Nghia Duong‐Trung

Nghia Duong-Trung, Stefan Born, Jong Woo Kim et al.

Machine learning (ML) is becoming increasingly crucial in many fields of engineering but has not yet played out its full potential in bioprocess engineering. While experimentation has been accelerated by increasing levels of lab automation, experimental planning and data modeling are still largerly depend on human intervention. ML can be seen as a set of tools that contribute to the automation of the whole experimental cycle, including model building and practical planning, thus allowing human experts to focus on the more demanding and overarching cognitive tasks. First, probabilistic programming is used for the autonomous building of predictive models. Second, machine learning automatically assesses alternative decisions by planning experiments to test hypotheses and conducting investigations to gather informative data that focus on model selection based on the uncertainty of model predictions. This review provides a comprehensive overview of ML-based automation in bioprocess development. On the one hand, the biotech and bioengineering community should be aware of the potential and, most importantly, the limitation of existing ML solutions for their application in biotechnology and biopharma. On the other hand, it is essential to identify the missing links to enable the easy implementation of ML and Artificial Intelligence (AI) tools in valuable solutions for the bio-community.

Nghia Duong-Trung, Duc-Manh Nguyen, Danh Le-Phuoc

Despite the notable advancements in numerous Transformer-based models, the task of long multi-horizon time series forecasting remains a persistent challenge, especially towards explainability. Focusing on commonly used saliency maps in explaining DNN in general, our quest is to build attention-based architecture that can automatically encode saliency-related temporal patterns by establishing connections with appropriate attention heads. Hence, this paper introduces Temporal Saliency Detection (TSD), an effective approach that builds upon the attention mechanism and applies it to multi-horizon time series prediction. While our proposed architecture adheres to the general encoder-decoder structure, it undergoes a significant renovation in the encoder component, wherein we incorporate a series of information contracting and expanding blocks inspired by the U-Net style architecture. The TSD approach facilitates the multiresolution analysis of saliency patterns by condensing multi-heads, thereby progressively enhancing the forecasting of complex time series data. Empirical evaluations illustrate the superiority of our proposed approach compared to other models across multiple standard benchmark datasets in diverse far-horizon forecasting settings. The initial TSD achieves substantial relative improvements of 31% and 46% over several models in the context of multivariate and univariate prediction. We believe the comprehensive investigations presented in this study will offer valuable insights and benefits to future research endeavors.

Kiran Madhusudhanan, Johannes Burchert, Nghia Duong-Trung et al.

Time series data is ubiquitous in research as well as in a wide variety of industrial applications. Effectively analyzing the available historical data and providing insights into the far future allows us to make effective decisions. Recent research has witnessed the superior performance of transformer-based architectures, especially in the regime of far horizon time series forecasting. However, the current state of the art sparse Transformer architectures fail to couple down- and upsampling procedures to produce outputs in a similar resolution as the input. We propose the Yformer model, based on a novel Y-shaped encoder-decoder architecture that (1) uses direct connection from the downscaled encoder layer to the corresponding upsampled decoder layer in a U-Net inspired architecture, (2) Combines the downscaling/upsampling with sparse attention to capture long-range effects, and (3) stabilizes the encoder-decoder stacks with the addition of an auxiliary reconstruction loss. Extensive experiments have been conducted with relevant baselines on four benchmark datasets, demonstrating an average improvement of 19.82, 18.41 percentage MSE and 13.62, 11.85 percentage MAE in comparison to the current state of the art for the univariate and the multivariate settings respectively.

Martin Wistuba, Nghia Duong-Trung, Nicolas Schilling et al.

We describe the solution of team ISMLL for the ECML-PKDD 2016 Discovery Challenge on Bank Card Usage for both tasks. Our solution is based on three pillars. Gradient boosted decision trees as a strong regression and classification model, an intensive search for good hyperparameter configurations and strong features that exploit geolocation information. This approach achieved the best performance on the public leaderboard for the first task and a decent fourth position for the second task.