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Current robot platforms are being employed to collaborate with humans in a wide range of domestic and industrial tasks. These environments require autonomous systems that are able to classify and communicate anomalous situations such as fires, injured persons, car accidents; or generally, any potentially dangerous situation for humans. In this paper we introduce an anomaly detection dataset for the purpose of robot applications as well as the design and implementation of a deep learning architecture that classifies and describes dangerous situations using only a single image as input. We report a classification accuracy of 97 % and METEOR score of 16.2. We will make the dataset publicly available after this paper is accepted.
In this paper we introduce the Perception for Autonomous Systems (PAZ) software library. PAZ is a hierarchical perception library that allow users to manipulate multiple levels of abstraction in accordance to their requirements or skill level. More specifically, PAZ is divided into three hierarchical levels which we refer to as pipelines, processors, and backends. These abstractions allows users to compose functions in a hierarchical modular scheme that can be applied for preprocessing, data-augmentation, prediction and postprocessing of inputs and outputs of machine learning (ML) models. PAZ uses these abstractions to build reusable training and prediction pipelines for multiple robot perception tasks such as: 2D keypoint estimation, 2D object detection, 3D keypoint discovery, 6D pose estimation, emotion classification, face recognition, instance segmentation, and attention mechanisms.
In this paper we propose an implement a general convolutional neural network (CNN) building framework for designing real-time CNNs. We validate our models by creating a real-time vision system which accomplishes the tasks of face detection, gender classification and emotion classification simultaneously in one blended step using our proposed CNN architecture. After presenting the details of the training procedure setup we proceed to evaluate on standard benchmark sets. We report accuracies of 96% in the IMDB gender dataset and 66% in the FER-2013 emotion dataset. Along with this we also introduced the very recent real-time enabled guided back-propagation visualization technique. Guided back-propagation uncovers the dynamics of the weight changes and evaluates the learned features. We argue that the careful implementation of modern CNN architectures, the use of the current regularization methods and the visualization of previously hidden features are necessary in order to reduce the gap between slow performances and real-time architectures. Our system has been validated by its deployment on a Care-O-bot 3 robot used during RoboCup@Home competitions. All our code, demos and pre-trained architectures have been released under an open-source license in our public repository.
Humans exhibit flexible and robust behavior in achieving their goals. We make suitable substitutions for objects, actions, or tools to get the job done. When opportunities that would allow us to reach our goals with less effort arise, we often take advantage of them. Robots are not nearly as robust in handling such situations. Enabling a domestic service robot to find ways to get a job done by making substitutions is the goal of our work. In this paper, we highlight the challenges faced in our approach to combine Hierarchical Task Network planning, Description Logics, and the notions of affordances and conceptual similarity. We present open questions in modeling the necessary knowledge, creating planning problems, and enabling the system to handle cases where plan generation fails due to missing/unavailable objects.
Representing 3D surfaces as level sets of continuous functions over R3 is the common denominator of neural implicit representations, which recently enabled remarkable progress in geometric deep learning and computer vision tasks. In order to represent 3D motion within this framework, it is often assumed (either explicitly or implicitly) that the transformations which a surface may undergo are homeomorphic: this is not necessarily true, for instance, in the case of fluid dynamics. In order to represent more general classes of deformations, we propose to apply this theoretical framework as regularizers for the optimization of simple 4D implicit functions (such as signed distance fields). We show that our representation is capable of capturing both homeomorphic and topology-changing deformations, while also defining correspondences over the continuously-reconstructed surfaces.
