8,476 results on '"Hansen, Lars"'
Search Results
2. Danoliteracy of Generative, Large Language Models
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Holm, Søren Vejlgaard, Hansen, Lars Kai, and Nielsen, Martin Carsten
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning ,I.2.7 - Abstract
The language technology moonshot moment of Generative, Large Language Models (GLLMs) was not limited to English: These models brought a surge of technological applications, investments and hype to low-resource languages as well. However, the capabilities of these models in languages such as Danish were until recently difficult to verify beyond qualitative demonstrations due to a lack of applicable evaluation corpora. We present a GLLM benchmark to evaluate Danoliteracy, a measure of Danish language and cultural competency, across eight diverse scenarios such Danish citizenship tests and abstractive social media question answering. This limited-size benchmark is found to produce a robust ranking that correlates to human feedback at $\rho \sim 0.8$ with GPT-4 and Claude Opus models achieving the highest rankings. Analyzing these model results across scenarios, we find one strong underlying factor explaining $95\%$ of scenario performance variance for GLLMs in Danish, suggesting a $g$ factor of model consistency in language adaption., Comment: 16 pages, 13 figures, submitted to: NoDaLiDa/Baltic-HLT 2025
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- 2024
3. BiSSL: Bilevel Optimization for Self-Supervised Pre-Training and Fine-Tuning
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Zakarias, Gustav Wagner, Hansen, Lars Kai, and Tan, Zheng-Hua
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence - Abstract
In this work, we present BiSSL, a first-of-its-kind training framework that introduces bilevel optimization to enhance the alignment between the pretext pre-training and downstream fine-tuning stages in self-supervised learning. BiSSL formulates the pretext and downstream task objectives as the lower- and upper-level objectives in a bilevel optimization problem and serves as an intermediate training stage within the self-supervised learning pipeline. By more explicitly modeling the interdependence of these training stages, BiSSL facilitates enhanced information sharing between them, ultimately leading to a backbone parameter initialization that is better suited for the downstream task. We propose a training algorithm that alternates between optimizing the two objectives defined in BiSSL. Using a ResNet-18 backbone pre-trained with SimCLR on the STL10 dataset, we demonstrate that our proposed framework consistently achieves improved or competitive classification accuracies across various downstream image classification datasets compared to the conventional self-supervised learning pipeline. Qualitative analyses of the backbone features further suggest that BiSSL enhances the alignment of downstream features in the backbone prior to fine-tuning.
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- 2024
4. How Redundant Is the Transformer Stack in Speech Representation Models?
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Dorszewski, Teresa, Jacobsen, Albert Kjøller, Tětková, Lenka, and Hansen, Lars Kai
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Electrical Engineering and Systems Science - Audio and Speech Processing ,Computer Science - Computation and Language ,Computer Science - Machine Learning ,Computer Science - Sound - Abstract
Self-supervised speech representation models, particularly those leveraging transformer architectures, have demonstrated remarkable performance across various tasks such as speech recognition, speaker identification, and emotion detection. Recent studies on transformer models revealed a high redundancy between layers and the potential for significant pruning, which we will investigate here for transformer-based speech representation models. We perform a detailed analysis of layer similarity in speech representation models using three similarity metrics: cosine similarity, centered kernel alignment, and mutual nearest-neighbor alignment. Our findings reveal a block-like structure of high similarity, suggesting two main processing steps and significant redundancy of layers. We demonstrate the effectiveness of pruning transformer-based speech representation models without the need for post-training, achieving up to 40% reduction in transformer layers while maintaining over 95% of the model's predictive capacity. Furthermore, we employ a knowledge distillation method to substitute the entire transformer stack with mimicking layers, reducing the network size 95-98% and the inference time by up to 94%. This substantial decrease in computational load occurs without considerable performance loss, suggesting that the transformer stack is almost completely redundant for downstream applications of speech representation models.
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- 2024
5. Connecting Concept Convexity and Human-Machine Alignment in Deep Neural Networks
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Dorszewski, Teresa, Tětková, Lenka, Linhardt, Lorenz, and Hansen, Lars Kai
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence - Abstract
Understanding how neural networks align with human cognitive processes is a crucial step toward developing more interpretable and reliable AI systems. Motivated by theories of human cognition, this study examines the relationship between \emph{convexity} in neural network representations and \emph{human-machine alignment} based on behavioral data. We identify a correlation between these two dimensions in pretrained and fine-tuned vision transformer models. Our findings suggest that the convex regions formed in latent spaces of neural networks to some extent align with human-defined categories and reflect the similarity relations humans use in cognitive tasks. While optimizing for alignment generally enhances convexity, increasing convexity through fine-tuning yields inconsistent effects on alignment, which suggests a complex relationship between the two. This study presents a first step toward understanding the relationship between the convexity of latent representations and human-machine alignment., Comment: First two authors contributed equally
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- 2024
6. Convexity-based Pruning of Speech Representation Models
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Dorszewski, Teresa, Tětková, Lenka, and Hansen, Lars Kai
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Computer Science - Computation and Language ,Computer Science - Sound ,Electrical Engineering and Systems Science - Audio and Speech Processing - Abstract
Speech representation models based on the transformer architecture and trained by self-supervised learning have shown great promise for solving tasks such as speech and speaker recognition, keyword spotting, emotion detection, and more. Typically, it is found that larger models lead to better performance. However, the significant computational effort involved in such large transformer systems is a challenge for embedded and real-world applications. Recent work has shown that there is significant redundancy in the transformer models for NLP and massive layer pruning is feasible (Sajjad et al., 2023). Here, we investigate layer pruning in audio models. We base the pruning decision on a convexity criterion. Convexity of classification regions has recently been proposed as an indicator of subsequent fine-tuning performance in a range of application domains, including NLP and audio. In empirical investigations, we find a massive reduction in the computational effort with no loss of performance or even improvements in certain cases.
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- 2024
7. SPEED: Scalable Preprocessing of EEG Data for Self-Supervised Learning
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Gjølbye, Anders, Skerath, Lina, Lehn-Schiøler, William, Langer, Nicolas, and Hansen, Lars Kai
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Electrical Engineering and Systems Science - Signal Processing ,Computer Science - Artificial Intelligence - Abstract
Electroencephalography (EEG) research typically focuses on tasks with narrowly defined objectives, but recent studies are expanding into the use of unlabeled data within larger models, aiming for a broader range of applications. This addresses a critical challenge in EEG research. For example, Kostas et al. (2021) show that self-supervised learning (SSL) outperforms traditional supervised methods. Given the high noise levels in EEG data, we argue that further improvements are possible with additional preprocessing. Current preprocessing methods often fail to efficiently manage the large data volumes required for SSL, due to their lack of optimization, reliance on subjective manual corrections, and validation processes or inflexible protocols that limit SSL. We propose a Python-based EEG preprocessing pipeline optimized for self-supervised learning, designed to efficiently process large-scale data. This optimization not only stabilizes self-supervised training but also enhances performance on downstream tasks compared to training with raw data., Comment: To appear in proceedings of 2024 IEEE International workshop on Machine Learning for Signal Processing
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- 2024
8. Microstructural and Micromechanical Evolution of Olivine Aggregates During Transient Creep
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Wiesman, Harison S., Breithaupt, Thomas, Wallis, David, and Hansen, Lars N.
