Search

Obtaining effective representations of DNA sequences is crucial for genome analysis. Metagenomic binning, for instance, relies on genome representations to cluster complex mixtures of DNA fragments from biological samples with the aim of determining their microbial compositions. In this paper, we revisit k-mer-based representations of genomes and provide a theoretical analysis of their use in representation learning. Based on the analysis, we propose a lightweight and scalable model for performing metagenomic binning at the genome read level, relying only on the k-mer compositions of the DNA fragments. We compare the model to recent genome foundation models and demonstrate that while the models are comparable in performance, the proposed model is significantly more effective in terms of scalability, a crucial aspect for performing metagenomic binning of real-world datasets., Comment: Accepted to the Thirty-Eighth Annual Conference on Neural Information Processing Systems (NeurIPS 2024)

Superlattices from twisted graphene mono- and bi-layer systems give rise to on-demand many-body states such as Mott insulators and unconventional superconductors. These phenomena are ascribed to a combination of flat bands and strong Coulomb interactions. However, a comprehensive understanding is lacking because the low-energy band structure strongly changes when the electron filling is varied. Here, we gain direct access to the filling-dependent low energy bands of twisted bilayer graphene (TBG) and twisted double bilayer graphene (TDBG) by applying micro-focused angle-resolved photoemission spectroscopy to in situ gated devices. Our findings for the two systems are in stark contrast: The doping dependent dispersion for TBG can be described in a simple model, combining a filling-dependent rigid band shift with a many-body related bandwidth change. In TDBG, on the other hand, we find a complex behaviour of the low-energy bands, combining non-monotonous bandwidth changes and tuneable gap openings. Our work establishes the extent of electric field tunability of the low energy electronic states in twisted graphene superlattices and can serve to underpin the theoretical understanding of the resulting phenomena., Comment: 26 pages, 4 main figures and 7 supplementary figures

In recent years, mobile network operators are showing interest in reducing energy consumption. Toward this goal, in cooperation with the Danish company 2Operate we have developed a stochastic simulation environment for mobile networks. Our simulator interacts with historical data from 2Operate and allow us to turn on and off network cells, replay traffic loads, etc. We have developed an optimization tool which is based on stochastic and distributed controllers computed by \uppaal. We have conducted experiments in our simulation tool. Experiments show that there is a potential to save up to 10\% of energy. We observe that for larger networks, there exists a larger potential for saving energy. Our simulator and \uppaal controllers, have been constructed in accordance to the 2Operate data and infrastructure. However, a main difference is that current equipment do not support updating schedulers on hourly bases. Nevertheless, new equipment e.g. new Huawei equipment do support changing schedulers on hourly basis. Therefore, integrating our solution in the production server of 2Operate is possible. However, rigorous testing in the production system is required., Comment: Report for Energy Cluster Denmark project of the year. https://www.energycluster.dk/en/eco-ran-wins-innovation-project-of-the-year/

Predicting patients hospital length of stay (LOS) is essential for improving resource allocation and supporting decision-making in healthcare organizations. This paper proposes a novel approach for predicting LOS by modeling patient information as sequences of events. Specifically, we present a transformer-based model, termed Medic-BERT (M-BERT), for LOS prediction using the unique features describing patients medical event sequences. We performed empirical experiments on a cohort of more than 45k emergency care patients from a large Danish hospital. Experimental results show that M-BERT can achieve high accuracy on a variety of LOS problems and outperforms traditional nonsequence-based machine learning approaches., Comment: 11 pages, 5 figures

Microbes have a profound impact on our health and environment, but our understanding of the diversity and function of microbial communities is severely limited. Through DNA sequencing of microbial communities (metagenomics), DNA fragments (reads) of the individual microbes can be obtained, which through assembly graphs can be combined into long contiguous DNA sequences (contigs). Given the complexity of microbial communities, single contig microbial genomes are rarely obtained. Instead, contigs are eventually clustered into bins, with each bin ideally making up a full genome. This process is referred to as metagenomic binning. Current state-of-the-art techniques for metagenomic binning rely only on the local features for the individual contigs. These techniques therefore fail to exploit the similarities between contigs as encoded by the assembly graph, in which the contigs are organized. In this paper, we propose to use Graph Neural Networks (GNNs) to leverage the assembly graph when learning contig representations for metagenomic binning. Our method, VaeG-Bin, combines variational autoencoders for learning latent representations of the individual contigs, with GNNs for refining these representations by taking into account the neighborhood structure of the contigs in the assembly graph. We explore several types of GNNs and demonstrate that VaeG-Bin recovers more high-quality genomes than other state-of-the-art binners on both simulated and real-world datasets.