The majority of biomedical knowledge is stored in structured databases or as unstructured text in scientific publications. This vast amount of information has led to numerous machine learning-based biological applications using either text through natural language processing (NLP) or structured data through knowledge graph embedding models (KGEMs). However, representations based on a single modality are inherently limited. To generate better representations of biological knowledge, we propose STonKGs, a Sophisticated Transformer trained on biomedical text and Knowledge Graphs. This multimodal Transformer uses combined input sequences of structured information from KGs and unstructured text data from biomedical literature to learn joint representations. First, we pre-trained STonKGs on a knowledge base assembled by the Integrated Network and Dynamical Reasoning Assembler (INDRA) consisting of millions of text-triple pairs extracted from biomedical literature by multiple NLP systems. Then, we benchmarked STonKGs against two baseline models trained on either one of the modalities (i.e., text or KG) across eight different classification tasks, each corresponding to a different biological application. Our results demonstrate that STonKGs outperforms both baselines, especially on the more challenging tasks with respect to the number of classes, improving upon the F1-score of the best baseline by up to 0.083. Additionally, our pre-trained model as well as the model architecture can be adapted to various other transfer learning applications. Finally, the source code and pre-trained STonKGs models are available at https://github.com/stonkgs/stonkgs and https://huggingface.co/stonkgs/stonkgs-150k.
Suppose we have n keys, n access probabilities for the keys, and n+1 access probabilities for the gaps between the keys. Let h_min(n) be the minimal height of a binary search tree for n keys. We consider the problem to construct an optimal binary search tree with near minimal height, i.e.\ with height h <= h_min(n) + Delta for some fixed Delta. It is shown, that for any fixed Delta optimal binary search trees with near minimal height can be constructed in time O(n^2). This is as fast as in the unrestricted case. So far, the best known algorithms for the construction of height-restricted optimal binary search trees have running time O(L n^2), whereby L is the maximal permitted height. Compared to these algorithms our algorithm is at least faster by a factor of log n, because L is lower bounded by log n.
The lattice Boltzmann method (LBM) is an efficient simulation technique for computational fluid mechanics and beyond. It is based on a simple stream-and-collide algorithm on Cartesian grids, which is easily compatible with modern machine learning architectures. While it is becoming increasingly clear that deep learning can provide a decisive stimulus for classical simulation techniques, recent studies have not addressed possible connections between machine learning and LBM. Here, we introduce Lettuce, a PyTorch-based LBM code with a threefold aim. Lettuce enables GPU accelerated calculations with minimal source code, facilitates rapid prototyping of LBM models, and enables integrating LBM simulations with PyTorch's deep learning and automatic differentiation facility. As a proof of concept for combining machine learning with the LBM, a neural collision model is developed, trained on a doubly periodic shear layer and then transferred to a different flow, a decaying turbulence. We also exemplify the added benefit of PyTorch's automatic differentiation framework in flow control and optimization. To this end, the spectrum of a forced isotropic turbulence is maintained without further constraining the velocity field.
This paper addresses the classification of Arabic text data in the field of Natural Language Processing (NLP), with a particular focus on Natural Language Inference (NLI) and Contradiction Detection (CD). Arabic is considered a resource-poor language, meaning that there are few data sets available, which leads to limited availability of NLP methods. To overcome this limitation, we create a dedicated data set from publicly available resources. Subsequently, transformer-based machine learning models are being trained and evaluated. We find that a language-specific model (AraBERT) performs competitively with state-of-the-art multilingual approaches, when we apply linguistically informed pre-training methods such as Named Entity Recognition (NER). To our knowledge, this is the first large-scale evaluation for this task in Arabic, as well as the first application of multi-task pre-training in this context.
Fundamental hydrogen storage properties of TiFe-alloy with partial substitution of Fe by Ti and Mn
(2020)
TiFe intermetallic compound has been extensively studied, owing to its low cost, good volumetric hydrogen density, and easy tailoring of hydrogenation thermodynamics by elemental substitution. All these positive aspects make this material promising for large-scale applications of solid-state hydrogen storage. On the other hand, activation and kinetic issues should be amended and the role of elemental substitution should be further understood. This work investigates the thermodynamic changes induced by the variation of Ti content along the homogeneity range of the TiFe phase (Ti:Fe ratio from 1:1 to 1:0.9) and of the substitution of Mn for Fe between 0 and 5 at.%. In all considered alloys, the major phase is TiFe-type together with minor amounts of TiFe2 or \b{eta}-Ti-type and Ti4Fe2O-type at the Ti-poor and rich side of the TiFe phase domain, respectively. Thermodynamic data agree with the available literature but offer here a comprehensive picture of hydrogenation properties over an extended Ti and Mn compositional range. Moreover, it is demonstrated that Ti-rich alloys display enhanced storage capacities, as long as a limited amount of \b{eta}-Ti is formed. Both Mn and Ti substitutions increase the cell parameter by possibly substituting Fe, lowering the plateau pressures and decreasing the hysteresis of the isotherms. A full picture of the dependence of hydrogen storage properties as a function of the composition will be discussed, together with some observed correlations.