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Condensed Matter - Materials Science ,Physics - Geophysics - Abstract
To examine the microstructural evolution that occurs during transient creep, we deformed olivine aggregates to different strains that spanned the initial transient deformation. Two sets of samples with different initial grain sizes of 5 $\mu$m and 20 $\mu$m were deformed in torsion at T = 1523 K, P = 300 MPa, and a constant shear strain rate of 1.5 $\times$ 10$^{-4}$ s$^{-1}$. Both sets of samples experienced strain hardening during deformation. We characterized the microstructures at the end of each experiment using high-angular resolution electron backscatter diffraction (HR-EBSD) and dislocation decoration. In the coarse-grained samples, dislocation density increased from 1.5 $\times$ 10$^{11}$ m$^{-2}$ to 3.6 $\times$ 10$^{12}$ m$^{-2}$ with strain. Although the same final dislocation density was reached in the fine-grained samples, it did not vary significantly at small strains, potentially due to concurrent grain growth during deformation. In both sets of samples, HR-EBSD analysis revealed that intragranular stress heterogeneity increased in magnitude with strain and that elevated stresses are associated with regions of high geometrically necessary dislocation density. Further analysis of the stresses and their probability distributions indicate that the stresses are imparted by long-range elastic interactions among dislocations. These characteristics indicate that dislocation interactions were the primary cause of strain hardening during transient creep. A comparison of the results to predictions from three recent models reveals that the models do not correctly predict the evolution in stress and dislocation density with strain for our experiments due to a lack of previous such data in their calibrations.
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- 2024
9. Challenges in explaining deep learning models for data with biological variation
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Tětková, Lenka, Dreier, Erik Schou, Malm, Robin, and Hansen, Lars Kai
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence ,Computer Science - Computer Vision and Pattern Recognition - Abstract
Much machine learning research progress is based on developing models and evaluating them on a benchmark dataset (e.g., ImageNet for images). However, applying such benchmark-successful methods to real-world data often does not work as expected. This is particularly the case for biological data where we expect variability at multiple time and spatial scales. In this work, we are using grain data and the goal is to detect diseases and damages. Pink fusarium, skinned grains, and other diseases and damages are key factors in setting the price of grains or excluding dangerous grains from food production. Apart from challenges stemming from differences of the data from the standard toy datasets, we also present challenges that need to be overcome when explaining deep learning models. For example, explainability methods have many hyperparameters that can give different results, and the ones published in the papers do not work on dissimilar images. Other challenges are more general: problems with visualization of the explanations and their comparison since the magnitudes of their values differ from method to method. An open fundamental question also is: How to evaluate explanations? It is a non-trivial task because the "ground truth" is usually missing or ill-defined. Also, human annotators may create what they think is an explanation of the task at hand, yet the machine learning model might solve it in a different and perhaps counter-intuitive way. We discuss several of these challenges and evaluate various post-hoc explainability methods on grain data. We focus on robustness, quality of explanations, and similarity to particular "ground truth" annotations made by experts. The goal is to find the methods that overall perform well and could be used in this challenging task. We hope the proposed pipeline will be used as a framework for evaluating explainability methods in specific use cases.
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- 2024
10. Airborne DNA reveals predictable spatial and seasonal dynamics of fungi.
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Abrego, Nerea, Furneaux, Brendan, Hardwick, Bess, Somervuo, Panu, Palorinne, Isabella, Aguilar-Trigueros, Carlos, Andrew, Nigel, Babiy, Ulyana, Bao, Tan, Bazzano, Gisela, Bondarchuk, Svetlana, Bonebrake, Timothy, Brennan, Georgina, Bret-Harte, Syndonia, Bässler, Claus, Cagnolo, Luciano, Cameron, Erin, Chapurlat, Elodie, Creer, Simon, DAcqui, Luigi, de Vere, Natasha, Desprez-Loustau, Marie-Laure, Dongmo, Michel, Jacobsen, Ida, Fisher, Brian, Flores de Jesus, Miguel, Gilbert, Gregory, Griffith, Gareth, Gritsuk, Anna, Gross, Andrin, Grudd, Håkan, Halme, Panu, Hanna, Rachid, Hansen, Jannik, Hansen, Lars, Hegbe, Apollon, Hill, Sarah, Hogg, Ian, Hultman, Jenni, Hyde, Kevin, Hynson, Nicole, Ivanova, Natalia, Karisto, Petteri, Kerdraon, Deirdre, Knorre, Anastasia, Krisai-Greilhuber, Irmgard, Kurhinen, Juri, Kuzmina, Masha, Lecomte, Nicolas, Lecomte, Erin, Loaiza, Viviana, Lundin, Erik, Meire, Alexander, Mešić, Armin, Miettinen, Otto, Monkhouse, Norman, Mortimer, Peter, Müller, Jörg, Nilsson, R, Nonti, Puani, Nordén, Jenni, Nordén, Björn, Norros, Veera, Paz, Claudia, Pellikka, Petri, Pereira, Danilo, Petch, Geoff, Pitkänen, Juha-Matti, Popa, Flavius, Potter, Caitlin, Purhonen, Jenna, Pätsi, Sanna, Rafiq, Abdullah, Raharinjanahary, Dimby, Rakos, Niklas, Rathnayaka, Achala, Raundrup, Katrine, Rebriev, Yury, Rikkinen, Jouko, Rogers, Hanna, Rogovsky, Andrey, Rozhkov, Yuri, Runnel, Kadri, Saarto, Annika, Savchenko, Anton, Schlegel, Markus, Schmidt, Niels, Seibold, Sebastian, Skjøth, Carsten, Stengel, Elisa, Sutyrina, Svetlana, Syvänperä, Ilkka, Tedersoo, Leho, Timm, Jebidiah, Tipton, Laura, Toju, Hirokazu, Uscka-Perzanowska, Maria, van der Bank, Michelle, van der Bank, F, and Vandenbrink, Bryan
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Air Microbiology ,Biodiversity ,DNA ,Fungal ,Fungi ,Mycorrhizae ,Phylogeny ,Seasons ,Spatio-Temporal Analysis ,Spores ,Fungal ,Temperature ,Tropical Climate ,Geographic Mapping - Abstract
Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions1,2. To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sampling of fungal spores3. The vast majority of operational taxonomic units were detected within only one climatic zone, and the spatiotemporal patterns of species richness and community composition were mostly explained by annual mean air temperature. Tropical regions hosted the highest fungal diversity except for lichenized, ericoid mycorrhizal and ectomycorrhizal fungi, which reached their peak diversity in temperate regions. The sensitivity in climatic responses was associated with phylogenetic relatedness, suggesting that large-scale distributions of some fungal groups are partially constrained by their ancestral niche. There was a strong phylogenetic signal in seasonal sensitivity, suggesting that some groups of fungi have retained their ancestral trait of sporulating for only a short period. Overall, our results show that the hyperdiverse kingdom of fungi follows globally highly predictable spatial and temporal dynamics, with seasonality in both species richness and community composition increasing with latitude. Our study reports patterns resembling those described for other major groups of organisms, thus making a major contribution to the long-standing debate on whether organisms with a microbial lifestyle follow the global biodiversity paradigms known for macroorganisms4,5.
