Bayesian Uncertainty Estimation by Hamiltonian Monte Carlo: Applications to Cardiac MRI Segmentation

Deep learning (DL)-based methods have achieved state-of-the-art performance for a wide range of medical image segmentation tasks. Nevertheless, recent studies show that deep neural networks (DNNs) can be miscalibrated and overconfident, leading to "silent failures" that are risky} for clinical applications. Bayesian statistics provide an intuitive approach to DL failure detection, based on posterior probability estimation. However, Bayesian DL, and in particular the posterior estimation, is intractable for large medical image segmentation DNNs. To tackle this challenge, we propose a Bayesian learning framework by Hamiltonian Monte Carlo (HMC), tempered by cold posterior (CP) to accommodate medical data augmentation, named HMC-CP. For HMC computation, we further propose a cyclical annealing strategy, which captures both local and global geometries of the posterior distribution, enabling highly efficient Bayesian DNN training with the same computational budget requirements as training a single DNN. The resulting Bayesian DNN outputs an ensemble segmentation along with the segmentation uncertainty. We evaluate the proposed HMC-CP extensively on cardiac magnetic resonance image (MRI) segmentation, using in-domain steady-state free precession (SSFP) cine images as well as out-of-domain datasets of quantitative $T_1$ and $T_2$ mapping.

MachineLearnAthon: An Action-Oriented Machine Learning Didactic Concept

Machine Learning (ML) techniques are encountered nowadays across disciplines, from social sciences, through natural sciences to engineering. The broad application of ML and the accelerated pace of its evolution lead to an increasing need for dedicated teaching concepts aimed at making the application of this technology more reliable and responsible. However, teaching ML is a daunting task. Aside from the methodological complexity of ML algorithms, both with respect to theory and implementation, the interdisciplinary and empirical nature of the field need to be taken into consideration. This paper introduces the MachineLearnAthon format, an innovative didactic concept designed to be inclusive for students of different disciplines with heterogeneous levels of mathematics, programming and domain expertise. At the heart of the concept lie ML challenges, which make use of industrial data sets to solve real-world problems. These cover the entire ML pipeline, promoting data literacy and practical skills, from data preparation, through deployment, to evaluation.

Toward autocorrection of chemical process flowsheets using large language models

The process engineering domain widely uses Process Flow Diagrams (PFDs) and Process and Instrumentation Diagrams (P&IDs) to represent process flows and equipment configurations. However, the P&IDs and PFDs, hereafter called flowsheets, can contain errors causing safety hazards, inefficient operation, and unnecessary expenses. Correcting and verifying flowsheets is a tedious, manual process. We propose a novel generative AI methodology for automatically identifying errors in flowsheets and suggesting corrections to the user, i.e., autocorrecting flowsheets. Inspired by the breakthrough of Large Language Models (LLMs) for grammatical autocorrection of human language, we investigate LLMs for the autocorrection of flowsheets. The input to the model is a potentially erroneous flowsheet and the output of the model are suggestions for a corrected flowsheet. We train our autocorrection model on a synthetic dataset in a supervised manner. The model achieves a top-1 accuracy of 80% and a top-5 accuracy of 84% on an independent test dataset of synthetically generated flowsheets. The results suggest that the model can learn to autocorrect the synthetic flowsheets. We envision that flowsheet autocorrection will become a useful tool for chemical engineers.

Mixed-Integer Optimisation of Graph Neural Networks for Computer-Aided Molecular Design

ReLU neural networks have been modelled as constraints in mixed integer linear programming (MILP), enabling surrogate-based optimisation in various domains and efficient solution of machine learning certification problems. However, previous works are mostly limited to MLPs. Graph neural networks (GNNs) can learn from non-euclidean data structures such as molecular structures efficiently and are thus highly relevant to computer-aided molecular design (CAMD). We propose a bilinear formulation for ReLU Graph Convolutional Neural Networks and a MILP formulation for ReLU GraphSAGE models. These formulations enable solving optimisation problems with trained GNNs embedded to global optimality. We apply our optimization approach to an illustrative CAMD case study where the formulations of the trained GNNs are used to design molecules with optimal boiling points.

Deep reinforcement learning for process design: Review and perspective

The transformation towards renewable energy and feedstock supply in the chemical industry requires new conceptual process design approaches. Recently, breakthroughs in artificial intelligence offer opportunities to accelerate this transition. Specifically, deep reinforcement learning, a subclass of machine learning, has shown the potential to solve complex decision-making problems and aid sustainable process design. We survey state-of-the-art research in reinforcement learning for process design through three major elements: (i) information representation, (ii) agent architecture, and (iii) environment and reward. Moreover, we discuss perspectives on underlying challenges and promising future works to unfold the full potential of reinforcement learning for process design in chemical engineering.

