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Veronika Cheplygina

Machine learning (ML) competitions aim to improve healthcare algorithms, like detecting lung cancer in chest x-rays. Teams worldwide compete to develop such algorithms, driven by prizes or prestige. Competitions encourage innovation but often produce similar algorithms that excel in one accuracy metric but fail with diverse real-world data.

Relying on one accuracy metric is insufficient for measuring algorithm quality, for example for rare patient cases. It leads to many similar algorithms with high environmental cost. Moreover, competition can deter women and minorities from entering or staying in data science.

I propose competitions which look at multiple metrics across different patient subgroups, with applications in chest and cardiovascular disease. Using the latest ML techniques we will develop methods to improve evaluation of algorithm robustness while reducing the carbon footprint. We will also study how competitions affect women and other groups in data science.

Johannes Bjerva

Imagine a world where generative AI (GenAI) exists free from any concerns for safety, security, privacy, trustworthiness, misinformation, or bias. We are far from this vision today, where negative consequences from GenAI, such as deepfakes, are ever present in the news cycle. A new threat to GenAI has emerged recently, as large language models can be attacked by malicious actors, leading to leakage of private data, manipulation of end-users, and even risks of medical misdiagnosis. For instance, an attacker can modify prompts to ‘trick’ a model into releasing private data. The project aims to draw upon the field of linguistics to mitigate such attacks, relying on the hypothesis that there are identifiable linguistic patterns in signals that attempt to negatively affect a GenAI model. If we can identify such patterns, we may have the key for safe and secure language-driven AI in the future.

Kyung Mih Noh

Our research explores chromatin mechanisms in neurodevelopment and brain disorders. Chromatin comprises DNA and histone proteins and regulates gene expression, which has an impact on human health. Key questions guide our work: How do chromatin regulators impact neuronal identity and, contribute to neurodevelopmental disorders? (2) Do chromatin states causatively regulate gene expression and cellular function? (3) How do neuronal chromatin states respond to external stimuli, and is there chromatin memory in the neuronal process? (4) What chromatin mechanisms govern interactions between neurons and other brain cell types in neurodevelopment? Using cutting-edge functional genomics, human brain cell models, and single-cell sequencing, we aim to decode molecular networks, providing essential insights into the molecular basis of neurodevelopment and brain disorders. Our efforts hold the potential to advance drug development and personalized medicine.

Frederic Gachon

The circadian clock orchestrates human physiology, including when we eat and sleep, synchronizing it with the daily changes in our environment and the alteration of day and night. Modern western lifestyles, technology, and shift work disrupt our body clock. This disruption is associated with many diseases including obesity and liver and kidney diseases, but the mechanisms responsible are poorly understood, as well as the causal relationship: is this circadian disruption a cause or a consequence of these diseases? This project aims at deciphering the consequences of the disruption of the circadian clock, with the hypothesis that the associated perturbations of our hormones could play a role in the progression of these diseases. This will potentially define new strategies to diagnose, prevent, and treat metabolic dysfunction associated diseases.

Lisa Frankel

Throughout their lifetime, cells face many types of stress from the environment including pollution, UV radiation, pathogen infection and exposure to various toxins. In the face of stress, our cells must adapt to survive and maintain vital functions. If not properly managed, genetic mistakes accumulate and predispose to disease, including cancer. One mechanism for coping with stress is autophagy. This system is crucial for the removal and recycling of cellular waste in order to maintain cellular and tissue homeostasis. Autophagy is deeply conserved in evolution and enables cellular adaptation and survival in response to stress. Using state-of-the-art methods, my team will investigate completely new aspects of autophagy, including its ability to reprogram our genetic instructions in response to stress. By illuminating this new layer of gene expression control, we will provide fundamental understanding of cancer development and progression, with importance for therapeutic developments.

Yoshiki Narimatsu

Sugars cover surfaces of all living cells and these glycans are essential for many of the biological processes required for human life and our relationship with the microbial world. Glycans, much like DNA and proteins, contain information that needs to be decoded. Information in glycans is “read” by glycan-binding proteins and these direct biological signals and functions. The simple way we currently understand how proteins read glycans does not provide a plausible explanation for the great diversity of functions assigned to glycans. I therefore propose that glycans are read in more complex ways. I have developed a novel technology that enables analysis of such complex glycan motif, and recently I obtained the first experimental evidence to support my hypothesis. In this project, I will therefore explore how complex glycan motifs modulate our immune system and how bacteria and virus gain entry and cause pathologies through glycans. The project has wide biomedical perspectives.

Johan Larsbrink

Tree bark is a renewable resource produced in huge amounts every year, but it is today of low-value and poorly used. It is today typically burnt, though its high moisture and ash make this inefficient, and the bark’s different structure from regular wood also makes it unsuitable for regular pulping. The bark contains a high proportion of defensive compounds, known as extractives, which are generally toxic and protects the tree against attacks. The idea of this project is to enable biological conversion of the extractives into novel products that can replace fossil alternatives used today. However, there is virtually no existing knowledge on how bark is deconstructed in nature, which prevents such developments. We will generate the necessary knowledge by following bark degradation, and use identified enzymes and microorganisms to valorize bark, its extractives, and help mitigate material losses in industry.

Ditte Welner

Enzymes can be used to produce many of the things that our society needs with low environmental footprint compared to producing the same thing with conventional chemical methods. UGTs are enzymes that can attach a sugar molecule to a cosmetic ingredient, dye, food ingredient, and other chemicals, thereby increasing the water solubility and stability. However, most UGTs cannot withstand the conditions present in industrial processes, so it becomes very expensive and unsustainable to use them. But nature has a place to look for stable enzymes: the extremophiles. These are organisms living in extreme environments such as geysers, the arctic, the desert, or deep down in the sea. They have evolved to withstand these hard conditions, and so have their enzymes. This project discovers novel, robust enzymes from extremophiles, and uses these to learn something about what control an enzymes robustness. The project will also develop low-impact biosolutions.

Bjørn Panyella Pedersen

The project will uncover the secrets of how plants transport sugars and the hormone auxin across membranes. This process is crucial for proper plant growth and development, but despite extensive research, the details of how this functions remain unclear.
Here we explore the 3D structures of key transporters to help us understand how substrates – including herbicides which utilize these transport systems – affect plant growth. This will allow us to predict and modify plant responses to changing environments, with significant implications for agriculture and sustainability.

Beyond practical applications, this research will provide a breakthrough in our understanding of fundamental plant metabolism, specifically in maintaining sugar and hormone balance. This knowledge is essential for addressing global challenges, such as ensuring sufficient food production while minimizing environmental impact. In essence, this project holds a key to a more sustainable and food-secure future.

Oliver Van Aken

Perhaps surprisingly, plants are sensitive to mechanical stimulation caused by wind, water drops, and gentle touching by insects or neighboring plants. Mechanical stimuli can change the plant’s physical appearance and flowering. ‘Touching’ may also increase plant resistance to pathogens, insects and abiotic stresses by stimulating its defense systems.

Very little is known about how plants detect mechanical stimuli, and how they induce physiological and molecular changes. Mechanical stimulation also has clear application potential, as controlled rolling has been widely used in Japanese grain agriculture to improve yield for centuries. The practical usefulness in Nordic agriculture is, however, unknown. This project aims to reveal the processes that control touch responses in plants, and exploit the potential of controlled mechanical treatment to improve sustainable agriculture.