sets of decision trees for the discovery of combinatorial dependencies between attributes. Previous work on this issue has focused either on expensive computational methods or the interpretation of single decision trees a very limited exploitation of the data. This has led to incomplete or unstable results. That is why a new method is developed that uses sets of decision trees to overcome these limitations. Both the introduced methods are available as software tools. They can be applied consecutively or separately. That way they make up a package of analytical tools that usefully supplement existing methods. By means of these tools, the newly introduced methods were able to confirm existing knowledge and to suggest interesting and new relationships between metabolites.
RNA folding is assumed to be a hierarchical process. The secondary structure of an RNA molecule, signified by base-pairing and stacking interactions between the paired bases, is formed first. Subsequently, the RNA molecule adopts an energetically favorable three-dimensional conformation in the structural space determined mainly by the rotational degrees of freedom associated with the backbone of regions of unpaired nucleotides (loops). To what extent the backbone conformation of RNA loops also results from interactions within the local sequence context or rather follows global optimization constraints alone has not been addressed yet. Because the majority of base stacking interactions are exerted locally, a critical influence of local sequence on local structure appears plausible. Thus, local loop structure ought to be predictable, at least in part, from the local sequence context alone. To test this hypothesis, we used Random Forests on a nonredundant data set of unpaired nucleotides extracted from 97 X-ray structures from the Protein Data Bank (PDB) to predict discrete backbone angle conformations given by the discretized eta/theta-pseudo-torsional space. Predictions on balanced sets with four to six conformational classes using local sequence information yielded average accuracies of up to 55%, thus significantly better than expected by chance (17%-25%). Bases close to the central nucleotide appear to be most tightly linked to its conformation. Our results suggest that RNA loop structure does not only depend on long-range base-pairing interactions; instead, it appears that local sequence context exerts a significant influence on the formation of the local loop structure.
Learning a model for the relationship between the attributes and the annotated labels of data examples serves two purposes. Firstly, it enables the prediction of the label for examples without annotation. Secondly, the parameters of the model can provide useful insights into the structure of the data. If the data has an inherent partitioned structure, it is natural to mirror this structure in the model. Such mixture models predict by combining the individual predictions generated by the mixture components which correspond to the partitions in the data. Often the partitioned structure is latent, and has to be inferred when learning the mixture model. Directly evaluating the accuracy of the inferred partition structure is, in many cases, impossible because the ground truth cannot be obtained for comparison. However it can be assessed indirectly by measuring the prediction accuracy of the mixture model that arises from it. This thesis addresses the interplay between the improvement of predictive accuracy by uncovering latent cluster structure in data, and further addresses the validation of the estimated structure by measuring the accuracy of the resulting predictive model. In the application of filtering unsolicited emails, the emails in the training set are latently clustered into advertisement campaigns. Uncovering this latent structure allows filtering of future emails with very low false positive rates. In order to model the cluster structure, a Bayesian clustering model for dependent binary features is developed in this thesis. Knowing the clustering of emails into campaigns can also aid in uncovering which emails have been sent on behalf of the same network of captured hosts, so-called botnets. This association of emails to networks is another layer of latent clustering. Uncovering this latent structure allows service providers to further increase the accuracy of email filtering and to effectively defend against distributed denial-of-service attacks. To this end, a discriminative clustering model is derived in this thesis that is based on the graph of observed emails. The partitionings inferred using this model are evaluated through their capacity to predict the campaigns of new emails. Furthermore, when classifying the content of emails, statistical information about the sending server can be valuable. Learning a model that is able to make use of it requires training data that includes server statistics. In order to also use training data where the server statistics are missing, a model that is a mixture over potentially all substitutions thereof is developed. Another application is to predict the navigation behavior of the users of a website. Here, there is no a priori partitioning of the users into clusters, but to understand different usage scenarios and design different layouts for them, imposing a partitioning is necessary. The presented approach simultaneously optimizes the discriminative as well as the predictive power of the clusters. Each model is evaluated on real-world data and compared to baseline methods. The results show that explicitly modeling the assumptions about the latent cluster structure leads to improved predictions compared to the baselines. It is beneficial to incorporate a small number of hyperparameters that can be tuned to yield the best predictions in cases where the prediction accuracy can not be optimized directly.
In order to evade detection by network-traffic analysis, a growing proportion of malware uses the encrypted HTTPS protocol. We explore the problem of detecting malware on client computers based on HTTPS traffic analysis. In this setting, malware has to be detected based on the host IP address, ports, timestamp, and data volume information of TCP/IP packets that are sent and received by all the applications on the client. We develop a scalable protocol that allows us to collect network flows of known malicious and benign applications as training data and derive a malware-detection method based on a neural networks and sequence classification. We study the method's ability to detect known and new, unknown malware in a large-scale empirical study.
Referential Choice
(2016)
We report a study of referential choice in discourse production, understood as the choice between various types of referential devices, such as pronouns and full noun phrases. Our goal is to predict referential choice, and to explore to what extent such prediction is possible. Our approach to referential choice includes a cognitively informed theoretical component, corpus analysis, machine learning methods and experimentation with human participants. Machine learning algorithms make use of 25 factors, including referent’s properties (such as animacy and protagonism), the distance between a referential expression and its antecedent, the antecedent’s syntactic role, and so on. Having found the predictions of our algorithm to coincide with the original almost 90% of the time, we hypothesized that fully accurate prediction is not possible because, in many situations, more than one referential option is available. This hypothesis was supported by an experimental study, in which participants answered questions about either the original text in the corpus, or about a text modified in accordance with the algorithm’s prediction. Proportions of correct answers to these questions, as well as participants’ rating of the questions’ difficulty, suggested that divergences between the algorithm’s prediction and the original referential device in the corpus occur overwhelmingly in situations where the referential choice is not categorical.
