Object-Centric Scene Representations Using Active Inference.

Representing a scene and its constituent objects from raw sensory data is a core ability for enabling robots to interact with their environment. In this letter, we propose a novel approach for scene understanding, leveraging an object-centric generative model that enables an agent to infer object category and pose in an allocentric reference frame using active inference, a neuro-inspired framework for action and perception. For evaluating the behavior of an active vision agent, we also propose a new benchmark where, given a target viewpoint of a particular object, the agent needs to find the best matching viewpoint given a workspace with randomly positioned objects in 3D. We demonstrate that our active inference agent is able to balance epistemic foraging and goal-driven behavior, and quantitatively outperforms both supervised and reinforcement learning baselines by more than a factor of two in terms of success rate.

Spatial and Temporal Hierarchy for Autonomous Navigation Using Active Inference in Minigrid Environment.

Robust evidence suggests that humans explore their environment using a combination of topological landmarks and coarse-grained path integration. This approach relies on identifiable environmental features (topological landmarks) in tandem with estimations of distance and direction (coarse-grained path integration) to construct cognitive maps of the surroundings. This cognitive map is believed to exhibit a hierarchical structure, allowing efficient planning when solving complex navigation tasks. Inspired by human behaviour, this paper presents a scalable hierarchical active inference model for autonomous navigation, exploration, and goal-oriented behaviour. The model uses visual observation and motion perception to combine curiosity-driven exploration with goal-oriented behaviour. Motion is planned using different levels of reasoning, i.e., from context to place to motion. This allows for efficient navigation in new spaces and rapid progress toward a target. By incorporating these human navigational strategies and their hierarchical representation of the environment, this model proposes a new solution for autonomous navigation and exploration. The approach is validated through simulations in a mini-grid environment.

Dermatologist versus artificial intelligence confidence in dermoscopy diagnosis: Complementary information that may affect decision-making.

In dermatology, deep learning may be applied for skin lesion classification. However, for a given input image, a neural network only outputs a label, obtained using the class probabilities, which do not model uncertainty. Our group developed a novel method to quantify uncertainty in stochastic neural networks. In this study, we aimed to train such network for skin lesion classification and evaluate its diagnostic performance and uncertainty, and compare the results to the assessments by a group of dermatologists. By passing duplicates of an image through such a stochastic neural network, we obtained distributions per class, rather than a single probability value. We interpreted the overlap between these distributions as the output uncertainty, where a high overlap indicated a high uncertainty, and vice versa. We had 29 dermatologists diagnose a series of skin lesions and rate their confidence. We compared these results to those of the network. The network achieved a sensitivity and specificity of 50% and 88%, comparable to the average dermatologist (respectively 68% and 73%). Higher confidence/less uncertainty was associated with better diagnostic performance both in the neural network and in dermatologists. We found no correlation between the uncertainty of the neural network and the confidence of dermatologists (R = -0.06, p = 0.77). Dermatologists should not blindly trust the output of a neural network, especially when its uncertainty is high. The addition of an uncertainty score may stimulate the human-computer interaction.

Symmetry and complexity in object-centric deep active inference models.

Humans perceive and interact with hundreds of objects every day. In doing so, they need to employ mental models of these objects and often exploit symmetries in the object's shape and appearance in order to learn generalizable and transferable skills. Active inference is a first principles approach to understanding and modelling sentient agents. It states that agents entertain a generative model of their environment, and learn and act by minimizing an upper bound on their surprisal, i.e. their free energy. The free energy decomposes into an accuracy and complexity term, meaning that agents favour the least complex model that can accurately explain their sensory observations. In this paper, we investigate how inherent symmetries of particular objects also emerge as symmetries in the latent state space of the generative model learnt under deep active inference. In particular, we focus on object-centric representations, which are trained from pixels to predict novel object views as the agent moves its viewpoint. First, we investigate the relation between model complexity and symmetry exploitation in the state space. Second, we do a principal component analysis to demonstrate how the model encodes the principal axis of symmetry of the object in the latent space. Finally, we also demonstrate how more symmetrical representations can be exploited for better generalization in the context of manipulation.

