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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.
Background: Virtual reality combined with spherical treadmills is used across species for studying neural circuits underlying navigation.
New Method: We developed an optical flow-based method for tracking treadmil ball motion in real-time using a single high-resolution camera.
Results: Tracking accuracy and timing were determined using calibration data. Ball tracking was performed at 500 Hz and integrated with an open source game engine for virtual reality projection. The projection was updated at 120 Hz with a latency with respect to ball motion of 30 ± 8 ms.
Comparison: with Existing Method(s) Optical flow based tracking of treadmill motion is typically achieved using optical mice. The camera-based optical flow tracking system developed here is based on off-the-shelf components and offers control over the image acquisition and processing parameters. This results in flexibility with respect to tracking conditions – such as ball surface texture, lighting conditions, or ball size – as well as camera alignment and calibration.
Conclusions: A fast system for rotational ball motion tracking suitable for virtual reality animal behavior across different scales was developed and characterized.
Application of underwater robots are on the rise, most of them are dependent on sonar for underwater vision, but the lack of strong perception capabilities limits them in this task. An important issue in sonar perception is matching image patches, which can enable other techniques like localization, change detection, and mapping. There is a rich literature for this problem in color images, but for acoustic images, it is lacking, due to the physics that produce these images. In this paper we improve on our previous results for this problem (Valdenegro-Toro et al, 2017), instead of modeling features manually, a Convolutional Neural Network (CNN) learns a similarity function and predicts if two input sonar images are similar or not. With the objective of improving the sonar image matching problem further, three state of the art CNN architectures are evaluated on the Marine Debris dataset, namely DenseNet, and VGG, with a siamese or two-channel architecture, and contrastive loss. To ensure a fair evaluation of each network, thorough hyper-parameter optimization is executed. We find that the best performing models are DenseNet Two-Channel network with 0.955 AUC, VGG-Siamese with contrastive loss at 0.949 AUC and DenseNet Siamese with 0.921 AUC. By ensembling the top performing DenseNet two-channel and DenseNet-Siamese models overall highest prediction accuracy obtained is 0.978 AUC, showing a large improvement over the 0.91 AUC in the state of the art.
Loading of shipping containers for dairy products often includes a press-fit task, which involves manually stacking milk cartons in a container without using pallets or packaging. Automating this task with a mobile manipulator can reduce worker strain, and also enhance the efficiency and safety of the container loading process. This paper proposes an approach called Adaptive Compliant Control with Integrated Failure Recovery (ACCIFR), which enables a mobile manipulator to reliably perform the press-fit task. We base the approach on a demonstration learning-based compliant control framework, such that we integrate a monitoring and failure recovery mechanism for successful task execution. Concretely, we monitor the execution through distance and force feedback, detect collisions while the robot is performing the press-fit task, and use wrench measurements to classify the direction of collision; this information informs the subsequent recovery process. We evaluate the method on a miniature container setup, considering variations in the (i) starting position of the end effector, (ii) goal configuration, and (iii) object grasping position. The results demonstrate that the proposed approach outperforms the baseline demonstration-based learning framework regarding adaptability to environmental variations and the ability to recover from collision failures, making it a promising solution for practical press-fit applications.
Saliency methods are frequently used to explain Deep Neural Network-based models. Adebayo et al.'s work on evaluating saliency methods for classification models illustrate certain explanation methods fail the model and data randomization tests. However, on extending the tests for various state of the art object detectors we illustrate that the ability to explain a model is more dependent on the model itself than the explanation method. We perform sanity checks for object detection and define new qualitative criteria to evaluate the saliency explanations, both for object classification and bounding box decisions, using Guided Backpropagation, Integrated Gradients, and their Smoothgrad versions, together with Faster R-CNN, SSD, and EfficientDet-D0, trained on COCO. In addition, the sensitivity of the explanation method to model parameters and data labels varies class-wise motivating to perform the sanity checks for each class. We find that EfficientDet-D0 is the most interpretable method independent of the saliency method, which passes the sanity checks with little problems.
Deep learning models are extensively used in various safety critical applications. Hence these models along with being accurate need to be highly reliable. One way of achieving this is by quantifying uncertainty. Bayesian methods for UQ have been extensively studied for Deep Learning models applied on images but have been less explored for 3D modalities such as point clouds often used for Robots and Autonomous Systems. In this work, we evaluate three uncertainty quantification methods namely Deep Ensembles, MC-Dropout and MC-DropConnect on the DarkNet21Seg 3D semantic segmentation model and comprehensively analyze the impact of various parameters such as number of models in ensembles or forward passes, and drop probability values, on task performance and uncertainty estimate quality. We find that Deep Ensembles outperforms other methods in both performance and uncertainty metrics. Deep ensembles outperform other methods by a margin of 2.4% in terms of mIOU, 1.3% in terms of accuracy, while providing reliable uncertainty for decision making.
