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New Publication: Automated Process Synthesis Using Reinforcement Learning @ ESCAPE31

New Publication: Automated Process Synthesis Using Reinforcement Learning @ ESCAPE31

A novel method for automated flowsheet synthesis based on reinforcement learning (RL) is presented. Using the interaction with a process simulator as the learning environment, an agent is trained to solve the task of synthesizing process flowsheets without any heuristics or prior knowledge. The developed RL method models the task as a competitive two-player game that the agent plays against itself during training. The concept is proven to work along an example with a quaternary mixture that is processed using a reactor or distillation units.

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New Publication: Automated synthesis of steady-state continuous processes using reinforcement learning

New Publication: Automated Process Synthesis Using Reinforcement Learning @ ESCAPE31

Automated flowsheet synthesis is an important field in computer-aided process engineering. The present work demonstrates how reinforcement learning can be used for automated flowsheet synthesis without any heuristics or prior knowledge of conceptual design. The environment consists of a steady-state flowsheet simulator that contains all physical knowledge. An agent is trained to take discrete actions and sequentially build up flowsheets that solve a given process problem. A novel method named SynGameZero is developed to ensure good exploration schemes in the complex problem. Therein, flowsheet synthesis is modelled as a game of two competing players. The agent plays this game against itself during training and consists of an artificial neural network and a tree search for forward planning. The method is applied successfully to a reaction-distillation process in a quaternary system.

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New Book Chapter: Design and Analysis of RNA Sequencing Data

New Book Chapter:  Design and Analysis of RNA Sequencing Data

In this chapter, we introduce the concept of RNA-Seq analyses. First, we start to provide an overview of a typical RNA-Seq experiment that includes extraction of sample RNA, enrichment, and cDNA library preparation. Next, we review tools for quality control and data pre-processing followed by a standard workflow to perform RNA-Seq analyses. For this purpose, we discuss two common RNA-Seq strategies, that is a reference-based alignment and a de novo assembly approach. We learn how to do basic downstream analyses of RNA-Seq data, including quantification of expressed genes, differential gene expression (DE) between different groups as well as functional gene analysis. Eventually, we provide a best-practice example for a reference-based RNA-Seq analysis from beginning to end, including all necessary tools and steps on GitHub: https://github.com/grimmlab/BookChapter-RNA-Seq-Analyses.

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New Publication in Plant Methods

New Publication in Plant Methods

New publication about “Accurate machine learning-based germination detection, prediction and quality assessment of three grain crops” just got published in Plant Methods.

Our proposed machine learning-based method can help to speed up the assessment of seed germination experiments for different seed cultivars. It has lower error rates and a higher performance compared to conventional and manual methods, leading to more accurate germination indices and quality assessments of seeds.

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New Publication in Bioinformatics

New Publication in Bioinformatics

New publication about “Network-guided search for genetic heterogeneity between gene pairs” just got published in Bioinformatics: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa581/5861532

We propose a novel method for finding pairs of interacting genes that are, upon combination, associated with a phenotype of interest under a model of genetic heterogeneity. We guide the interaction search using biological prior knowledge in the form of protein-protein interaction networks. Our method controls type I error and outperforms state-of-the-art methods with respect to statistical power. Additionally, we find novel associations for multiple A. thaliana phenotypes, and for a study of rare variants in migraine patients.

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Kontakt

Professorship Bioinformatics

Petersgasse 18
94315 Straubing

Head

Prof. Dr. Dominik Grimm

Phone: +49 (0) 9421 187-230
Fax: +49 (0) 9421 187-285
E-Mail: dominik.grimm@hswt.de

Team Assistant

Anna Fischer

Phone: +49 (0) 9421 187-231
Fax: +49 (0) 9421 187-285
E-Mail: anna.fischer@hswt.de