EAP4EMSIG -- Experiment Automation Pipeline for Event-Driven Microscopy to Smart Microfluidic Single-Cells Analysis

Microfluidic Live-Cell Imaging (MLCI) generates high-quality data that allows biotechnologists to study cellular growth dynamics in detail. However, obtaining these continuous data over extended periods is challenging, particularly in achieving accurate and consistent real-time event classification at the intersection of imaging and stochastic biology. To address this issue, we introduce the Experiment Automation Pipeline for Event-Driven Microscopy to Smart Microfluidic Single-Cells Analysis (EAP4EMSIG). In particular, we present initial zero-shot results from the real-time segmentation module of our approach. Our findings indicate that among four State-Of-The- Art (SOTA) segmentation methods evaluated, Omnipose delivers the highest Panoptic Quality (PQ) score of 0.9336, while Contour Proposal Network (CPN) achieves the fastest inference time of 185 ms with the second-highest PQ score of 0.8575. Furthermore, we observed that the vision foundation model Segment Anything is unsuitable for this particular use case.

Generating peak-aware pseudo-measurements for low-voltage feeders using metadata of distribution system operators

Distribution system operators (DSOs) must cope with new challenges such as the reconstruction of distribution grids along climate neutrality pathways or the ability to manage and control consumption and generation in the grid. In order to meet the challenges, measurements within the distribution grid often form the basis for DSOs. Hence, it is an urgent problem that measurement devices are not installed in many low-voltage (LV) grids. In order to overcome this problem, we present an approach to estimate pseudo-measurements for non-measured LV feeders based on the metadata of the respective feeder using regression models. The feeder metadata comprise information about the number of grid connection points, the installed power of consumers and producers, and billing data in the downstream LV grid. Additionally, we use weather data, calendar data and timestamp information as model features. The existing measurements are used as model target. We extensively evaluate the estimated pseudo-measurements on a large real-world dataset with 2,323 LV feeders characterized by both consumption and feed-in. For this purpose, we introduce peak metrics inspired by the BigDEAL challenge for the peak magnitude, timing and shape for both consumption and feed-in. As regression models, we use XGBoost, a multilayer perceptron (MLP) and a linear regression (LR). We observe that XGBoost and MLP outperform the LR. Furthermore, the results show that the approach adapts to different weather, calendar and timestamp conditions and produces realistic load curves based on the feeder metadata. In the future, the approach can be adapted to other grid levels like substation transformers and can supplement research fields like load modeling, state estimation and LV load forecasting.

Coverage Path Planning for Thermal Interface Materials

Thermal management of power electronics and Electronic Control Units is crucial in times of increasing power densities and limited assembly space. Electric and autonomous vehicles are a prominent application field. Thermal Interface Materials are used to transfer heat from a semiconductor to a heatsink. They are applied along a dispense path onto the semiconductor and spread over its entire surface once the heatsink is joined. To plan this application path, design engineers typically perform an iterative trial-and-error procedure of elaborate simulations and manual experiments. We propose a fully automated optimization approach, which clearly outperforms the current manual path planning and respects all relevant manufacturing constraints. An optimum dispense path increases the reliability of the thermal interface and makes the manufacturing more sustainable by reducing material waste. We show results on multiple real products from automotive series production, including an experimental validation on actual series manufacturing equipment.

Iterative Cluster Harvesting for Wafer Map Defect Patterns

Unsupervised clustering of wafer map defect patterns is challenging because the appearance of certain defect patterns varies significantly. This includes changing shape, location, density, and rotation of the defect area on the wafer. We present a harvesting approach, which can cluster even challenging defect patterns of wafer maps well. Our approach makes use of a well-known, three-step procedure: feature extraction, dimension reduction, and clustering. The novelty in our approach lies in repeating dimensionality reduction and clustering iteratively while filtering out one cluster per iteration according to its silhouette score. This method leads to an improvement of clustering performance in general and is especially useful for difficult defect patterns. The low computational effort allows for a quick assessment of large datasets and can be used to support manual labeling efforts. We benchmark against related approaches from the literature and show improved results on a real-world industrial dataset.

AI-based automated active learning for discovery of hidden dynamic processes: A use case in light microscopy

In the biomedical environment, experiments assessing dynamic processes are primarily performed by a human acquisition supervisor. Contemporary implementations of such experiments frequently aim to acquire a maximum number of relevant events from sometimes several hundred parallel, non-synchronous processes. Since in some high-throughput experiments, only one or a few instances of a given process can be observed simultaneously, a strategy for planning and executing an efficient acquisition paradigm is essential. To address this problem, we present two new methods in this paper. The first method, Encoded Dynamic Process (EDP), is Artificial Intelligence (AI)-based and represents dynamic processes so as to allow prediction of pseudo-time values from single still images. Second, with Experiment Automation Pipeline for Dynamic Processes (EAPDP), we present a Machine Learning Operations (MLOps)-based pipeline that uses the extracted knowledge from EDP to efficiently schedule acquisition in biomedical experiments for dynamic processes in practice. In a first experiment, we show that the pre-trained State-Of-The- Art (SOTA) object segmentation method Contour Proposal Networks (CPN) works reliably as a module of EAPDP to extract the relevant object for EDP from the acquired three-dimensional image stack.