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- 2024
11. Knowledge graphs for empirical concept retrieval
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Tětková, Lenka, Scheidt, Teresa Karen, Fogh, Maria Mandrup, Jørgensen, Ellen Marie Gaunby, Nielsen, Finn Årup, and Hansen, Lars Kai
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence - Abstract
Concept-based explainable AI is promising as a tool to improve the understanding of complex models at the premises of a given user, viz.\ as a tool for personalized explainability. An important class of concept-based explainability methods is constructed with empirically defined concepts, indirectly defined through a set of positive and negative examples, as in the TCAV approach (Kim et al., 2018). While it is appealing to the user to avoid formal definitions of concepts and their operationalization, it can be challenging to establish relevant concept datasets. Here, we address this challenge using general knowledge graphs (such as, e.g., Wikidata or WordNet) for comprehensive concept definition and present a workflow for user-driven data collection in both text and image domains. The concepts derived from knowledge graphs are defined interactively, providing an opportunity for personalization and ensuring that the concepts reflect the user's intentions. We test the retrieved concept datasets on two concept-based explainability methods, namely concept activation vectors (CAVs) and concept activation regions (CARs) (Crabbe and van der Schaar, 2022). We show that CAVs and CARs based on these empirical concept datasets provide robust and accurate explanations. Importantly, we also find good alignment between the models' representations of concepts and the structure of knowledge graphs, i.e., human representations. This supports our conclusion that knowledge graph-based concepts are relevant for XAI., Comment: Preprint. Accepted to The 2nd World Conference on eXplainable Artificial Intelligence
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- 2024
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12. Assessing the Effectiveness of a Short Form Screening Tool (COPs) for Body Dysmorphic Disorder in Cosmetic Surgery Patients: A Study of Pre- and Post-Operative Outcomes
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Brown, Tim, de la Paz, Jacob, Murphy, Tracey, and Hansen, Lars
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- 2024
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13. Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA.
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Ovaskainen, Otso, Abrego, Nerea, Furneaux, Brendan, Hardwick, Bess, Somervuo, Panu, Palorinne, Isabella, Andrew, Nigel, Babiy, Ulyana, Bao, Tan, Bazzano, Gisela, Bondarchuk, Svetlana, Bonebrake, Timothy, Brennan, Georgina, Bret-Harte, Syndonia, Bässler, Claus, Cagnolo, Luciano, Cameron, Erin, Chapurlat, Elodie, Creer, Simon, DAcqui, Luigi, de Vere, Natasha, Desprez-Loustau, Marie-Laure, Dongmo, Michel, Dyrholm Jacobsen, Ida, Fisher, Brian, Flores de Jesus, Miguel, Griffith, Gareth, Gritsuk, Anna, Gross, Andrin, Grudd, Håkan, Halme, Panu, Hanna, Rachid, Hansen, Jannik, Hansen, Lars, Hegbe, Apollon, Hill, Sarah, Hogg, Ian, Hultman, Jenni, Hyde, Kevin, Hynson, Nicole, Ivanova, Natalia, Karisto, Petteri, Kerdraon, Deirdre, Knorre, Anastasia, Krisai-Greilhuber, Irmgard, Kurhinen, Juri, Kuzmina, Masha, Lecomte, Nicolas, Lecomte, Erin, Loaiza, Viviana, Lundin, Erik, Meire, Alexander, Mešić, Armin, Miettinen, Otto, Monkhause, Norman, Mortimer, Peter, Müller, Jörg, Nilsson, R, Nonti, Puani, Nordén, Jenni, Nordén, Björn, Paz, Claudia, Pellikka, Petri, Pereira, Danilo, Petch, Geoff, Pitkänen, Juha-Matti, Popa, Flavius, Potter, Caitlin, Purhonen, Jenna, Pätsi, Sanna, Rafiq, Abdullah, Raharinjanahary, Dimby, Rakos, Niklas, Rathnayaka, Achala, Raundrup, Katrine, Rebriev, Yury, Rikkinen, Jouko, Rogers, Hanna, Rogovsky, Andrey, Rozhkov, Yuri, Runnel, Kadri, Saarto, Annika, Savchenko, Anton, Schlegel, Markus, Schmidt, Niels, Seibold, Sebastian, Skjøth, Carsten, Stengel, Elisa, Sutyrina, Svetlana, Syvänperä, Ilkka, Tedersoo, Leho, Timm, Jebidiah, Tipton, Laura, Toju, Hirokazu, Uscka-Perzanowska, Maria, van der Bank, Michelle, Herman van der Bank, F, Vandenbrink, Bryan, Ventura, Stefano, and Vignisson, Solvi
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Air Microbiology ,Spores ,Fungal ,DNA ,Fungal ,Fungi ,Biodiversity - Abstract
Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. Here we present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world. Each sample represents fungal DNA extracted from 24 m3 of air. We applied a conservative bioinformatics pipeline that filtered out sequences that did not show strong evidence of representing a fungal species. The pipeline yielded 27,954 species-level operational taxonomic units (OTUs). Each OTU is accompanied by a probabilistic taxonomic classification, validated through comparison with expert evaluations. To examine the potential of the data for ecological analyses, we partitioned the variation in species distributions into spatial and seasonal components, showing a strong effect of the annual mean temperature on community composition.
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- 2024
14. Sea ice as habitat for microalgae, bacteria, virus, fungi, meio- and macrofauna: A review of an extreme environment
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Lund-Hansen, Lars Chresten, Gradinger, Rolf, Hassett, Brandon, Jayasinghe, Sahan, Kennedy, Fraser, Martin, Andrew, McMinn, Andrew, Søgaard, Dorte H., and Sorrell, Brian K.