We derive rates of convergence for limit theorems that reveal the intricate structure of the phase transitions in a mean-field version of the Blume-Emery-Griffith model. The theorems consist of scaling limits for the total spin. The model depends on the inverse temperature β and the interaction strength K. The rates of convergence results are obtained as (β,K) converges along appropriate sequences (βn,Kn) to points belonging to various subsets of the phase diagram which include a curve of second-order points and a tricritical point. We apply Stein's method for normal and non-normal approximation avoiding the use of transforms and supplying bounds, such as those of Berry-Esseen quality, on approximation error. We observe an additional phase transition phenomenon in the sense that depending on how fast Kn and βn are converging to points in various subsets of the phase diagram, different rates of convergences to one and the same limiting distribution occur.
The latest trends in inverse rendering techniques for reconstruction use neural networks to learn 3D representations as neural fields. NeRF-based techniques fit multi-layer perceptrons (MLPs) to a set of training images to estimate a radiance field which can then be rendered from any virtual camera by means of volume rendering algorithms. Major drawbacks of these representations are the lack of well-defined surfaces and non-interactive rendering times, as wide and deep MLPs must be queried millions of times per single frame. These limitations have recently been singularly overcome, but managing to accomplish this simultaneously opens up new use cases. We present KiloNeuS, a new neural object representation that can be rendered in path-traced scenes at interactive frame rates. KiloNeuS enables the simulation of realistic light interactions between neural and classic primitives in shared scenes, and it demonstrably performs in real-time with plenty of room for future optimizations and extensions.
Recent experimental evidence suggest that mebendazole, a popular antiparasitic drug, binds to heat shock protein 90 (Hsp90) and inhibit acute myeloid leukemia cell growth. In this study we use quantum mechanics (QM), molecular similarity and molecular dynamics (MD) calculations to predict possible binding poses of mebendazole to the adenosine triphosphate (ATP) binding site of Hsp90. Extensive conformational searches and minimization of the five tautomers of mebendazole using MP2/aug-cc-pVTZ theory level resulting in 152 minima being identified. Mebendazole-Hsp90 complex models were created using the QM optimized conformations and protein coordinates obtained from experimental crystal structures that were chosen through similarity calculations. Nine different poses were identified from a total of 600 ns of explicit solvent, all-atom MD simulations using two different force fields. All simulations support the hypothesis that mebendazole is able to bind to the ATP binding site of Hsp90.
Comparative Evaluation of Pretrained Transfer Learning Models on Automatic Short Answer Grading
(2020)
Automatic Short Answer Grading (ASAG) is the process of grading the student answers by computational approaches given a question and the desired answer. Previous works implemented the methods of concept mapping, facet mapping, and some used the conventional word embeddings for extracting semantic features. They extracted multiple features manually to train on the corresponding datasets. We use pretrained embeddings of the transfer learning models, ELMo, BERT, GPT, and GPT-2 to assess their efficiency on this task. We train with a single feature, cosine similarity, extracted from the embeddings of these models. We compare the RMSE scores and correlation measurements of the four models with previous works on Mohler dataset. Our work demonstrates that ELMo outperformed the other three models. We also, briefly describe the four transfer learning models and conclude with the possible causes of poor results of transfer learning models.
The MAP-Elites algorithm produces a set of high-performing solutions that vary according to features defined by the user. This technique has the potential to be a powerful tool for design space exploration, but is limited by the need for numerous evaluations. The Surrogate-Assisted Illumination algorithm (SAIL), introduced here, integrates approximative models and intelligent sampling of the objective function to minimize the number of evaluations required by MAP-Elites.
