403 research outputs found

    Collision avoidance on unmanned aerial vehicles using neural network pipelines and flow clustering techniques

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    UIDB/04111/2020 PCIF/SSI/0102/2017 IF/00325/2015Unmanned Autonomous Vehicles (UAV), while not a recent invention, have recently acquired a prominent position in many industries, and they are increasingly used not only by avid customers, but also in high-demand technical use-cases, and will have a significant societal effect in the coming years. However, the use of UAVs is fraught with significant safety threats, such as collisions with dynamic obstacles (other UAVs, birds, or randomly thrown objects). This research focuses on a safety problem that is often overlooked due to a lack of technology and solutions to address it: collisions with non-stationary objects. A novel approach is described that employs deep learning techniques to solve the computationally intensive problem of real-time collision avoidance with dynamic objects using off-the-shelf commercial vision sensors. The suggested approach’s viability was corroborated by multiple experiments, firstly in simulation, and afterward in a concrete real-world case, that consists of dodging a thrown ball. A novel video dataset was created and made available for this purpose, and transfer learning was also tested, with positive results.publishersversionpublishe

    Learning the Structure of Continuous Markov Decision Processes

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    There is growing interest in artificial, intelligent agents which can operate autonomously for an extended period of time in complex environments and fulfill a variety of different tasks. Such agents will face different problems during their lifetime which may not be foreseeable at the time of their deployment. Thus, the capacity for lifelong learning of new behaviors is an essential prerequisite for this kind of agents as it enables them to deal with unforeseen situations. However, learning every complex behavior anew from scratch would be cumbersome for the agent. It is more plausible to consider behavior to be modular and let the agent acquire a set of reusable building blocks for behavior, the so-called skills. These skills might, once acquired, facilitate fast learning and adaptation of behavior to new situations. This work focuses on computational approaches for skill acquisition, namely which kind of skills shall be acquired and how to acquire them. The former is commonly denoted as skill discovery and the latter as skill learning . The main contribution of this thesis is a novel incremental skill acquisition approach which is suited for lifelong learning. In this approach, the agent learns incrementally a graph-based representation of a domain and exploits certain properties of this graph such as its bottlenecks for skill discovery. This thesis proposes a novel approach for learning a graph-based representation of continuous domains based on formalizing the problem as a probabilistic generative model. Furthermore, a new incremental agglomerative clustering approach for identifying bottlenecks of such graphs is presented. Thereupon, the thesis proposes a novel intrinsic motivation system which enables an agent to intelligently allocate time between skill discovery and skill learning in developmental settings, where the agent is not constrained by external tasks. The results of this thesis show that the resulting skill acquisition approach is suited for continuous domains and can deal with domain stochasticity and different explorative behavior of the agent. The acquired skills are reusable and versatile and can be used in multi-task and lifelong learning settings in high-dimensional problems