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- 2024
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15. A Deep Learning Analysis of Climate Change, Innovation, and Uncertainty
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Barnett, Michael, Brock, William, Hansen, Lars Peter, Hu, Ruimeng, and Huang, Joseph
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Economics - General Economics ,Computer Science - Machine Learning - Abstract
We study the implications of model uncertainty in a climate-economics framework with three types of capital: "dirty" capital that produces carbon emissions when used for production, "clean" capital that generates no emissions but is initially less productive than dirty capital, and knowledge capital that increases with R\&D investment and leads to technological innovation in green sector productivity. To solve our high-dimensional, non-linear model framework we implement a neural-network-based global solution method. We show there are first-order impacts of model uncertainty on optimal decisions and social valuations in our integrated climate-economic-innovation framework. Accounting for interconnected uncertainty over climate dynamics, economic damages from climate change, and the arrival of a green technological change leads to substantial adjustments to investment in the different capital types in anticipation of technological change and the revelation of climate damage severity.
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- 2023
16. Granular dilatancy and non-local fluidity of partially molten rock
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Katz, Richard F., Rudge, John F., and Hansen, Lars N.
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Physics - Fluid Dynamics ,Physics - Geophysics - Abstract
Partially molten rock is a densely packed, melt-saturated, granular medium, but it has seldom been considered in these terms. In this manuscript, we extend the continuum theory of partially molten rock to incorporate the physics of granular media. Our formulation includes dilatancy in a viscous constitutive law and introduces a non-local fluidity. We analyse the resulting poro-viscous--granular theory in terms of two modes of liquid--solid segregation that are observed in published torsion experiments: localisation of liquid into high-porosity sheets and radially inward liquid flow. We show that the newly incorporated granular physics brings the theory into agreement with experiments. We discuss these results in the context of grain-scale physics across the nominal jamming fraction at the high homologous temperatures relevant in geological systems., Comment: 31 pages, 9 figures, 4 appendicies
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- 2023
17. Concept-based explainability for an EEG transformer model
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Gjølbye, Anders, Lehn-Schiøler, William, Jónsdóttir, Áshildur, Arnardóttir, Bergdís, and Hansen, Lars Kai
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Computer Science - Machine Learning ,Electrical Engineering and Systems Science - Signal Processing ,Statistics - Machine Learning - Abstract
Deep learning models are complex due to their size, structure, and inherent randomness in training procedures. Additional complexity arises from the selection of datasets and inductive biases. Addressing these challenges for explainability, Kim et al. (2018) introduced Concept Activation Vectors (CAVs), which aim to understand deep models' internal states in terms of human-aligned concepts. These concepts correspond to directions in latent space, identified using linear discriminants. Although this method was first applied to image classification, it was later adapted to other domains, including natural language processing. In this work, we attempt to apply the method to electroencephalogram (EEG) data for explainability in Kostas et al.'s BENDR (2021), a large-scale transformer model. A crucial part of this endeavor involves defining the explanatory concepts and selecting relevant datasets to ground concepts in the latent space. Our focus is on two mechanisms for EEG concept formation: the use of externally labeled EEG datasets, and the application of anatomically defined concepts. The former approach is a straightforward generalization of methods used in image classification, while the latter is novel and specific to EEG. We present evidence that both approaches to concept formation yield valuable insights into the representations learned by deep EEG models., Comment: To appear in proceedings of 2023 IEEE International workshop on Machine Learning for Signal Processing
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- 2023
18. Using Sequences of Life-events to Predict Human Lives
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Savcisens, Germans, Eliassi-Rad, Tina, Hansen, Lars Kai, Mortensen, Laust, Lilleholt, Lau, Rogers, Anna, Zettler, Ingo, and Lehmann, Sune
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Statistics - Machine Learning ,Computer Science - Machine Learning ,Statistics - Applications - Abstract
Over the past decade, machine learning has revolutionized computers' ability to analyze text through flexible computational models. Due to their structural similarity to written language, transformer-based architectures have also shown promise as tools to make sense of a range of multi-variate sequences from protein-structures, music, electronic health records to weather-forecasts. We can also represent human lives in a way that shares this structural similarity to language. From one perspective, lives are simply sequences of events: People are born, visit the pediatrician, start school, move to a new location, get married, and so on. Here, we exploit this similarity to adapt innovations from natural language processing to examine the evolution and predictability of human lives based on detailed event sequences. We do this by drawing on arguably the most comprehensive registry data in existence, available for an entire nation of more than six million individuals across decades. Our data include information about life-events related to health, education, occupation, income, address, and working hours, recorded with day-to-day resolution. We create embeddings of life-events in a single vector space showing that this embedding space is robust and highly structured. Our models allow us to predict diverse outcomes ranging from early mortality to personality nuances, outperforming state-of-the-art models by a wide margin. Using methods for interpreting deep learning models, we probe the algorithm to understand the factors that enable our predictions. Our framework allows researchers to identify new potential mechanisms that impact life outcomes and associated possibilities for personalized interventions.
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- 2023
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19. Masked Autoencoders with Multi-Window Local-Global Attention Are Better Audio Learners
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Yadav, Sarthak, Theodoridis, Sergios, Hansen, Lars Kai, and Tan, Zheng-Hua
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Computer Science - Sound ,Computer Science - Artificial Intelligence ,Electrical Engineering and Systems Science - Audio and Speech Processing - Abstract
In this work, we propose a Multi-Window Masked Autoencoder (MW-MAE) fitted with a novel Multi-Window Multi-Head Attention (MW-MHA) module that facilitates the modelling of local-global interactions in every decoder transformer block through attention heads of several distinct local and global windows. Empirical results on ten downstream audio tasks show that MW-MAEs consistently outperform standard MAEs in overall performance and learn better general-purpose audio representations, along with demonstrating considerably better scaling characteristics. Investigating attention distances and entropies reveals that MW-MAE encoders learn heads with broader local and global attention. Analyzing attention head feature representations through Projection Weighted Canonical Correlation Analysis (PWCCA) shows that attention heads with the same window sizes across the decoder layers of the MW-MAE learn correlated feature representations which enables each block to independently capture local and global information, leading to a decoupled decoder feature hierarchy. Code for feature extraction and downstream experiments along with pre-trained models will be released publically.
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- 2023
20. Mapping RANKL- and OPG-expressing cells in bone tissue: the bone surface cells as activators of osteoclastogenesis and promoters of the denosumab rebound effect
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El-Masri, Bilal M., Andreasen, Christina M., Laursen, Kaja S., Kofod, Viktoria B., Dahl, Xenia G., Nielsen, Malene H., Thomsen, Jesper S., Brüel, Annemarie, Sørensen, Mads S., Hansen, Lars J., Kim, Albert S., Taylor, Victoria E., Massarotti, Caitlyn, McDonald, Michelle M., You, Xiaomeng, Charles, Julia F., Delaisse, Jean-Marie, and Andersen, Thomas L.
