Improving 3D deep learning segmentation with biophysically motivated cell synthesis

Biomedical research increasingly relies on 3D cell culture models and AI-based analysis can potentially facilitate a detailed and accurate feature extraction on a single-cell level. However, this requires for a precise segmentation of 3D cell datasets, which in turn demands high-quality ground truth for training. Manual annotation, the gold standard for ground truth data, is too time-consuming and thus not feasible for the generation of large 3D training datasets. To address this, we present a novel framework for generating 3D training data, which integrates biophysical modeling for realistic cell shape and alignment. Our approach allows the in silico generation of coherent membrane and nuclei signals, that enable the training of segmentation models utilizing both channels for improved performance. Furthermore, we present a new GAN training scheme that generates not only image data but also matching labels. Quantitative evaluation shows superior performance of biophysical motivated synthetic training data, even outperforming manual annotation and pretrained models. This underscores the potential of incorporating biophysical modeling for enhancing synthetic training data quality.

Assessing Political Bias in Large Language Models

The assessment of societal biases within Large Language Models (LLMs) has emerged as a critical concern in the contemporary discourse surrounding Artificial Intelligence (AI) ethics and their impact. Especially, recognizing and considering political biases is important for practical applications to gain a deeper understanding of the possibilities and behaviors and to prevent unwanted statements. As the upcoming elections of the European Parliament will not remain unaffected by LLMs, we evaluate the bias of the current most popular open-source models concerning political issues within the European Union (EU) from a German perspective. To do so, we use the "Wahl-O-Mat", a voting advice application used in Germany, to determine which political party is the most aligned for the respective LLM. We show that larger models, such as Llama3-70B, tend to align more closely with left-leaning political parties like GR\"UNE and Volt, while smaller models often remain neutral, particularly in English. This highlights the nuanced behavior of LLMs and the importance of language in shaping their political stances. Our findings underscore the importance of rigorously assessing and addressing societal bias in LLMs to safeguard the integrity and fairness of applications that employ the power of modern machine learning methods.

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.

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.

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.

A universal synthetic dataset for machine learning on spectroscopic data

To assist in the development of machine learning methods for automated classification of spectroscopic data, we have generated a universal synthetic dataset that can be used for model validation. This dataset contains artificial spectra designed to represent experimental measurements from techniques including X-ray diffraction, nuclear magnetic resonance, and Raman spectroscopy. The dataset generation process features customizable parameters, such as scan length and peak count, which can be adjusted to fit the problem at hand. As an initial benchmark, we simulated a dataset containing 35,000 spectra based on 500 unique classes. To automate the classification of this data, eight different machine learning architectures were evaluated. From the results, we shed light on which factors are most critical to achieve optimal performance for the classification task. The scripts used to generate synthetic spectra, as well as our benchmark dataset and evaluation routines, are made publicly available to aid in the development of improved machine learning models for spectroscopic analysis.

ciscNet -- A Single-Branch Cell Instance Segmentation and Classification Network

Automated cell nucleus segmentation and classification are required to assist pathologists in their decision making. The Colon Nuclei Identification and Counting Challenge 2022 (CoNIC Challenge 2022) supports the development and comparability of segmentation and classification methods for histopathological images. In this contribution, we describe our CoNIC Challenge 2022 method ciscNet to segment, classify and count cell nuclei, and report preliminary evaluation results. Our code is available at https://git.scc.kit.edu/ciscnet/ciscnet-conic-2022.

Label Assistant: A Workflow for Assisted Data Annotation in Image Segmentation Tasks

Recent research in the field of computer vision strongly focuses on deep learning architectures to tackle image processing problems. Deep neural networks are often considered in complex image processing scenarios since traditional computer vision approaches are expensive to develop or reach their limits due to complex relations. However, a common criticism is the need for large annotated datasets to determine robust parameters. Annotating images by human experts is time-consuming, burdensome, and expensive. Thus, support is needed to simplify annotation, increase user efficiency, and annotation quality. In this paper, we propose a generic workflow to assist the annotation process and discuss methods on an abstract level. Thereby, we review the possibilities of focusing on promising samples, image pre-processing, pre-labeling, label inspection, or post-processing of annotations. In addition, we present an implementation of the proposal by means of a developed flexible and extendable software prototype nested in hybrid touchscreen/laptop device.

Towards DeepSpray: Using Convolutional Neural Network to post-process Shadowgraphy Images of Liquid Atomization

This technical report investigates the potential of Convolutional Neural Networks to post-process images from primary atomization. Three tasks are investigated. First, the detection and segmentation of liquid droplets in degraded optical conditions. Second, the detection of overlapping ellipses and the prediction of their geometrical characteristics. This task corresponds to extrapolate the hidden contour of an ellipse with reduced visual information. Third, several features of the liquid surface during primary breakup (ligaments, bags, rims) are manually annotated on 15 experimental images. The detector is trained on this minimal database using simple data augmentation and then applied to other images from numerical simulation and from other experiment. In these three tasks, models from the literature based on Convolutional Neural Networks showed very promising results, thus demonstrating the high potential of Deep Learning to post-process liquid atomization. The next step is to embed these models into a unified framework DeepSpray.

Distributed traffic light control at uncoupled intersections with real-world topology by deep reinforcement learning

This work examines the implications of uncoupled intersections with local real-world topology and sensor setup on traffic light control approaches. Control approaches are evaluated with respect to: Traffic flow, fuel consumption and noise emission at intersections. The real-world road network of Friedrichshafen is depicted, preprocessed and the present traffic light controlled intersections are modeled with respect to state space and action space. Different strategies, containing fixed-time, gap-based and time-based control approaches as well as our deep reinforcement learning based control approach, are implemented and assessed. Our novel DRL approach allows for modeling the TLC action space, with respect to phase selection as well as selection of transition timings. It was found that real-world topologies, and thus irregularly arranged intersections have an influence on the performance of traffic light control approaches. This is even to be observed within the same intersection types (n-arm, m-phases). Moreover we could show, that these influences can be efficiently dealt with by our deep reinforcement learning based control approach.