Gaussian processes (GPs) are powerful but computationally expensive machine learning models, requiring an estimate of the kernel covariance matrix for every prediction. In large and complex domains, such as graphs, sets, or images, the choice of suitable kernel can also be non-trivial to determine, providing an additional obstacle to the learning task. Over the last decade, these challenges have resulted in significant advances being made in terms of scalability and expressivity, exemplified by, e.g., the use of inducing points and neural network kernel approximations. In this paper, we propose inducing Gaussian process networks (IGN), a simple framework for simultaneously learning the feature space as well as the inducing points. The inducing points, in particular, are learned directly in the feature space, enabling a seamless representation of complex structured domains while also facilitating scalable gradient-based learning methods. We consider both regression and (binary) classification tasks and report on experimental results for real-world data sets showing that IGNs provide significant advances over state-of-the-art methods. We also demonstrate how IGNs can be used to effectively model complex domains using neural network architectures.

Travel time or speed estimation are part of many intelligent transportation applications. Existing estimation approaches rely on either function fitting or aggregation and represent different trade-offs between generalizability and accuracy. Function-fitting approaches learn functions that map feature vectors of, e.g., routes, to travel time or speed estimates, which enables generalization to unseen routes. However, mapping functions are imperfect and offer poor accuracy in practice. Aggregation-based approaches instead form estimates by aggregating historical data, e.g., traversal data for routes. This enables very high accuracy given sufficient data. However, they rely on simplistic heuristics when insufficient data is available, yielding poor generalizability. We present a Unifying approach to Travel time and speed Estimation (UniTE) that combines function-fitting and aggregation-based approaches into a unified framework that aims to achieve the generalizability of function-fitting approaches and the accuracy of aggregation-based approaches. An empirical study finds that an instance of UniTE can improve the accuracies of travel speed distribution and travel time estimation by $40-64\%$ and $3-23\%$, respectively, compared to using function fitting or aggregation alone

Storm water detention ponds are used to manage the discharge of rainfall runoff from urban areas to nearby streams. Their purpose is to reduce the hydraulic impact and sediment loads of the receiving waters. Detention ponds are currently designed based on static controls: the output flow of a pond is capped at a fixed value. This is not optimal with respect to the current infrastructure capacity and for some detention ponds it might even violate current regulations set by the European Water Framework Directive. We apply formal methods to synthesize (i.e., derive automatically) a safe and optimal active controller. We model the storm water detention pond, including the urban catchment area and the rain forecasts, as a hybrid Markov decision process. Subsequently, we use the tool Uppaal Stratego to synthesize a control strategy minimizing the cost related to pollution (optimality) while guaranteeing no emergency overflow of the detention pond (safety). Simulation results for an existing pond show that Uppaal Stratego can learn optimal strategies that prevent emergency overflows, where the current static control is not always able to prevent it. At the same time, our approach can improve sedimentation during low rain periods., Comment: Accepted for the IFAC Conference on Analysis and Design of Hybrid Systems 2021. Full paper version

The application of machine learning techniques in the setting of road networks holds the potential to facilitate many important intelligent transportation applications. Graph Convolutional Networks (GCNs) are neural networks that are capable of leveraging the structure of a network. However, many implicit assumptions of GCNs do not apply to road networks. We introduce the Relational Fusion Network (RFN), a novel type of GCN designed specifically for road networks. In particular, we propose methods that outperform state-of-the-art GCNs by 21%-40% on two machine learning tasks in road networks. Furthermore, we show that state-of-the-art GCNs may fail to effectively leverage road network structure and may not generalize well to other road networks., Comment: IEEE Transactions on Intelligent Transportation Systems (2020). arXiv admin note: substantial text overlap with arXiv:1908.11567