Referential Choice
(2016)
We report a study of referential choice in discourse production, understood as the choice between various types of referential devices, such as pronouns and full noun phrases. Our goal is to predict referential choice, and to explore to what extent such prediction is possible. Our approach to referential choice includes a cognitively informed theoretical component, corpus analysis, machine learning methods and experimentation with human participants. Machine learning algorithms make use of 25 factors, including referent’s properties (such as animacy and protagonism), the distance between a referential expression and its antecedent, the antecedent’s syntactic role, and so on. Having found the predictions of our algorithm to coincide with the original almost 90% of the time, we hypothesized that fully accurate prediction is not possible because, in many situations, more than one referential option is available. This hypothesis was supported by an experimental study, in which participants answered questions about either the original text in the corpus, or about a text modified in accordance with the algorithm’s prediction. Proportions of correct answers to these questions, as well as participants’ rating of the questions’ difficulty, suggested that divergences between the algorithm’s prediction and the original referential device in the corpus occur overwhelmingly in situations where the referential choice is not categorical.
Classification of clouds, cirrus, snow, shadows and clear sky areas is a crucial step in the pre-processing of optical remote sensing images and is a valuable input for their atmospheric correction. The Multi-Spectral Imager on board the Sentinel-2's of the Copernicus program offers optimized bands for this task and delivers unprecedented amounts of data regarding spatial sampling, global coverage, spectral coverage, and repetition rate. Efficient algorithms are needed to process, or possibly reprocess, those big amounts of data. Techniques based on top-of-atmosphere reflectance spectra for single-pixels without exploitation of external data or spatial context offer the largest potential for parallel data processing and highly optimized processing throughput. Such algorithms can be seen as a baseline for possible trade-offs in processing performance when the application of more sophisticated methods is discussed. We present several ready-to-use classification algorithms which are all based on a publicly available database of manually classified Sentinel-2A images. These algorithms are based on commonly used and newly developed machine learning techniques which drastically reduce the amount of time needed to update the algorithms when new images are added to the database. Several ready-to-use decision trees are presented which allow to correctly label about 91% of the spectra within a validation dataset. While decision trees are simple to implement and easy to understand, they offer only limited classification skill. It improves to 98% when the presented algorithm based on the classical Bayesian method is applied. This method has only recently been used for this task and shows excellent performance concerning classification skill and processing performance. A comparison of the presented algorithms with other commonly used techniques such as random forests, stochastic gradient descent, or support vector machines is also given. Especially random forests and support vector machines show similar classification skill as the classical Bayesian method.
We report a study of referential choice in discourse production, understood as the choice between various types of referential devices, such as pronouns and full noun phrases. Our goal is to predict referential choice, and to explore to what extent such prediction is possible. Our approach to referential choice includes a cognitively informed theoretical component, corpus analysis, machine learning methods and experimentation with human participants. Machine learning algorithms make use of 25 factors, including referent’s properties (such as animacy and protagonism), the distance between a referential expression and its antecedent, the antecedent’s syntactic role, and so on. Having found the predictions of our algorithm to coincide with the original almost 90% of the time, we hypothesized that fully accurate prediction is not possible because, in many situations, more than one referential option is available. This hypothesis was supported by an experimental study, in which participants answered questions about either the original text in the corpus, or about a text modified in accordance with the algorithm’s prediction. Proportions of correct answers to these questions, as well as participants’ rating of the questions’ difficulty, suggested that divergences between the algorithm’s prediction and the original referential device in the corpus occur overwhelmingly in situations where the referential choice is not categorical.
HPI Future SOC Lab
(2016)
The “HPI Future SOC Lab” is a cooperation of the Hasso Plattner Institute (HPI) and industrial partners. Its mission is to enable and promote exchange and interaction between the research community and the industrial partners.
The HPI Future SOC Lab provides researchers with free of charge access to a complete infrastructure of state of the art hard and software. This infrastructure includes components, which might be too expensive for an ordinary research environment, such as servers with up to 64 cores and 2 TB main memory. The offerings address researchers particularly from but not limited to the areas of computer science and business information systems. Main areas of research include cloud computing, parallelization, and In-Memory technologies.
This technical report presents results of research projects executed in 2016. Selected projects have presented their results on April 5th and November 3th 2016 at the Future SOC Lab Day events.
Potato (Solanum tuberosum L.) is one of the most important food crops worldwide. Current potato varieties are highly susceptible to drought stress. In view of global climate change, selection of cultivars with improved drought tolerance and high yield potential is of paramount importance. Drought tolerance breeding of potato is currently based on direct selection according to yield and phenotypic traits and requires multiple trials under drought conditions. Marker-assisted selection (MAS) is cheaper, faster and reduces classification errors caused by noncontrolled environmental effects. We analysed 31 potato cultivars grown under optimal and reduced water supply in six independent field trials. Drought tolerance was determined as tuber starch yield. Leaf samples from young plants were screened for preselected transcript and nontargeted metabolite abundance using qRT-PCR and GC-MS profiling, respectively. Transcript marker candidates were selected from a published RNA-Seq data set. A Random Forest machine learning approach extracted metabolite and transcript markers for drought tolerance prediction with low error rates of 6% and 9%, respectively. Moreover, by combining transcript and metabolite markers, the prediction error was reduced to 4.3%. Feature selection from Random Forest models allowed model minimization, yielding a minimal combination of only 20 metabolite and transcript markers that were successfully tested for their reproducibility in 16 independent agronomic field trials. We demonstrate that a minimum combination of transcript and metabolite markers sampled at early cultivation stages predicts potato yield stability under drought largely independent of seasonal and regional agronomic conditions.