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In IBM Research AI4ScR team, our focus is on understanding the spatiotemporal heterogeneity of biological organization. To achieve this, we combine AI, especially Deep learning, with spatial single-cell measurements for modeling the complexity of tumor microenvironment (TME).
Graph representation learning has recently become popular in single-cell biology to understand the spatial cell distribution in TME [1,2,3,4,5]. Encoding the spatial arrangement of cells in form of a graph allows to capture the inter-cellular interactions and map the topological distribution to downstream biological metadata. Though the downstream performance for using cell-graphs is encouraging, the explainability of the findings in terms of the functional capabilities of the cells is missing.
To bridge this gap, the project aims at exploring a novel concept-paradigm, that builds on prior biological knowledge to construct explainable representation of TME. The paradigm is expected to identify various entities of interest in tissue, i.e., cells, and engineer entity-guided abstract concepts to encode the TME. Subsequently, the multitudes of information in terms of the designed concepts are to be integrated via attention-based Graph Neural Networks (GNNs) for tumor characterization. Eventually, the objective is to decipher the learned networks via post-hoc interpretability techniques  to comprehend the concept-space.
- Computational Biology and Bioinformatics, Computer Vision, Knowledge Representation and Machine Learning
- Master Thesis
Ultrasound contrast agent microbubbles have been recently promoted as potential drug carriers for ultrasound-guided targeted drug administration. A full understanding of their mechanical behaviour is therefore sought. Unfortunately, experiments with bubbles suffer from interference with walls because of buoyancy. In this regard, holographic optical tweezers enable for contact-free positioning of microbubbles in the three-dimensional space. In this project we aim to upgrade an optical tweezers setup to simultaneously trap multiple microbubbles.
- Electrical and Electronic Engineering, Mechanical and Industrial Engineering, Optical Physics
- Semester Project
Design, build, and implement the control of a multi-DOF robot joint actuated by multiple pneumatic artificial muscles (PAMs). We will explore behaviors that can be produced by over-actuating a sequence of multi-dof joints with muscle-actuated tendons, and investigate how levels of coupling between actuated degrees of freedom can be used to simplify actuation.
- Intelligent Robotics, Knowledge Representation and Machine Learning, Modeling and Simulation, Robotics and Mechatronics
- Master Thesis
Be part of an interdisciplinary team and contribute to a project investigating the vocal repertoire of free-ranging
killer whale calls using bioacoustics and machine learning techniques.
- Behavioural and Cognitive Sciences, Environmental Sciences, Pattern Recognition, Signal Processing, Sociobiology and Behavioural Ecology, Speech Recognition
- Master Thesis
High-Speed Laser Cladding (HSLC) is a new laser cladding process with high productivity, low heat input and excellent bonding. At inspire, a new HSLC demo production unit is being set up to further develop the process for application of new materials, especially aluminium alloys, and their optimization to the specific process conditions.
HSLC exhibits solidification rates in a range between conventional laser cladding and SLM, and much higher than for standard processes such as casting. Subsequently, alloys that are designed for those processes cannot be applied by HSLC. Therefore, alloys must be specifically designed to the production process to yield high-performance results. It is our aim to develop aluminium alloys specifically for the HSLC process, as it is an ideal material for many lightweight applications.
- Automotive Engineering, Manufacturing Engineering, Materials Engineering, Mechanical and Industrial Engineering, Metallurgy
- PhD Placement
To better understand the spread of bacteria and viruses in an acute care hospital, this project aims at combining deep learning-based methods, such as activity recognition and object detection to automatically collect and analyze data on all hand-to-surface exposures by doctors, nurses and patients.
- Artificial Intelligence and Signal and Image Processing
- Master Thesis
Microbubble contrast agents and superheated nanodroplets for acoustic vaporization are nowadays collecting much interest due to their promising performance in medical applications such as ultrasound imaging and drug delivery. Those agents are usually coated with a surfactant, which reduces the effective interfacial tension (thereby improving emulsion stability) and affect their dynamic response to ultrasound. Stimuli-responsive surfactants change their properties according to external signals and can be greatly effective in dynamically controlling contrast agents surface characteristics and dynamic. Moreover, the use of solid particles as a substitute for a surfactant can improve the stability of the emulsion.
- Chemistry, Engineering and Technology, Physics
- Bachelor Thesis, Semester Project
The imaging of high-speed small-scale flow phenomena such as cavitation shock waves inception or microbubble ultrasound contrast agents dynamics require both a low exposure time and a high optical magnification and therefore extremely intense and short light pulses. In this project we aim to make use of lasers to create a sufficiently powerful and versatile illumination system for studying high-speed phenomena in fluids.
- Electrical and Electronic Engineering, Mechanical and Industrial Engineering, Physics
- Semester Project
The Advanced Manufacturing Lab (am|z) performs internationally leading research in the field of manufacturing engineering. A recent research focus is put on sustainable manufacturing and low-waste production. Near-net shaping of hard materials could benefit the tool making industry to become more sustainable. For a new industry related research project, we are looking for a motivated student.
- Engineering and Technology
- Bachelor Thesis, Master Thesis, Semester Project
This project aims to develop an automated pipeline to localise bone cells from histology slices.
- Biomedical Engineering, Computational Biology and Bioinformatics, Computer Hardware, Electrical and Electronic Engineering, Interdisciplinary Engineering, Mathematics, Mechanical and Industrial Engineering, Medical Biotechnology, Statistics
- Bachelor Thesis, Internship, Master Thesis, Semester Project