Computational Optimization of Image-Based Reinforcement Learning for Robotics.

The robotics field has been deeply influenced by the advent of deep learning. In recent years, this trend has been characterized by the adoption of large, pretrained models for robotic use cases, which are not compatible with the computational hardware available in robotic systems. Moreover, such large, computationally intensive models impede the low-latency execution which is required for many closed-loop control systems. In this work, we propose different strategies for improving the computational efficiency of the deep-learning models adopted in reinforcement-learning (RL) scenarios. As a use-case project, we consider an image-based RL method on the synergy between push-and-grasp actions. As a first optimization step, we reduce the model architecture in complexity, by decreasing the number of layers and by altering the architecture structure. Second, we consider downscaling the input resolution to reduce the computational load. Finally, we perform weight quantization, where we compare post-training quantization and quantized-aware training. We benchmark the improvements introduced in each optimization by running a standard testing routine. We show that the optimization strategies introduced can improve the computational efficiency by around 300 times, while also slightly improving the functional performance of the system. In addition, we demonstrate closed-loop control behaviour on a real-world robot, while processing everything on a Jetson Xavier NX edge device.

Embodied Object Representation Learning and Recognition.

Scene understanding and decomposition is a crucial challenge for intelligent systems, whether it is for object manipulation, navigation, or any other task. Although current machine and deep learning approaches for object detection and classification obtain high accuracy, they typically do not leverage interaction with the world and are limited to a set of objects seen during training. Humans on the other hand learn to recognize and classify different objects by actively engaging with them on first encounter. Moreover, recent theories in neuroscience suggest that cortical columns in the neocortex play an important role in this process, by building predictive models about objects in their reference frame. In this article, we present an enactive embodied agent that implements such a generative model for object interaction. For each object category, our system instantiates a deep neural network, called Cortical Column Network (CCN), that represents the object in its own reference frame by learning a generative model that predicts the expected transform in pixel space, given an action. The model parameters are optimized through the active inference paradigm, i.e., the minimization of variational free energy. When provided with a visual observation, an ensemble of CCNs each vote on their belief of observing that specific object category, yielding a potential object classification. In case the likelihood on the selected category is too low, the object is detected as an unknown category, and the agent has the ability to instantiate a novel CCN for this category. We validate our system in an simulated environment, where it needs to learn to discern multiple objects from the YCB dataset. We show that classification accuracy improves as an embodied agent can gather more evidence, and that it is able to learn about novel, previously unseen objects. Finally, we show that an agent driven through active inference can choose their actions to reach a preferred observation.

Model Reduction Through Progressive Latent Space Pruning in Deep Active Inference.

Although still not fully understood, sleep is known to play an important role in learning and in pruning synaptic connections. From the active inference perspective, this can be cast as learning parameters of a generative model and Bayesian model reduction, respectively. In this article, we show how to reduce dimensionality of the latent space of such a generative model, and hence model complexity, in deep active inference during training through a similar process. While deep active inference uses deep neural networks for state space construction, an issue remains in that the dimensionality of the latent space must be specified beforehand. We investigate two methods that are able to prune the latent space of deep active inference models. The first approach functions similar to sleep and performs model reduction post hoc. The second approach is a novel method which is more similar to reflection, operates during training and displays "aha" moments when the model is able to reduce latent space dimensionality. We show for two well-known simulated environments that model performance is retained in the first approach and only diminishes slightly in the second approach. We also show that reconstructions from a real world example are indistinguishable before and after reduction. We conclude that the most important difference constitutes a trade-off between training time and model performance in terms of accuracy and the ability to generalize, via minimization of model complexity.

The Free Energy Principle for Perception and Action: A Deep Learning Perspective.