MLOps for Scarce Image Data: A Use Case in Microscopic Image Analysis

Nowadays, Machine Learning (ML) is experiencing tremendous popularity that has never been seen before. The operationalization of ML models is governed by a set of concepts and methods referred to as Machine Learning Operations (MLOps). Nevertheless, researchers, as well as professionals, often focus more on the automation aspect and neglect the continuous deployment and monitoring aspects of MLOps. As a result, there is a lack of continuous learning through the flow of feedback from production to development, causing unexpected model deterioration over time due to concept drifts, particularly when dealing with scarce data. This work explores the complete application of MLOps in the context of scarce data analysis. The paper proposes a new holistic approach to enhance biomedical image analysis. Our method includes: a fingerprinting process that enables selecting the best models, datasets, and model development strategy relative to the image analysis task at hand; an automated model development stage; and a continuous deployment and monitoring process to ensure continuous learning. For preliminary results, we perform a proof of concept for fingerprinting in microscopic image datasets.

Context-Aware Composition of Agent Policies by Markov Decision Process Entity Embeddings and Agent Ensembles

Computational agents support humans in many areas of life and are therefore found in heterogeneous contexts. This means they operate in rapidly changing environments and can be confronted with huge state and action spaces. In order to perform services and carry out activities in a goal-oriented manner, agents require prior knowledge and therefore have to develop and pursue context-dependent policies. However, prescribing policies in advance is limited and inflexible, especially in dynamically changing environments. Moreover, the context of an agent determines its choice of actions. Since the environments can be stochastic and complex in terms of the number of states and feasible actions, activities are usually modelled in a simplified way by Markov decision processes so that, e.g., agents with reinforcement learning are able to learn policies, that help to capture the context and act accordingly to optimally perform activities. However, training policies for all possible contexts using reinforcement learning is time-consuming. A requirement and challenge for agents is to learn strategies quickly and respond immediately in cross-context environments and applications, e.g., the Internet, service robotics, cyber-physical systems. In this work, we propose a novel simulation-based approach that enables a) the representation of heterogeneous contexts through knowledge graphs and entity embeddings and b) the context-aware composition of policies on demand by ensembles of agents running in parallel. The evaluation we conducted with the "Virtual Home" dataset indicates that agents with a need to switch seamlessly between different contexts, can request on-demand composed policies that lead to the successful completion of context-appropriate activities without having to learn these policies in lengthy training steps and episodes, in contrast to agents that use reinforcement learning.

Transformer Training Strategies for Forecasting Multiple Load Time Series

Recent work uses Transformers for load forecasting, which are the state of the art for sequence modeling tasks in data-rich domains. In the smart grid of the future, accurate load forecasts must be provided on the level of individual clients of an energy supplier. While the total amount of electrical load data available to an energy supplier will increase with the ongoing smart meter rollout, the amount of data per client will always be limited. We test whether the Transformer benefits from a transfer learning strategy, where a global model is trained on the load time series data from multiple clients. We find that the global model is superior to two other training strategies commonly used in related work: multivariate models and local models. A comparison to linear models and multi-layer perceptrons shows that Transformers are effective for electrical load forecasting when they are trained with the right strategy.

CoNIC Challenge: Pushing the Frontiers of Nuclear Detection, Segmentation, Classification and Counting

Nuclear detection, segmentation and morphometric profiling are essential in helping us further understand the relationship between histology and patient outcome. To drive innovation in this area, we setup a community-wide challenge using the largest available dataset of its kind to assess nuclear segmentation and cellular composition. Our challenge, named CoNIC, stimulated the development of reproducible algorithms for cellular recognition with real-time result inspection on public leaderboards. We conducted an extensive post-challenge analysis based on the top-performing models using 1,658 whole-slide images of colon tissue. With around 700 million detected nuclei per model, associated features were used for dysplasia grading and survival analysis, where we demonstrated that the challenge's improvement over the previous state-of-the-art led to significant boosts in downstream performance. Our findings also suggest that eosinophils and neutrophils play an important role in the tumour microevironment. We release challenge models and WSI-level results to foster the development of further methods for biomarker discovery.

ProbPNN: Enhancing Deep Probabilistic Forecasting with Statistical Information

Probabilistic forecasts are essential for various downstream applications such as business development, traffic planning, and electrical grid balancing. Many of these probabilistic forecasts are performed on time series data that contain calendar-driven periodicities. However, existing probabilistic forecasting methods do not explicitly take these periodicities into account. Therefore, in the present paper, we introduce a deep learning-based method that considers these calendar-driven periodicities explicitly. The present paper, thus, has a twofold contribution: First, we apply statistical methods that use calendar-driven prior knowledge to create rolling statistics and combine them with neural networks to provide better probabilistic forecasts. Second, we benchmark ProbPNN with state-of-the-art benchmarks by comparing the achieved normalised continuous ranked probability score (nCRPS) and normalised Pinball Loss (nPL) on two data sets containing in total more than 1000 time series. The results of the benchmarks show that using statistical forecasting components improves the probabilistic forecast performance and that ProbPNN outperforms other deep learning forecasting methods whilst requiring less computation costs.