Data augmentation for machine learning of chemical process flowsheets

Artificial intelligence has great potential for accelerating the design and engineering of chemical processes. Recently, we have shown that transformer-based language models can learn to auto-complete chemical process flowsheets using the SFILES 2.0 string notation. Also, we showed that language translation models can be used to translate Process Flow Diagrams (PFDs) into Process and Instrumentation Diagrams (P&IDs). However, artificial intelligence methods require big data and flowsheet data is currently limited. To mitigate this challenge of limited data, we propose a new data augmentation methodology for flowsheet data that is represented in the SFILES 2.0 notation. We show that the proposed data augmentation improves the performance of artificial intelligence-based process design models. In our case study flowsheet data augmentation improved the prediction uncertainty of the flowsheet autocompletion model by 14.7%. In the future, our flowsheet data augmentation can be used for other machine learning algorithms on chemical process flowsheets that are based on SFILES notation.

Transfer learning for process design with reinforcement learning

Process design is a creative task that is currently performed manually by engineers. Artificial intelligence provides new potential to facilitate process design. Specifically, reinforcement learning (RL) has shown some success in automating process design by integrating data-driven models that learn to build process flowsheets with process simulation in an iterative design process. However, one major challenge in the learning process is that the RL agent demands numerous process simulations in rigorous process simulators, thereby requiring long simulation times and expensive computational power. Therefore, typically short-cut simulation methods are employed to accelerate the learning process. Short-cut methods can, however, lead to inaccurate results. We thus propose to utilize transfer learning for process design with RL in combination with rigorous simulation methods. Transfer learning is an established approach from machine learning that stores knowledge gained while solving one problem and reuses this information on a different target domain. We integrate transfer learning in our RL framework for process design and apply it to an illustrative case study comprising equilibrium reactions, azeotropic separation, and recycles, our method can design economically feasible flowsheets with stable interaction with DWSIM. Our results show that transfer learning enables RL to economically design feasible flowsheets with DWSIM, resulting in a flowsheet with an 8% higher revenue. And the learning time can be reduced by a factor of 2.

Learning from flowsheets: A generative transformer model for autocompletion of flowsheets

We propose a novel method enabling autocompletion of chemical flowsheets. This idea is inspired by the autocompletion of text. We represent flowsheets as strings using the text-based SFILES 2.0 notation and learn the grammatical structure of the SFILES 2.0 language and common patterns in flowsheets using a transformer-based language model. We pre-train our model on synthetically generated flowsheets to learn the flowsheet language grammar. Then, we fine-tune our model in a transfer learning step on real flowsheet topologies. Finally, we use the trained model for causal language modeling to autocomplete flowsheets. Eventually, the proposed method can provide chemical engineers with recommendations during interactive flowsheet synthesis. The results demonstrate a high potential of this approach for future AI-assisted process synthesis.

Physical Pooling Functions in Graph Neural Networks for Molecular Property Prediction

Graph neural networks (GNNs) are emerging in chemical engineering for the end-to-end learning of physicochemical properties based on molecular graphs. A key element of GNNs is the pooling function which combines atom feature vectors into molecular fingerprints. Most previous works use a standard pooling function to predict a variety of properties. However, unsuitable pooling functions can lead to unphysical GNNs that poorly generalize. We compare and select meaningful GNN pooling methods based on physical knowledge about the learned properties. The impact of physical pooling functions is demonstrated with molecular properties calculated from quantum mechanical computations. We also compare our results to the recent set2set pooling approach. We recommend using sum pooling for the prediction of properties that depend on molecular size and compare pooling functions for properties that are molecular size-independent. Overall, we show that the use of physical pooling functions significantly enhances generalization.

SFILES 2.0: An extended text-based flowsheet representation

SFILES is a text-based notation for chemical process flowsheets. It was originally proposed by d'Anterroches (2006) who was inspired by the text-based SMILES notation for molecules. The text-based format has several advantages compared to flowsheet images regarding the storage format, computational accessibility, and eventually for data analysis and processing. However, the original SFILES version cannot describe essential flowsheet configurations unambiguously, such as the distinction between top and bottom products. Neither is it capable of describing the control structure required for the safe and reliable operation of chemical processes. Also, there is no publicly available software for decoding or encoding chemical process topologies to SFILES. We propose the SFILES 2.0 with a complete description of the extended notation and naming conventions. Additionally, we provide open-source software for the automated conversion between flowsheet graphs and SFILES 2.0 strings. This way, we hope to encourage researchers and engineers to publish their flowsheet topologies as SFILES 2.0 strings. The ultimate goal is to set the standards for creating a FAIR database of chemical process flowsheets, which would be of great value for future data analysis and processing.