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- 2024
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21. Prices versus Quantities in Fisheries Models: Comment
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Hansen, Lars Gårn
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- 2012
22. A family of di-glutamate mucin-degrading enzymes that bridges glycan hydrolases and peptidases
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Narimatsu, Yoshiki, Büll, Christian, Taleb, Víctor, Liao, Qinghua, Compañón, Ismael, Sánchez-Navarro, David, Durbesson, Fabien, Vincentelli, Renaud, Hansen, Lars, Corzana, Francisco, Rovira, Carme, Henrissat, Bernard, Clausen, Henrik, Joshi, Hiren J., and Hurtado-Guerrero, Ramon
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- 2024
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23. On convex decision regions in deep network representations
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Tětková, Lenka, Brüsch, Thea, Scheidt, Teresa Karen, Mager, Fabian Martin, Aagaard, Rasmus Ørtoft, Foldager, Jonathan, Alstrøm, Tommy Sonne, and Hansen, Lars Kai
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence - Abstract
Current work on human-machine alignment aims at understanding machine-learned latent spaces and their correspondence to human representations. G{\"a}rdenfors' conceptual spaces is a prominent framework for understanding human representations. Convexity of object regions in conceptual spaces is argued to promote generalizability, few-shot learning, and interpersonal alignment. Based on these insights, we investigate the notion of convexity of concept regions in machine-learned latent spaces. We develop a set of tools for measuring convexity in sampled data and evaluate emergent convexity in layered representations of state-of-the-art deep networks. We show that convexity is robust to basic re-parametrization and, hence, meaningful as a quality of machine-learned latent spaces. We find that approximate convexity is pervasive in neural representations in multiple application domains, including models of images, audio, human activity, text, and medical images. Generally, we observe that fine-tuning increases the convexity of label regions. We find evidence that pretraining convexity of class label regions predicts subsequent fine-tuning performance.
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- 2023
24. Robustness of Visual Explanations to Common Data Augmentation
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Tětková, Lenka and Hansen, Lars Kai
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning - Abstract
As the use of deep neural networks continues to grow, understanding their behaviour has become more crucial than ever. Post-hoc explainability methods are a potential solution, but their reliability is being called into question. Our research investigates the response of post-hoc visual explanations to naturally occurring transformations, often referred to as augmentations. We anticipate explanations to be invariant under certain transformations, such as changes to the colour map while responding in an equivariant manner to transformations like translation, object scaling, and rotation. We have found remarkable differences in robustness depending on the type of transformation, with some explainability methods (such as LRP composites and Guided Backprop) being more stable than others. We also explore the role of training with data augmentation. We provide evidence that explanations are typically less robust to augmentation than classification performance, regardless of whether data augmentation is used in training or not., Comment: Accepted to The 2nd Explainable AI for Computer Vision (XAI4CV) Workshop at CVPR 2023
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- 2023
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25. Calibration and data analysis routines for nanoindentation with spherical tips
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Avadanii, Diana, Kareer, Anna, Hansen, Lars, and Wilkinson, Angus
- Subjects
Condensed Matter - Materials Science - Abstract
Instrumented spherical nanoindentation with a continuous stiffness measurement has gained increased popularity in material science studies in brittle and ductile materials alike. These investigations span hypotheses related to a wide range of microphysics involving grain boundaries, twins, dislocation densities, ion-induced damage and more. These studies rely on the implementation of different methodologies for instrument calibration and for circumventing tip shape imperfections. In this study, we test, integrate, and re-adapt published strategies for tip and machine-stiffness calibration for spherical tips. We propose a routine for independently calibrating the effective tip radius and the machine stiffness using three reference materials (fused silica, sapphire, glassy carbon), which requires the parametrization of the effective radius as a function of load. We validate our proposed workflow against key benchmarks, such as variation of Young's modulus with depth. We apply the resulting calibrations to data collected in materials with varying ductility (olivine, titanium, and tungsten) to extract indentation stress-strain curves. We also test the impact of the machine stiffness on recently proposed methods for identification of yield stress, and compare the influence of different conventions on assessing the indentation size effect. Finally, we synthesize these analysis routines in a single workflow for use in future studies aiming to extract and process data from spherical nanoindentation.
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- 2023
- Full Text
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26. On the role of Model Uncertainties in Bayesian Optimization
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Foldager, Jonathan, Jordahn, Mikkel, Hansen, Lars Kai, and Andersen, Michael Riis
- Subjects
Statistics - Machine Learning ,Computer Science - Machine Learning - Abstract
Bayesian optimization (BO) is a popular method for black-box optimization, which relies on uncertainty as part of its decision-making process when deciding which experiment to perform next. However, not much work has addressed the effect of uncertainty on the performance of the BO algorithm and to what extent calibrated uncertainties improve the ability to find the global optimum. In this work, we provide an extensive study of the relationship between the BO performance (regret) and uncertainty calibration for popular surrogate models and compare them across both synthetic and real-world experiments. Our results confirm that Gaussian Processes are strong surrogate models and that they tend to outperform other popular models. Our results further show a positive association between calibration error and regret, but interestingly, this association disappears when we control for the type of model in the analysis. We also studied the effect of re-calibration and demonstrate that it generally does not lead to improved regret. Finally, we provide theoretical justification for why uncertainty calibration might be difficult to combine with BO due to the small sample sizes commonly used., Comment: 14 pages, 4 figures, 2 tables
- Published
- 2023
27. Using sequences of life-events to predict human lives
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Savcisens, Germans, Eliassi-Rad, Tina, Hansen, Lars Kai, Mortensen, Laust Hvas, Lilleholt, Lau, Rogers, Anna, Zettler, Ingo, and Lehmann, Sune
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- 2024
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28. Impact of Lipidic Plaque on In-Stent and Stent Edge–Related Events After PCI in Myocardial Infarction: A PROSPECT II Substudy
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Kjøller-Hansen, Lars, Maehara, Akiko, Kelbæk, Henning, Matsumura, Mitsuaki, Maeng, Michael, Engstrøm, Thomas, Fröbert, Ole, Persson, Jonas, Wiseth, Rune, Larsen, Alf Inge, Jensen, Lisette Okkels, Nordrehaug, Jan Erik, Omerovic, Elmir, Held, Claes, James, Stefan, Mintz, Gary S., Ali, Ziad A., Stone, Gregg W., and Erlinge, David
- Published
- 2024
- Full Text
- View/download PDF
29. Cotadutide promotes glycogenolysis in people with overweight or obesity diagnosed with type 2 diabetes
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Parker, Victoria E. R., Robertson, Darren, Erazo-Tapia, Edmundo, Havekes, Bas, Phielix, Esther, de Ligt, Marlies, Roumans, Kay H. M., Mevenkamp, Julian, Sjoberg, Folke, Schrauwen-Hinderling, Vera B., Johansson, Edvin, Chang, Yi-Ting, Esterline, Russell, Smith, Kenneth, Wilkinson, Daniel J., Hansen, Lars, Johansson, Lars, Ambery, Philip, Jermutus, Lutz, and Schrauwen, Patrick
- Published
- 2023
- Full Text
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30. Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria
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Dougherty, Peter Erdmann, Nielsen, Tue Kjærgaard, Riber, Leise, Lading, Helen Helgå, Forero-Junco, Laura Milena, Kot, Witold, Raaijmakers, Jos M., and Hansen, Lars Hestbjerg
- Published
- 2023
- Full Text
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31. A family with ulcerative colitis maps to 7p21.1 and comprises a region with regulatory activity for the aryl hydrocarbon receptor gene
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Eiberg, Hans, Olsson, Josephine B., Bak, Mads, Bang-Berthelsen, Claus Heiner, Troelsen, Jesper T., and Hansen, Lars
- Published
- 2023
- Full Text
- View/download PDF
32. Clustering of antipsychotic-naïve patients with schizophrenia based on functional connectivity from resting-state electroencephalography
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Ambrosen, Karen S., Fredriksson, Fanny, Anhøj, Simon, Bak, Nikolaj, van Dellen, Edwin, Dominicus, Livia, Lemvigh, Cecilie K., Sørensen, Mikkel E., Nielsen, Mette Ø., Bojesen, Kirsten B., Fagerlund, Birgitte, Glenthøj, Birte Y., Oranje, Bob, Hansen, Lars K., and Ebdrup, Bjørn H.