The free energy principle, and its corollary active inference, constitute a bio-inspired theory that assumes biological agents act to remain in a restricted set of preferred states of the world, i.e., they minimize their free energy. Under this principle, biological agents learn a generative model of the world and plan actions in the future that will maintain the agent in an homeostatic state that satisfies its preferences. This framework lends itself to being realized in silico, as it comprehends important aspects that make it computationally affordable, such as variational inference and amortized planning. In this work, we investigate the tool of deep learning to design and realize artificial agents based on active inference, presenting a deep-learning oriented presentation of the free energy principle, surveying works that are relevant in both machine learning and active inference areas, and discussing the design choices that are involved in the implementation process. This manuscript probes newer perspectives for the active inference framework, grounding its theoretical aspects into more pragmatic affairs, offering a practical guide to active inference newcomers and a starting point for deep learning practitioners that would like to investigate implementations of the free energy principle.

Data-Efficient Sensor Upgrade Path Using Knowledge Distillation.

Deep neural networks have achieved state-of-the-art performance in image classification. Due to this success, deep learning is now also being applied to other data modalities such as multispectral images, lidar and radar data. However, successfully training a deep neural network requires a large reddataset. Therefore, transitioning to a new sensor modality (e.g., from regular camera images to multispectral camera images) might result in a drop in performance, due to the limited availability of data in the new modality. This might hinder the adoption rate and time to market for new sensor technologies. In this paper, we present an approach to leverage the knowledge of a teacher network, that was trained using the original data modality, to improve the performance of a student network on a new data modality: a technique known in literature as knowledge distillation. By applying knowledge distillation to the problem of sensor transition, we can greatly speed up this process. We validate this approach using a multimodal version of the MNIST dataset. Especially when little data is available in the new modality (i.e., 10 images), training with additional teacher supervision results in increased performance, with the student network scoring a test set accuracy of 0.77, compared to an accuracy of 0.37 for the baseline. We also explore two extensions to the default method of knowledge distillation, which we evaluate on a multimodal version of the CIFAR-10 dataset: an annealing scheme for the hyperparameter α and selective knowledge distillation. Of these two, the first yields the best results. Choosing the optimal annealing scheme results in an increase in test set accuracy of 6%. Finally, we apply our method to the real-world use case of skin lesion classification.

Robot navigation as hierarchical active inference.

Localization and mapping has been a long standing area of research, both in neuroscience, to understand how mammals navigate their environment, as well as in robotics, to enable autonomous mobile robots. In this paper, we treat navigation as inferring actions that minimize (expected) variational free energy under a hierarchical generative model. We find that familiar concepts like perception, path integration, localization and mapping naturally emerge from this active inference formulation. Moreover, we show that this model is consistent with models of hippocampal functions, and can be implemented in silico on a real-world robot. Our experiments illustrate that a robot equipped with our hierarchical model is able to generate topologically consistent maps, and correct navigation behaviour is inferred when a goal location is provided to the system.

Active Vision for Robot Manipulators Using the Free Energy Principle.

Occlusions, restricted field of view and limited resolution all constrain a robot's ability to sense its environment from a single observation. In these cases, the robot first needs to actively query multiple observations and accumulate information before it can complete a task. In this paper, we cast this problem of active vision as active inference, which states that an intelligent agent maintains a generative model of its environment and acts in order to minimize its surprise, or expected free energy according to this model. We apply this to an object-reaching task for a 7-DOF robotic manipulator with an in-hand camera to scan the workspace. A novel generative model using deep neural networks is proposed that is able to fuse multiple views into an abstract representation and is trained from data by minimizing variational free energy. We validate our approach experimentally for a reaching task in simulation in which a robotic agent starts without any knowledge about its workspace. Each step, the next view pose is chosen by evaluating the expected free energy. We find that by minimizing the expected free energy, exploratory behavior emerges when the target object to reach is not in view, and the end effector is moved to the correct reach position once the target is located. Similar to an owl scavenging for prey, the robot naturally prefers higher ground for exploring, approaching its target once located.

Learning Generative State Space Models for Active Inference.