Road networks are a type of spatial network, where edges may be associated with qualitative information such as road type and speed limit. Unfortunately, such information is often incomplete; for instance, OpenStreetMap only has speed limits for 13% of all Danish road segments. This is problematic for analysis tasks that rely on such information for machine learning. To enable machine learning in such circumstances, one may consider the application of network embedding methods to extract structural information from the network. However, these methods have so far mostly been used in the context of social networks, which differ significantly from road networks in terms of, e.g., node degree and level of homophily (which are key to the performance of many network embedding methods). We analyze the use of network embedding methods, specifically node2vec, for learning road segment embeddings in road networks. Due to the often limited availability of information on other relevant road characteristics, the analysis focuses on leveraging the spatial network structure. Our results suggest that network embedding methods can indeed be used for deriving relevant network features (that may, e.g, be used for predicting speed limits), but that the qualities of the embeddings differ from embeddings for social networks., Comment: Best Paper at the 3rd IEEE International Workshop on Big Spatial Data (BSD 2018)

Machine learning techniques for road networks hold the potential to facilitate many important transportation applications. Graph Convolutional Networks (GCNs) are neural networks that are capable of leveraging the structure of a road network by utilizing information of, e.g., adjacent road segments. While state-of-the-art GCNs target node classification tasks in social, citation, and biological networks, machine learning tasks in road networks differ substantially from such tasks. In road networks, prediction tasks concern edges representing road segments, and many tasks involve regression. In addition, road networks differ substantially from the networks assumed in the GCN literature in terms of the attribute information available and the network characteristics. Many implicit assumptions of GCNs do therefore not apply. We introduce the notion of Relational Fusion Network (RFN), a novel type of GCN designed specifically for machine learning on road networks. In particular, we propose methods that outperform state-of-the-art GCNs on both a road segment regression task and a road segment classification task by 32-40% and 21-24%, respectively. In addition, we provide experimental evidence of the short-comings of state-of-the-art GCNs in the context of road networks: unlike our method, they cannot effectively leverage the road network structure for road segment classification and fail to outperform a regular multi-layer perceptron., Comment: Ten-page pre-print version of a four-page ACM SIGSPATIAL 2019 poster paper

Recent advances in statistical inference have significantly expanded the toolbox of probabilistic modeling. Historically, probabilistic modeling has been constrained to (i) very restricted model classes where exact or approximate probabilistic inference were feasible, and (ii) small or medium-sized data sets which fit within the main memory of the computer. However, developments in variational inference, a general form of approximate probabilistic inference originated in statistical physics, are allowing probabilistic modeling to overcome these restrictions: (i) Approximate probabilistic inference is now possible over a broad class of probabilistic models containing a large number of parameters, and (ii) scalable inference methods based on stochastic gradient descent and distributed computation engines allow to apply probabilistic modeling over massive data sets. One important practical consequence of these advances is the possibility to include deep neural networks within a probabilistic model to capture complex non-linear stochastic relationships between random variables. These advances in conjunction with the release of novel probabilistic modeling toolboxes have greatly expanded the scope of application of probabilistic models, and allow these models to take advantage of the recent strides made by the deep learning community. In this paper we review the main concepts, methods and tools needed to use deep neural networks within a probabilistic modeling framework.

Demand Response (DR) schemes are effective tools to maintain a dynamic balance in energy markets with higher integration of fluctuating renewable energy sources. DR schemes can be used to harness residential devices' flexibility and to utilize it to achieve social and financial objectives. However, existing DR schemes suffer from low user participation as they fail at taking into account the users' requirements. First, DR schemes are highly demanding for the users, as users need to provide direct information, e.g. via surveys, on their energy consumption preferences. Second, the user utility models based on these surveys are hard-coded and do not adapt over time. Third, the existing scheduling techniques require the users to input their energy requirements on a daily basis. As an alternative, this paper proposes a DR scheme for user-oriented direct load-control of residential appliances operations. Instead of relying on user surveys to evaluate the user utility, we propose an online data-driven approach for estimating user utility functions, purely based on available load consumption data, that adaptively models the users' preference over time. Our scheme is based on a day-ahead scheduling technique that transparently prescribes the users with optimal device operation schedules that take into account both financial benefits and user-perceived quality of service. To model day-ahead user energy demand and flexibility, we propose a probabilistic approach for generating flexibility models under uncertainty. Results on both real-world and simulated datasets show that our DR scheme can provide significant financial benefits while preserving the user-perceived quality of service., Comment: 10 pages plus 1 page references, 11 figures, conference: ACM e-Energy 2018