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.

Creating Probabilistic Forecasts from Arbitrary Deterministic Forecasts using Conditional Invertible Neural Networks

In various applications, probabilistic forecasts are required to quantify the inherent uncertainty associated with the forecast. However, numerous modern forecasting methods are still designed to create deterministic forecasts. Transforming these deterministic forecasts into probabilistic forecasts is often challenging and based on numerous assumptions that may not hold in real-world situations. Therefore, the present article proposes a novel approach for creating probabilistic forecasts from arbitrary deterministic forecasts. In order to implement this approach, we use a conditional Invertible Neural Network (cINN). More specifically, we apply a cINN to learn the underlying distribution of the data and then combine the uncertainty from this distribution with an arbitrary deterministic forecast to generate accurate probabilistic forecasts. Our approach enables the simple creation of probabilistic forecasts without complicated statistical loss functions or further assumptions. Besides showing the mathematical validity of our approach, we empirically show that our approach noticeably outperforms traditional methods for including uncertainty in deterministic forecasts and generally outperforms state-of-the-art probabilistic forecasting benchmarks.

AutoPV: Automated photovoltaic forecasts with limited information using an ensemble of pre-trained models

Accurate PhotoVoltaic (PV) power generation forecasting is vital for the efficient operation of Smart Grids. The automated design of such accurate forecasting models for individual PV plants includes two challenges: First, information about the PV mounting configuration (i.e. inclination and azimuth angles) is often missing. Second, for new PV plants, the amount of historical data available to train a forecasting model is limited (cold-start problem). We address these two challenges by proposing a new method for day-ahead PV power generation forecasts called AutoPV. AutoPV is a weighted ensemble of forecasting models that represent different PV mounting configurations. This representation is achieved by pre-training each forecasting model on a separate PV plant and by scaling the model's output with the peak power rating of the corresponding PV plant. To tackle the cold-start problem, we initially weight each forecasting model in the ensemble equally. To tackle the problem of missing information about the PV mounting configuration, we use new data that become available during operation to adapt the ensemble weights to minimize the forecasting error. AutoPV is advantageous as the unknown PV mounting configuration is implicitly reflected in the ensemble weights, and only the PV plant's peak power rating is required to re-scale the ensemble's output. AutoPV also allows to represent PV plants with panels distributed on different roofs with varying alignments, as these mounting configurations can be reflected proportionally in the weighting. Additionally, the required computing memory is decoupled when scaling AutoPV to hundreds of PV plants, which is beneficial in Smart Grids with limited computing capabilities. For a real-world data set with 11 PV plants, the accuracy of AutoPV is comparable to a model trained on two years of data and outperforms an incrementally trained model.

EasyMLServe: Easy Deployment of REST Machine Learning Services

Various research domains use machine learning approaches because they can solve complex tasks by learning from data. Deploying machine learning models, however, is not trivial and developers have to implement complete solutions which are often installed locally and include Graphical User Interfaces (GUIs). Distributing software to various users on-site has several problems. Therefore, we propose a concept to deploy software in the cloud. There are several frameworks available based on Representational State Transfer (REST) which can be used to implement cloud-based machine learning services. However, machine learning services for scientific users have special requirements that state-of-the-art REST frameworks do not cover completely. We contribute an EasyMLServe software framework to deploy machine learning services in the cloud using REST interfaces and generic local or web-based GUIs. Furthermore, we apply our framework on two real-world applications, \ie, energy time-series forecasting and cell instance segmentation. The EasyMLServe framework and the use cases are available on GitHub.