    Computational methods for large-scale single-cell RNA-seq and multimodal data

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    Emerging single cell genomics technologies such as single cell RNA-seq (scRNA-seq) and single cell ATAC-seq provide new opportunities for discovery of previously unknown cell types, facilitating the study of biological processes such as tumor progression, and delineating molecular mechanism differences between species. Due to the high dimensionality of the data produced by the technologies, computation and mathematics have been the cornerstone in decoding meaningful information from the data. Computational models have been challenged by the exponential growth of the data thanks to the continuing decrease in sequencing costs and growth of large-scale genomic projects such as the Human Cell Atlas. In addition, recent single-cell technologies have enabled us to measure multiple modalities such as transcriptome, protome, and epigenome in the same cell. This requires us to establish new computational methods which can cope with multiple layers of the data. To address these challenges, the main goal of this thesis was to develop computational methods and mathematical models for analyzing large-scale scRNA-seq and multimodal omics data. In particular, I have focused on fundamental single-cell analysis such as clustering and visualization. The most common task in scRNA-seq data analysis is the identification of cell types. Numerous methods have been proposed for this problem with a current focus on methods for the analysis of large scale scRNA-seq data. I developed Specter, a computational method that utilizes recent algorithmic advances in fast spectral clustering and ensemble learning. Specter achieves a substantial improvement in accuracy over existing methods and identifies rare cell types with high sensitivity. Specter allows us to process a dataset comprising 2 million cells in just 26 minutes. Moreover, the analysis of CITE-seq data, that simultaneously provides gene expression and protein levels, showed that Specter is able to incorporate multimodal omics measurements to resolve subtle transcriptomic differences between subpopulations of cells. We have effectively handled big data for clustering analysis using Specter. The question is how to cope with the big data for other downstream analyses such as trajectory inference and data integration. The most simple scheme is to shrink the data by selecting a subset of cells (the sketch) that best represents the full data set. Therefore I developed an algorithm called Sphetcher that makes use of the thresholding technique to efficiently pick representative cells that evenly cover the transcriptomic space occupied by the original data set. I showed that the sketch computed by Sphetcher constitutes a more accurate presentation of the original transcriptomic landscape than existing methods, which leads to a more balanced composition of cell types and a large fraction of rare cell types in the sketch. Sphetcher bridges the gap between the scalability of computational methods and the volume of the data. Moreover, I demonstrated that Sphetcher can incorporate prior information (e.g. cell labels) to inform the inference of the trajectory of human skeletal muscle myoblast differentiation. The biological processes such as development, differentiation, and cell cycle can be monitored by performing single cell sequencing at different time points, each corresponding to a snapshot of the process. A class of computational methods called trajectory inference aims to reconstruct the developmental trajectories from these snapshots. Trajectory inference (TI) methods such as Monocle, can computationally infer a pseudotime variable which serves as a proxy for developmental time. In order to compare two trajectories inferred by TI methods, we need to align the pseudotime between two trajectories. Current methods for aligning trajectories are based on the concept of dynamic time warping, which is limited to simple linear trajectories. Since complex trajectories are common in developmental processes, I adopted arboreal matchings to compare and align complex trajectories with multiple branch points diverting cells into alternative fates. Arboreal matchings were originally proposed in the context of phylogenetic trees and I theoretically linked them to dynamic time warping. A suite of exact and heuristic algorithms for aligning complex trajectories was implemented in a software Trajan. When aligning single-cell trajectories describing human muscle differentiation and myogenic reprogramming, Trajan automatically identifies the core paths from which we are able to reproduce recently reported barriers to reprogramming. In a perturbation experiment, I showed that Trajan correctly maps identical cells in a global view of trajectories, as opposed to a pairwise application of dynamic time warping. Visualization using dimensionality reduction techniques such as t-SNE and UMAP is a fundamental step in the analysis of high-dimensional data. Visualization has played a pivotal role in discovering the dynamic trends in single cell genomics data. I developed j-SNE and j-UMAP as their generalizations to the joint visualization of multimodal omics data, e.g., CITE-seq data. The approach automatically learns the relative importance of each modality in order to obtain a concise representation of the data. When comparing with the conventional approaches, I demonstrated that j-SNE and j-UMAP produce unified embeddings that better agree with known cell types and that harmonize RNA and protein velocity landscapes

    iMODS: internal coordinates normal mode analysis server

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    Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends its applicability while implicitly maintaining stereochemistry. Vibrational analysis, motion animationś and morphing trajectories can be easily carried out at different resolution scales almost interactively. The server is versatile; non-specialists can rapidly characterize potential conformational changes, whereas advanced users can customize the model resolution with multiple coarse-grained atomic representations and elastic network potentials. iMODS supports advanced visualization capabilities for illustrating collective motions, including an improved affine-model-based arrow representation of domain dynamics. The generated all-heavy-atoms conformations can be used to introduce flexibility for more advanced modeling or sampling strategies.Human Frontier Science Program—RGP0039/2008, Ministerio de Economía y Competitividad—BFU2013-44306P and Comunidad de Madrid—CAM-S2010/BMD

    Visualization of large molecular trajectories

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    The analysis of protein-ligand interactions is a time-intensive task. Researchers have to analyze multiple physico-chemical properties of the protein at once and combine them to derive conclusions about the protein-ligand interplay. Typically, several charts are inspected, and 3D animations can be played side-by-side to obtain a deeper understanding of the data. With the advances in simulation techniques, larger and larger datasets are available, with up to hundreds of thousands of steps. Unfortunately, such large trajectories are very difficult to investigate with traditional approaches. Therefore, the need for special tools that facilitate inspection of these large trajectories becomes substantial. In this paper, we present a novel system for visual exploration of very large trajectories in an interactive and user-friendly way. Several visualization motifs are automatically derived from the data to give the user the information about interactions between protein and ligand. Our system offers specialized widgets to ease and accelerate data inspection and navigation to interesting parts of the simulation. The system is suitable also for simulations where multiple ligands are involved. We have tested the usefulness of our tool on a set of datasets obtained from protein engineers, and we describe the expert feedback.Peer ReviewedPostprint (author's final draft
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