The development of robot control programs is a complex task. Many robots are different in their electrical and mechanical structure which is also reflected in the software. Specific robot software environments support the program development, but are mainly text-based and usually applied by experts in the field with profound knowledge of the target robot. This paper presents a graphical programming environment which aims to ease the development of robot control programs. In contrast to existing graphical robot programming environments, our approach focuses on the composition of parallel action sequences. The developed environment allows to schedule independent robot actions on parallel execution lines and provides mechanism to avoid side-effects of parallel actions. The developed environment is platform-independent and based on the model-driven paradigm. The feasibility of our approach is shown by the application of the sequencer to a simulated service robot and a robot for educational purpose.
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 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.
Object detectors have improved considerably in the last years by using advanced CNN architectures. However, many detector hyper-parameters are generally manually tuned, or they are used with values set by the detector authors. Automatic Hyper-parameter optimization has not been explored in improving CNN-based object detectors hyper-parameters. In this work, we propose the use of Black-box optimization methods to tune the prior/default box scales in Faster R-CNN and SSD, using Bayesian Optimization, SMAC, and CMA-ES. We show that by tuning the input image size and prior box anchor scale on Faster R-CNN mAP increases by 2% on PASCAL VOC 2007, and by 3% with SSD. On the COCO dataset with SSD there are mAP improvement in the medium and large objects, but mAP decreases by 1% in small objects. We also perform a regression analysis to find the significant hyper-parameters to tune.
Grasp verification is advantageous for autonomous manipulation robots as they provide the feedback required for higher level planning components about successful task completion. However, a major obstacle in doing grasp verification is sensor selection. In this paper, we propose a vision based grasp verification system using machine vision cameras, with the verification problem formulated as an image classification task. Machine vision cameras consist of a camera and a processing unit capable of on-board deep learning inference. The inference in these low-power hardware are done near the data source, reducing the robot's dependence on a centralized server, leading to reduced latency, and improved reliability. Machine vision cameras provide the deep learning inference capabilities using different neural accelerators. Although, it is not clear from the documentation of these cameras what is the effect of these neural accelerators on performance metrics such as latency and throughput. To systematically benchmark these machine vision cameras, we propose a parameterized model generator that generates end to end models of Convolutional Neural Networks(CNN). Using these generated models we benchmark latency and throughput of two machine vision cameras, JeVois A33 and Sipeed Maix Bit. Our experiments demonstrate that the selected machine vision camera and the deep learning models can robustly verify grasp with 97% per frame accuracy.
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.
In robot-assisted therapy for individuals with Autism Spectrum Disorder, the workload of therapists during a therapeutic session is increased if they have to control the robot manually. To allow therapists to focus on the interaction with the person instead, the robot should be more autonomous, namely it should be able to interpret the person's state and continuously adapt its actions according to their behaviour. In this paper, we develop a personalised robot behaviour model that can be used in the robot decision-making process during an activity; this behaviour model is trained with the help of a user model that has been learned from real interaction data. We use Q-learning for this task, such that the results demonstrate that the policy requires about 10,000 iterations to converge. We thus investigate policy transfer for improving the convergence speed; we show that this is a feasible solution, but an inappropriate initial policy can lead to a suboptimal final return.
Robots applied in therapeutic scenarios, for instance in the therapy of individuals with Autism Spectrum Disorder, are sometimes used for imitation learning activities in which a person needs to repeat motions by the robot. To simplify the task of incorporating new types of motions that a robot can perform, it is desirable that the robot has the ability to learn motions by observing demonstrations from a human, such as a therapist. In this paper, we investigate an approach for acquiring motions from skeleton observations of a human, which are collected by a robot-centric RGB-D camera. Given a sequence of observations of various joints, the joint positions are mapped to match the configuration of a robot before being executed by a PID position controller. We evaluate the method, in particular the reproduction error, by performing a study with QTrobot in which the robot acquired different upper-body dance moves from multiple participants. The results indicate the method's overall feasibility, but also indicate that the reproduction quality is affected by noise in the skeleton observations.
This paper presents the b-it-bots RoboCup@Work team and its current hardware and functional architecture for the KUKA youBot robot. We describe the underlying software framework and the developed capabilities required for operating in industrial environments including features such as reliable and precise navigation, flexible manipulation, robust object recognition and task planning. New developments include an approach to grasp vertical objects, placement of objects by considering the empty space on a workstation, and the process of porting our code to ROS2.