In this paper we investigate the active inference framework as a means to enable autonomous behavior in artificial agents. Active inference is a theoretical framework underpinning the way organisms act and observe in the real world. In active inference, agents act in order to minimize their so called free energy, or prediction error. Besides being biologically plausible, active inference has been shown to solve hard exploration problems in various simulated environments. However, these simulations typically require handcrafting a generative model for the agent. Therefore we propose to use recent advances in deep artificial neural networks to learn generative state space models from scratch, using only observation-action sequences. This way we are able to scale active inference to new and challenging problem domains, whilst still building on the theoretical backing of the free energy principle. We validate our approach on the mountain car problem to illustrate that our learnt models can indeed trade-off instrumental value and ambiguity. Furthermore, we show that generative models can also be learnt using high-dimensional pixel observations, both in the OpenAI Gym car racing environment and a real-world robotic navigation task. Finally we show that active inference based policies are an order of magnitude more sample efficient than Deep Q Networks on RL tasks.

BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements.

MOTIVATION: The accurate discovery and annotation of regulatory elements remains a challenging problem. The growing number of sequenced genomes creates new opportunities for comparative approaches to motif discovery. Putative binding sites are then considered to be functional if they are conserved in orthologous promoter sequences of multiple related species. Existing methods for comparative motif discovery usually rely on pregenerated multiple sequence alignments, which are difficult to obtain for more diverged species such as plants. As a consequence, misaligned regulatory elements often remain undetected. RESULTS: We present a novel algorithm that supports both alignment-free and alignment-based motif discovery in the promoter sequences of related species. Putative motifs are exhaustively enumerated as words over the IUPAC alphabet and screened for conservation using the branch length score. Additionally, a confidence score is established in a genome-wide fashion. In order to take advantage of a cloud computing infrastructure, the MapReduce programming model is adopted. The method is applied to four monocotyledon plant species and it is shown that high-scoring motifs are significantly enriched for open chromatin regions in Oryza sativa and for transcription factor binding sites inferred through protein-binding microarrays in O.sativa and Zea mays. Furthermore, the method is shown to recover experimentally profiled ga2ox1-like KN1 binding sites in Z.mays. AVAILABILITY AND IMPLEMENTATION: BLSSpeller was written in Java. Source code and manual are available at http://bioinformatics.intec.ugent.be/blsspeller CONTACT: Klaas.Vandepoele@psb.vib-ugent.be or jan.fostier@intec.ugent.be. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Multi-criteria anomaly detection in urban noise sensor networks.

The growing concern of citizens about the quality of their living environment and the emergence of low-cost microphones and data acquisition systems triggered the deployment of numerous noise monitoring networks spread over large geographical areas. Due to the local character of noise pollution in an urban environment, a dense measurement network is needed in order to accurately assess the spatial and temporal variations. The use of consumer grade microphones in this context appears to be very cost-efficient compared to the use of measurement microphones. However, the lower reliability of these sensing units requires a strong quality control of the measured data. To automatically validate sensor (microphone) data, prior to their use in further processing, a multi-criteria measurement quality assessment model for detecting anomalies such as microphone breakdowns, drifts and critical outliers was developed. Each of the criteria results in a quality score between 0 and 1. An ordered weighted average (OWA) operator combines these individual scores into a global quality score. The model is validated on datasets acquired from a real-world, extensive noise monitoring network consisting of more than 50 microphones. Over a period of more than a year, the proposed approach successfully detected several microphone faults and anomalies.

i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets.

Comparative genomics is a powerful means to gain insight into the evolutionary processes that shape the genomes of related species. As the number of sequenced genomes increases, the development of software to perform accurate cross-species analyses becomes indispensable. However, many implementations that have the ability to compare multiple genomes exhibit unfavorable computational and memory requirements, limiting the number of genomes that can be analyzed in one run. Here, we present a software package to unveil genomic homology based on the identification of conservation of gene content and gene order (collinearity), i-ADHoRe 3.0, and its application to eukaryotic genomes. The use of efficient algorithms and support for parallel computing enable the analysis of large-scale data sets. Unlike other tools, i-ADHoRe can process the Ensembl data set, containing 49 species, in 1 h. Furthermore, the profile search is more sensitive to detect degenerate genomic homology than chaining pairwise collinearity information based on transitive homology. From ultra-conserved collinear regions between mammals and birds, by integrating coexpression information and protein-protein interactions, we identified more than 400 regions in the human genome showing significant functional coherence. The different algorithmical improvements ensure that i-ADHoRe 3.0 will remain a powerful tool to study genome evolution.