- Published
- 2023
- Full Text
- View/download PDF
33. Reconstructing the exit wave of 2D materials in high-resolution transmission electron microscopy using machine learning
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Leth Larsen, Matthew Helmi, Dahl, Frederik, Hansen, Lars P, Barton, Bastian, Kisielowski, Christian, Helveg, Stig, Winther, Ole, Hansen, Thomas W, and Schiøtz, Jakob
- Subjects
Physical Sciences ,Condensed Matter Physics ,Networking and Information Technology R&D (NITRD) ,Bioengineering ,Machine Learning and Artificial Intelligence ,2D materials ,Exit wave reconstruction ,HRTEM ,Machine learning ,Atomic ,Molecular ,Nuclear ,Particle and Plasma Physics ,Optical Physics ,Other Physical Sciences ,Microscopy ,Biochemistry and cell biology ,Physical chemistry ,Condensed matter physics - Abstract
Reconstruction of the exit wave function is an important route to interpreting high-resolution transmission electron microscopy (HRTEM) images. Here we demonstrate that convolutional neural networks can be used to reconstruct the exit wave from a short focal series of HRTEM images, with a fidelity comparable to conventional exit wave reconstruction. We use a fully convolutional neural network based on the U-Net architecture, and demonstrate that we can train it on simulated exit waves and simulated HRTEM images of graphene-supported molybdenum disulphide (an industrial desulfurization catalyst). We then apply the trained network to analyse experimentally obtained images from similar samples, and obtain exit waves that clearly show the atomically resolved structure of both the MoS2 nanoparticles and the graphene support. We also show that it is possible to successfully train the neural networks to reconstruct exit waves for 3400 different two-dimensional materials taken from the Computational 2D Materials Database of known and proposed two-dimensional materials.
- Published
- 2023
34. Non-target analysis of Danish wastewater treatment plant effluent: Statistical analysis of chemical fingerprinting as a step toward a future monitoring tool
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Aggerbeck, Marie Rønne, Frøkjær, Emil Egede, Johansen, Anders, Ellegaard-Jensen, Lea, Hansen, Lars Hestbjerg, and Hansen, Martin
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- 2024
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35. A novel genus of Pectobacterium bacteriophages display broad host range by targeting several species of Danish soft rot isolates
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Pedersen, Julie Stenberg, Carstens, Alexander Byth, Rothgard, Magnus Mulbjerg, Roy, Chayan, Viry, Anouk, Papudeshi, Bhavya, Kot, Witold, Hille, Frank, Franz, Charles M.A.P., Edwards, Robert, and Hansen, Lars Hestbjerg
- Published
- 2024
- Full Text
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36. CUX1-related neurodevelopmental disorder: deep insights into phenotype-genotype spectrum and underlying pathology
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Oppermann, Henry, Marcos-Grañeda, Elia, Weiss, Linnea A., Gurnett, Christina A., Jelsig, Anne Marie, Vineke, Susanne H., Isidor, Bertrand, Mercier, Sandra, Magnussen, Kari, Zacher, Pia, Hashim, Mona, Pagnamenta, Alistair T., Race, Simone, Srivastava, Siddharth, Frazier, Zoë, Maiwald, Robert, Pergande, Matthias, Milani, Donatella, Rinelli, Martina, Levy, Jonathan, Krey, Ilona, Fontana, Paolo, Lonardo, Fortunato, Riley, Stephanie, Kretzer, Jasmine, Rankin, Julia, Reis, Linda M., Semina, Elena V., Reuter, Miriam S., Scherer, Stephen W., Iascone, Maria, Weis, Denisa, Fagerberg, Christina R., Brasch-Andersen, Charlotte, Hansen, Lars Kjaersgaard, Kuechler, Alma, Noble, Nathan, Gardham, Alice, Tenney, Jessica, Rathore, Geetanjali, Beck-Woedl, Stefanie, Haack, Tobias B., Pavlidou, Despoina C., Atallah, Isis, Vodopiutz, Julia, Janecke, Andreas R., Hsieh, Tzung-Chien, Lesmann, Hellen, Klinkhammer, Hannah, Krawitz, Peter M., Lemke, Johannes R., Jamra, Rami Abou, Nieto, Marta, Tümer, Zeynep, and Platzer, Konrad
- Published
- 2023
- Full Text
- View/download PDF
37. Reconstructing the exit wave in high-resolution transmission electron microscopy using machine learning
- Author
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Larsen, Matthew Helmi Leth, Dahl, Frederik, Hansen, Lars P., Barton, Bastian, Kisielowski, Christian, Helveg, Stig, Winther, Ole, Hansen, Thomas W., and Schiøtz, Jakob
- Subjects
Condensed Matter - Materials Science ,Condensed Matter - Disordered Systems and Neural Networks - Abstract
Reconstruction of the exit wave function is an important route to interpreting high-resolution transmission electron microscopy (HRTEM) images. Here we demonstrate that convolutional neural networks can be used to reconstruct the exit wave from a short focal series of HRTEM images, with a fidelity comparable to conventional exit wave reconstruction. We use a fully convolutional neural network based on the U-Net architecture, and demonstrate that we can train it on simulated exit waves and simulated HRTEM images of graphene-supported molybdenum disulphide (an industrial desulfurization catalyst). We then apply the trained network to analyse experimentally obtained images from similar samples, and obtain exit waves that clearly show the atomically resolved structure of both the MoS$_2$ nanoparticles and the graphene support. We also show that it is possible to successfully train the neural networks to reconstruct exit waves for 3400 different two-dimensional materials taken from the Computational 2D Materials Database of known and proposed two-dimensional materials., Comment: 16 pages, 24 figures
- Published
- 2021
- Full Text
- View/download PDF
38. Economics of New Zealand planted kauri forestry - a model exercise
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Steward, Gregory A., Hansen, Lars, and Dungey, Heidi S.