The ability of SAIL to efficiently produce both accurate models and diverse high performing solutions is illustrated on a 2D airfoil design problem. The search space is divided into bins, each holding a design with a different combination of features. In each bin SAIL produces a better performing solution than MAP-Elites, and requires several orders of magnitude fewer evaluations. The CMA-ES algorithm was used to produce an optimal design in each bin: with the same number of evaluations required by CMA-ES to find a near-optimal solution in a single bin, SAIL finds solutions of similar quality in every bin.
The way solutions are represented, or encoded, is usually the result of domain knowledge and experience. In this work, we combine MAP-Elites with Variational Autoencoders to learn a Data-Driven Encoding (DDE) that captures the essence of the highest-performing solutions while still able to encode a wide array of solutions. Our approach learns this data-driven encoding during optimization by balancing between exploiting the DDE to generalize the knowledge contained in the current archive of elites and exploring new representations that are not yet captured by the DDE. Learning representation during optimization allows the algorithm to solve high-dimensional problems, and provides a low-dimensional representation which can be then be re-used. We evaluate the DDE approach by evolving solutions for inverse kinematics of a planar arm (200 joint angles) and for gaits of a 6-legged robot in action space (a sequence of 60 positions for each of the 12 joints). We show that the DDE approach not only accelerates and improves optimization, but produces a powerful encoding that captures a bias for high performance while expressing a variety of solutions.
The Covid-19 pandemic has challenged educators across the world to move their teaching and mentoring from in-person to remote. During nonpandemic semesters at their institutes (e.g. universities), educators can directly provide students the software environment needed to support their learning - either in specialized computer laboratories (e.g. computational chemistry labs) or shared computer spaces. These labs are often supported by staff that maintains the operating systems (OS) and software. But how does one provide a specialized software environment for remote teaching? One solution is to provide students a customized operating system (e.g., Linux) that includes open-source software for supporting your teaching goals. However, such a solution should not require students to install the OS alongside their existing one (i.e. dual/multi-booting) or be used as a complete replacement. Such approaches are risky because of a) the students' possible lack of software expertise, b) the possible disruption of an existing software workflow that is needed in other classes or by other family members, and c) the importance of maintaining a working computer when isolated (e.g. societal restrictions). To illustrate possible solutions, we discuss our approach that used a customized Linux OS and a Docker container in a course that teaches computational chemistry and Python3.
Background 3-hydroxy-3-methylglutaryl-coenzyme A lyase deficiency (HMGCLD) is an autosomal recessive disorder of ketogenesis and leucine degradation due to mutations in HMGCL .
Method We performed a systematic literature search to identify all published cases. 211 patients of whom relevant clinical data were available were included in this analysis. Clinical course, biochemical findings and mutation data are highlighted and discussed. An overview on all published HMGCL variants is provided.
Results More than 95% of patients presented with acute metabolic decompensation. Most patients manifested within the first year of life, 42.4% already neonatally. Very few individuals remained asymptomatic. The neurologic long-term outcome was favorable with 62.6% of patients showing normal development.
Conclusion This comprehensive data analysis provides a systematic overview on all published cases with HMGCLD including a list of all known HMGCL mutations.
2-methylacetoacetyl-coenzyme A thiolase (beta-ketothiolase) deficiency: one disease - two pathways
(2019)
Background: 2-methylacetoacetyl-coenzyme A thiolase deficiency (MATD; deficiency of mitochondrial acetoacetyl-coenzyme A thiolase T2/ “beta-ketothiolase”) is an autosomal recessive disorder of ketone body utilization and isoleucine degradation due to mutations in ACAT1.
Methods: We performed a systematic literature search for all available clinical descriptions of patients with MATD. 244 patients were identified and included in this analysis. Clinical course and biochemical data are presented and discussed.
Results: For 89.6 % of patients at least one acute metabolic decompensation was reported. Age at first symptoms ranged from 2 days to 8 years (median 12 months). More than 82% of patients presented in the first two years of life, while manifestation in the neonatal period was the exception (3.4%). 77.0% (157 of 204 patients) of patients showed normal psychomotor development without neurologic abnormalities.
Conclusion: This comprehensive data analysis provides a systematic overview on all cases with MATD identified in the literature. It demonstrates that MATD is a rather benign disorder with often favourable outcome, when compared with many other organic acidurias.