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists.

MOTIVATION: Many comparative genomics studies rely on the correct identification of homologous genomic regions using accurate alignment tools. In such case, the alphabet of the input sequences consists of complete genes, rather than nucleotides or amino acids. As optimal multiple sequence alignment is computationally impractical, a progressive alignment strategy is often employed. However, such an approach is susceptible to the propagation of alignment errors in early pairwise alignment steps, especially when dealing with strongly diverged genomic regions. In this article, we present a novel accurate and efficient greedy, graph-based algorithm for the alignment of multiple homologous genomic segments, represented as ordered gene lists. RESULTS: Based on provable properties of the graph structure, several heuristics are developed to resolve local alignment conflicts that occur due to gene duplication and/or rearrangement events on the different genomic segments. The performance of the algorithm is assessed by comparing the alignment results of homologous genomic segments in Arabidopsis thaliana to those obtained by using both a progressive alignment method and an earlier graph-based implementation. Especially for datasets that contain strongly diverged segments, the proposed method achieves a substantially higher alignment accuracy, and proves to be sufficiently fast for large datasets including a few dozens of eukaryotic genomes. AVAILABILITY: http://bioinformatics.psb.ugent.be/software. The algorithm is implemented as a part of the i-ADHoRe 3.0 package.

On the ability of consumer electronics microphones for environmental noise monitoring.

The massive production of microphones for consumer electronics, and the shift from dedicated processing hardware to PC-based systems, opens the way to build affordable, extensive noise measurement networks. Applications include e.g. noise limit and urban soundscape monitoring, and validation of calculated noise maps. Microphones are the critical components of such a network. Therefore, in a first step, some basic characteristics of 8 microphones, distributed over a wide range of price classes, were measured in a standardized way in an anechoic chamber. In a next step, a thorough evaluation was made of the ability of these microphones to be used for environmental noise monitoring. This was done during a continuous, half-year lasting outdoor experiment, characterized by a wide variety of meteorological conditions. While some microphones failed during the course of this test, it was shown that it is possible to identify cheap microphones that highly correlate to the reference microphone during the full test period. When the deviations are expressed in total A-weighted (road traffic) noise levels, values of less than 1 dBA are obtained, in excess to the deviation amongst reference microphones themselves.

Design and implementation of a secure and user-friendly broker platform supporting the end-to-end provisioning of e-homecare services.

We designed a broker platform for e-homecare services using web service technology. The broker allows efficient data communication and guarantees quality requirements such as security, availability and cost-efficiency by dynamic selection of services, minimizing user interactions and simplifying authentication through a single user sign-on. A prototype was implemented, with several e-homecare services (alarm, telemonitoring, audio diary and video-chat). It was evaluated by patients with diabetes and multiple sclerosis. The patients found that the start-up time and overhead imposed by the platform was satisfactory. Having all e-homecare services integrated into a single application, which required only one login, resulted in a high quality of experience for the patients.

Design of a JAIN SLEE/ESB-based platform for routing medical data in the ICU.

The importance of computer aided decision making is continuously increasing. In the ICU, medical decision support services gather and process medical data of patients and present results and suggestions to the medical staff. The medical decision support services can monitor for example blood pressure, creatinine levels or the usage of antibiotics. If certain levels are crossed, they raise alerts so that the medical staff can take appropriate actions if required. This significantly reduces the amount of data needing to be processed by the medical staff. To handle the large amount of data that is generated by the ICU on a daily basis, a platform for routing and processing this data is necessary. In this paper we propose a platform based on JAIN SLEE and an Enterprise Service Bus. The platform takes care of the routing of the data to the appropriate services and allows to easily deploy and manage services. In this paper, we present the design details and the evaluation results. Furthermore, it is shown that the platform is capable of routing and processing all the events generated by the ICU within strict time constraints.