- Published
- 2014
39. A randomized phase 2b trial examined the effects of the glucagon-like peptide-1 and glucagon receptor agonist cotadutide on kidney outcomes in patients with diabetic kidney disease
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Selvarajah, Viknesh, Robertson, Darren, Hansen, Lars, Jermutus, Lutz, Smith, Kirsten, Coggi, Angela, Sánchez, José, Chang, Yi-Ting, Yu, Hongtao, Parkinson, Joanna, Khan, Anis, Chung, H. Sophia, Hess, Sonja, Dumas, Richard, Duck, Tabbatha, Jolly, Simran, Elliott, Tom G., Baker, John, Lecube, Albert, Derwahl, Karl-Michael, Scott, Russell, Morales, Cristobal, Peters, Carl, Goldenberg, Ronald, Parker, Victoria E.R., and Heerspink, Hiddo J.L.
- Published
- 2024
- Full Text
- View/download PDF
40. Noise-Assisted Variational Quantum Thermalization
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Foldager, Jonathan, Pesah, Arthur, and Hansen, Lars Kai
- Subjects
Quantum Physics ,Physics - Computational Physics - Abstract
Preparing thermal states on a quantum computer can have a variety of applications, from simulating many-body quantum systems to training machine learning models. Variational circuits have been proposed for this task on near-term quantum computers, but several challenges remain, such as finding a scalable cost-function, avoiding the need of purification, and mitigating noise effects. We propose a new algorithm for thermal state preparation that tackles those three challenges by exploiting the noise of quantum circuits. We consider a variational architecture containing a depolarizing channel after each unitary layer, with the ability to directly control the level of noise. We derive a closed-form approximation for the free-energy of such circuit and use it as a cost function for our variational algorithm. By evaluating our method on a variety of Hamiltonians and system sizes, we find several systems for which the thermal state can be approximated with a high fidelity. However, we also show that the ability for our algorithm to learn the thermal state strongly depends on the temperature: while a high fidelity can be obtained for high and low temperatures, we identify a specific range for which the problem becomes more challenging. We hope that this first study on noise-assisted thermal state preparation will inspire future research on exploiting noise in variational algorithms., Comment: 13 pages, 7 figures. Submitted to Scientific Reports
- Published
- 2021
41. Topic Model Robustness to Automatic Speech Recognition Errors in Podcast Transcripts
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Fetic, Raluca Alexandra, Jordahn, Mikkel, Lima, Lucas Chaves, Egebæk, Rasmus Arpe Fogh, Nielsen, Martin Carsten, Biering, Benjamin, and Hansen, Lars Kai
- Subjects
Computer Science - Information Retrieval ,Computer Science - Machine Learning - Abstract
For a multilingual podcast streaming service, it is critical to be able to deliver relevant content to all users independent of language. Podcast content relevance is conventionally determined using various metadata sources. However, with the increasing quality of speech recognition in many languages, utilizing automatic transcriptions to provide better content recommendations becomes possible. In this work, we explore the robustness of a Latent Dirichlet Allocation topic model when applied to transcripts created by an automatic speech recognition engine. Specifically, we explore how increasing transcription noise influences topics obtained from transcriptions in Danish; a low resource language. First, we observe a baseline of cosine similarity scores between topic embeddings from automatic transcriptions and the descriptions of the podcasts written by the podcast creators. We then observe how the cosine similarities decrease as transcription noise increases and conclude that even when automatic speech recognition transcripts are erroneous, it is still possible to obtain high-quality topic embeddings from the transcriptions.
- Published
- 2021
42. 21st century accelerating neurological deaths in UK and major Western countries: - Demographic and/or multiple-interactive-environmental causes?
- Author
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Pritchard, Colin, Silk, Anne, Hansen, Lars, Panesar, Harpal, and Berendt, Therese
- Published
- 2024
- Full Text
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43. Robust inference for moment condition models without rational expectations
- Author
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Chen, Xiaohong, Hansen, Lars Peter, and Hansen, Peter G.
