Reischl, Markus
Energy-Based Prior Latent Space Diffusion model for Reconstruction of Lumbar Vertebrae from Thick Slice MRI
Wang, Yanke, Lee, Yolanne Y. R., Dolfini, Aurelio, Reischl, Markus, Konukoglu, Ender, Flouris, Kyriakos
Lumbar spine problems are ubiquitous, motivating research into targeted imaging for treatment planning and guided interventions. While high resolution and high contrast CT has been the modality of choice, MRI can capture both bone and soft tissue without the ionizing radiation of CT albeit longer acquisition time. The critical trade-off between contrast quality and acquisition time has motivated 'thick slice MRI', which prioritises faster imaging with high in-plane resolution but variable contrast and low through-plane resolution. We investigate a recently developed post-acquisition pipeline which segments vertebrae from thick-slice acquisitions and uses a variational autoencoder to enhance quality after an initial 3D reconstruction. We instead propose a latent space diffusion energy-based prior to leverage diffusion models, which exhibit high-quality image generation. Crucially, we mitigate their high computational cost and low sample efficiency by learning an energy-based latent representation to perform the diffusion processes. Our resulting method outperforms existing approaches across metrics including Dice and VS scores, and more faithfully captures 3D features.
Assessing Political Bias in Large Language Models
Rettenberger, Luca, Reischl, Markus, Schutera, Mark
The assessment of bias within Large Language Models (LLMs) has emerged as a critical concern in the contemporary discourse surrounding Artificial Intelligence (AI) in the context of their potential impact on societal dynamics. Recognizing and considering political bias within LLM applications is especially important when closing in on the tipping point toward performative prediction. Then, being educated about potential effects and the societal behavior LLMs can drive at scale due to their interplay with human operators. In this way, the upcoming elections of the European Parliament will not remain unaffected by LLMs. We evaluate the political bias of the currently most popular open-source LLMs (instruct or assistant models) concerning political issues within the European Union (EU) from a German voter's perspective. To do so, we use the "Wahl-O-Mat," a voting advice application used in Germany. From the voting advice of the "Wahl-O-Mat" we quantize the degree of alignment of LLMs with German political parties. We show that larger models, such as Llama3-70B, tend to align more closely with left-leaning political parties, while smaller models often remain neutral, particularly when prompted in English. The central finding is that LLMs are similarly biased, with low variances in the alignment concerning a specific party. Our findings underline the importance of rigorously assessing and making bias transparent in LLMs to safeguard the integrity and trustworthiness of applications that employ the capabilities of performative prediction and the invisible hand of machine learning prediction and language generation.
MLOps for Scarce Image Data: A Use Case in Microscopic Image Analysis
Sitcheu, Angelo Yamachui, Friederich, Nils, Baeuerle, Simon, Neumann, Oliver, Reischl, Markus, Mikut, Ralf
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
Graham, Simon, Vu, Quoc Dang, Jahanifar, Mostafa, Weigert, Martin, Schmidt, Uwe, Zhang, Wenhua, Zhang, Jun, Yang, Sen, Xiang, Jinxi, Wang, Xiyue, Rumberger, Josef Lorenz, Baumann, Elias, Hirsch, Peter, Liu, Lihao, Hong, Chenyang, Aviles-Rivero, Angelica I., Jain, Ayushi, Ahn, Heeyoung, Hong, Yiyu, Azzuni, Hussam, Xu, Min, Yaqub, Mohammad, Blache, Marie-Claire, Piégu, Benoît, Vernay, Bertrand, Scherr, Tim, Böhland, Moritz, Löffler, Katharina, Li, Jiachen, Ying, Weiqin, Wang, Chixin, Kainmueller, Dagmar, Schönlieb, Carola-Bibiane, Liu, Shuolin, Talsania, Dhairya, Meda, Yughender, Mishra, Prakash, Ridzuan, Muhammad, Neumann, Oliver, Schilling, Marcel P., Reischl, Markus, Mikut, Ralf, Huang, Banban, Chien, Hsiang-Chin, Wang, Ching-Ping, Lee, Chia-Yen, Lin, Hong-Kun, Liu, Zaiyi, Pan, Xipeng, Han, Chu, Cheng, Jijun, Dawood, Muhammad, Deshpande, Srijay, Bashir, Raja Muhammad Saad, Shephard, Adam, Costa, Pedro, Nunes, João D., Campilho, Aurélio, Cardoso, Jaime S., S, Hrishikesh P, Puthussery, Densen, G, Devika R, C, Jiji V, Zhang, Ye, Fang, Zijie, Lin, Zhifan, Zhang, Yongbing, Lin, Chunhui, Zhang, Liukun, Mao, Lijian, Wu, Min, Vo, Vi Thi-Tuong, Kim, Soo-Hyung, Lee, Taebum, Kondo, Satoshi, Kasai, Satoshi, Dumbhare, Pranay, Phuse, Vedant, Dubey, Yash, Jamthikar, Ankush, Vuong, Trinh Thi Le, Kwak, Jin Tae, Ziaei, Dorsa, Jung, Hyun, Miao, Tianyi, Snead, David, Raza, Shan E Ahmed, Minhas, Fayyaz, Rajpoot, Nasir M.
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
Neumann, Oliver, Schilling, Marcel, Reischl, Markus, Mikut, Ralf
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, i. e., energy time-series forecasting and cell instance segmentation. The EasyMLServe framework and the use cases are available on GitHub.
Label Assistant: A Workflow for Assisted Data Annotation in Image Segmentation Tasks
Schilling, Marcel P., Rettenberger, Luca, Münke, Friedrich, Cui, Haijun, Popova, Anna A., Levkin, Pavel A., Mikut, Ralf, Reischl, Markus
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.
Distributed traffic light control at uncoupled intersections with real-world topology by deep reinforcement learning
Schutera, Mark, Goby, Niklas, Smolarek, Stefan, Reischl, Markus
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.
Transfer Learning versus Multi-agent Learning regarding Distributed Decision-Making in Highway Traffic
Schutera, Mark, Goby, Niklas, Neumann, Dirk, Reischl, Markus
Transportation and traffic are currently undergoing a rapid increase in terms of both scale and complexity. At the same time, an increasing share of traffic participants are being transformed into agents driven or supported by artificial intelligence resulting in mixed-intelligence traffic. This work explores the implications of distributed decision-making in mixed-intelligence traffic. The investigations are carried out on the basis of an online-simulated highway scenario, namely the MIT \emph{DeepTraffic} simulation. In the first step traffic agents are trained by means of a deep reinforcement learning approach, being deployed inside an elitist evolutionary algorithm for hyperparameter search. The resulting architectures and training parameters are then utilized in order to either train a single autonomous traffic agent and transfer the learned weights onto a multi-agent scenario or else to conduct multi-agent learning directly. Both learning strategies are evaluated on different ratios of mixed-intelligence traffic. The strategies are assessed according to the average speed of all agents driven by artificial intelligence. Traffic patterns that provoke a reduction in traffic flow are analyzed with respect to the different strategies.