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Jochen Knaus

Publications and source records attributed to Jochen Knaus.

2 recordsLinked to original sources

GottBERT: a pure German Language Model

Pre-trained language models have significantly advanced natural language processing (NLP), especially with the introduction of BERT and its optimized version, RoBERTa. While initial research focused on English, single-language models can be advantageous compared to multilingual ones in terms of pre-training effort, overall resource efficiency or downstream task performance. Despite the growing popularity of prompt-based LLMs, more compute-efficient BERT-like models remain highly relevant. In this work, we present the first German single-language RoBERTa model, GottBERT, pre-trained exclusively on the German portion of the OSCAR dataset. Additionally, we investigated the impact of filtering the OSCAR corpus. GottBERT was pre-trained using fairseq and standard hyperparameters. We evaluated its performance on two Named Entity Recognition (NER) tasks (Conll 2003 and GermEval 2014) and three text classification tasks (GermEval 2018 fine and coarse, and 10kGNAD) against existing German BERT models and two multilingual models. Performance was measured using the $F_{1}$ score and accuracy. The GottBERT base and large models showed competitive performance, with GottBERT leading among the base models in 4 of 6 tasks. Contrary to our expectation, the applied filtering did not significantly affect the results. To support the German NLP research community, we are releasing the GottBERT models under the MIT license.

cs.CL

Netboost: Boosting-supported network analysis improves high-dimensional omics prediction in acute myeloid leukemia and Huntington's disease

Background: State-of-the art selection methods fail to identify weak but cumulative effects of features found in many high-dimensional omics datasets. Nevertheless, these features play an important role in certain diseases. Results: We present Netboost, a three-step dimension reduction technique. First, a boosting-based filter is combined with the topological overlap measure to identify the essential edges of the network. Second, sparse hierarchical clustering is applied on the selected edges to identify modules and finally module information is aggregated by the first principal components. The primary analysis is than carried out on these summary measures instead of the original data. We demonstrate the application of the newly developed Netboost in combination with CoxBoost for survival prediction of DNA methylation and gene expression data from 180 acute myeloid leukemia (AML) patients and show, based on cross-validated prediction error curve estimates, its prediction superiority over variable selection on the full dataset as well as over an alternative clustering approach. The identified signature related to chromatin modifying enzymes was replicated in an independent dataset of AML patients in the phase II AMLSG 12-09 study. In a second application we combine Netboost with Random Forest classification and improve the disease classification error in RNA-sequencing data of Huntington's disease mice. Conclusion: Netboost improves definition of predictive variables for survival analysis and classification. It is a freely available Bioconductor R package for dimension reduction and hypothesis generation in high-dimensional omics applications.

q-bio.GN