- Published
- 2024
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44. Machine-learning vs. logistic regression for preoperative prediction of medical morbidity after fast-track hip and knee arthroplasty—a comparative study
- Author
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Michelsen, Christian, Jørgensen, Christoffer C., Heltberg, Mathias, Jensen, Mogens H., Lucchetti, Alessandra, Petersen, Pelle B., Petersen, Troels, Kehlet, Henrik, Madsen, Frank, Hansen, Torben B., Gromov, Kirill, Jakobsen, Thomas, Varnum, Claus, Overgaard, Soren, Rathsach, Mikkel, and Hansen, Lars
- Published
- 2023
- Full Text
- View/download PDF
45. Critical Assessment of Metagenome Interpretation: the second round of challenges
- Author
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Meyer, Fernando, Fritz, Adrian, Deng, Zhi-Luo, Koslicki, David, Lesker, Till Robin, Gurevich, Alexey, Robertson, Gary, Alser, Mohammed, Antipov, Dmitry, Beghini, Francesco, Bertrand, Denis, Brito, Jaqueline J, Brown, C Titus, Buchmann, Jan, Buluç, Aydin, Chen, Bo, Chikhi, Rayan, Clausen, Philip TLC, Cristian, Alexandru, Dabrowski, Piotr Wojciech, Darling, Aaron E, Egan, Rob, Eskin, Eleazar, Georganas, Evangelos, Goltsman, Eugene, Gray, Melissa A, Hansen, Lars Hestbjerg, Hofmeyr, Steven, Huang, Pingqin, Irber, Luiz, Jia, Huijue, Jørgensen, Tue Sparholt, Kieser, Silas D, Klemetsen, Terje, Kola, Axel, Kolmogorov, Mikhail, Korobeynikov, Anton, Kwan, Jason, LaPierre, Nathan, Lemaitre, Claire, Li, Chenhao, Limasset, Antoine, Malcher-Miranda, Fabio, Mangul, Serghei, Marcelino, Vanessa R, Marchet, Camille, Marijon, Pierre, Meleshko, Dmitry, Mende, Daniel R, Milanese, Alessio, Nagarajan, Niranjan, Nissen, Jakob, Nurk, Sergey, Oliker, Leonid, Paoli, Lucas, Peterlongo, Pierre, Piro, Vitor C, Porter, Jacob S, Rasmussen, Simon, Rees, Evan R, Reinert, Knut, Renard, Bernhard, Robertsen, Espen Mikal, Rosen, Gail L, Ruscheweyh, Hans-Joachim, Sarwal, Varuni, Segata, Nicola, Seiler, Enrico, Shi, Lizhen, Sun, Fengzhu, Sunagawa, Shinichi, Sørensen, Søren Johannes, Thomas, Ashleigh, Tong, Chengxuan, Trajkovski, Mirko, Tremblay, Julien, Uritskiy, Gherman, Vicedomini, Riccardo, Wang, Zhengyang, Wang, Ziye, Wang, Zhong, Warren, Andrew, Willassen, Nils Peder, Yelick, Katherine, You, Ronghui, Zeller, Georg, Zhao, Zhengqiao, Zhu, Shanfeng, Zhu, Jie, Garrido-Oter, Ruben, Gastmeier, Petra, Hacquard, Stephane, Häußler, Susanne, Khaledi, Ariane, Maechler, Friederike, Mesny, Fantin, Radutoiu, Simona, Schulze-Lefert, Paul, Smit, Nathiana, and Strowig, Till
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Networking and Information Technology R&D (NITRD) ,Archaea ,Metagenome ,Metagenomics ,Reproducibility of Results ,Sequence Analysis ,DNA ,Software ,Technology ,Medical and Health Sciences ,Developmental Biology ,Biological sciences - Abstract
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.
- Published
- 2022
46. Archival associations in Sweden
- Author
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Hansen, Lars-Erik, primary and Sundqvist, Anneli, additional
- Published
- 2023
- Full Text
- View/download PDF
47. Generalization by design: Shortcuts to Generalization in Deep Learning
- Author
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Taborsky, Petr and Hansen, Lars Kai
- Subjects
Computer Science - Machine Learning ,Mathematics - Differential Geometry ,Mathematics - Probability - Abstract
We take a geometrical viewpoint and present a unifying view on supervised deep learning with the Bregman divergence loss function - this entails frequent classification and prediction tasks. Motivated by simulations we suggest that there is principally no implicit bias of vanilla stochastic gradient descent training of deep models towards "simpler" functions. Instead, we show that good generalization may be instigated by bounded spectral products over layers leading to a novel geometric regularizer. It is revealed that in deep enough models such a regularizer enables both, extreme accuracy and generalization, to be reached. We associate popular regularization techniques like weight decay, drop out, batch normalization, and early stopping with this perspective. Backed up by theory we further demonstrate that "generalization by design" is practically possible and that good generalization may be encoded into the structure of the network. We design two such easy-to-use structural regularizers that insert an additional \textit{generalization layer} into a model architecture, one with a skip connection and another one with drop-out. We verify our theoretical results in experiments on various feedforward and convolutional architectures, including ResNets, and datasets (MNIST, CIFAR10, synthetic data). We believe this work opens up new avenues of research towards better generalizing architectures., Comment: 16 pages + 9 pages supplementary
- Published
- 2021
48. Weighted Burgers Vector analysis of orientation fields from high-angular resolution electron backscatter diffraction
- Author
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Gardner, Joe, Wallis, David, Hansen, Lars N., and Wheeler, John
- Published
- 2024
- Full Text
- View/download PDF
49. Dissecting structure-function of 3-O-sulfated heparin and engineered heparan sulfates
- Author
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Karlsson, Richard, Chopra, Pradeep, Joshi, Apoorva, Yang, Zhang, Vakhrushev, Sergey Y, Clausen, Thomas Mandel, Painter, Chelsea D, Szekeres, Gergo P, Chen, Yen-Hsi, Sandoval, Daniel R, Hansen, Lars, Esko, Jeffrey D, Pagel, Kevin, Dyer, Douglas P, Turnbull, Jeremy E, Clausen, Henrik, Boons, Geert-Jan, and Miller, Rebecca L
- Subjects
Hematology - Abstract
Heparan sulfate (HS) polysaccharides are master regulators of diverse biological processes via sulfated motifs that can recruit specific proteins. 3-O-sulfation of HS/heparin is crucial for anticoagulant activity, but despite emerging evidence for roles in many other functions, a lack of tools for deciphering structure-function relationships has hampered advances. Here, we describe an approach integrating synthesis of 3-O-sulfated standards, comprehensive HS disaccharide profiling, and cell engineering to address this deficiency. Its application revealed previously unseen differences in 3-O-sulfated profiles of clinical heparins and 3-O-sulfotransferase (HS3ST)–specific variations in cell surface HS profiles. The latter correlated with functional differences in anticoagulant activity and binding to platelet factor 4 (PF4), which underlies heparin-induced thrombocytopenia, a known side effect of heparin. Unexpectedly, cells expressing the HS3ST4 isoenzyme generated HS with potent anticoagulant activity but weak PF4 binding. The data provide new insights into 3-O-sulfate structure-function and demonstrate proof of concept for tailored cell-based synthesis of next-generation heparins.
- Published
- 2021
50. The role of grain-environment heterogeneity in normal grain growth: a stochastic approach
- Author
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Breithaupt, Thomas, Hansen, Lars N., Toppaladoddi, Srikanth, and Katz, Richard F.
- Subjects
Condensed Matter - Materials Science - Abstract
The size distribution of grains is a fundamental characteristic of polycrystalline solids. In the absence of deformation, the grain-size distribution is controlled by normal grain growth. The canonical model of normal grain growth, developed by Hillert, predicts a grain-size distribution that bears a systematic discrepancy with observed distributions. To address this, we propose a change to the Hillert model that accounts for the influence of heterogeneity in the local environment of grains. In our model, each grain evolves in response to its own local environment of neighbouring grains, rather than to the global population of grains. The local environment of each grain evolves according to an Ornstein-Uhlenbeck stochastic process. Our results are consistent with accepted grain-growth kinetics. Crucially, our model indicates that the size of relatively large grains evolves as a random walk due to the inherent variability in their local environments. This leads to a broader grain-size distribution than the Hillert model and indicates that heterogeneity has a critical influence on the evolution of microstructure., Comment: 24 pages, 8 figures, to be published in Acta Materialia
- Published
- 2021
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