Hippocampal formation-inspired global self-localization: quick recovery from the kidnapped robot problem from an egocentric perspective.

It remains difficult for mobile robots to continue accurate self-localization when they are suddenly teleported to a location that is different from their beliefs during navigation. Incorporating insights from neuroscience into developing a spatial cognition model for mobile robots may make it possible to acquire the ability to respond appropriately to changing situations, similar to living organisms. Recent neuroscience research has shown that during teleportation in rat navigation, neural populations of place cells in the cornu ammonis-3 region of the hippocampus, which are sparse representations of each other, switch discretely. In this study, we construct a spatial cognition model using brain reference architecture-driven development, a method for developing brain-inspired software that is functionally and structurally consistent with the brain. The spatial cognition model was realized by integrating the recurrent state-space model, a world model, with Monte Carlo localization to infer allocentric self-positions within the framework of neuro-symbol emergence in the robotics toolkit. The spatial cognition model, which models the cornu ammonis-1 and -3 regions with each latent variable, demonstrated improved self-localization performance of mobile robots during teleportation in a simulation environment. Moreover, it was confirmed that sparse neural activity could be obtained for the latent variables corresponding to cornu ammonis-3. These results suggest that spatial cognition models incorporating neuroscience insights can contribute to improving the self-localization technology for mobile robots. The project website is https://nakashimatakeshi.github.io/HF-IGL/.

Customized T-time inner sampling network with uncertainty-aware data augmentation strategy for multi-annotated lesion segmentation.

Segmentation in medical images is inherently ambiguous. It is crucial to capture the uncertainty in lesion segmentations to assist cancer diagnosis and further interventions. Recent works have made great progress in generating multiple plausible segmentation results as diversified references to account for the uncertainty in lesion segmentations. However, the efficiency of existing models is limited, and the uncertainty information lying in multi-annotated datasets remains to be fully utilized. In this study, we propose a series of methods to corporately deal with the above limitation and leverage the abundant information in multi-annotated datasets: (1) Customized T-time Inner Sampling Network to promote the modeling flexibility and efficiently generate samples matching the ground-truth distribution of a number of annotators; (2) Uncertainty Degree defined for quantitatively measuring the uncertainty of each sample and the imbalance of the whole multi-annotated dataset from a brand new perspective; (3) Uncertainty-aware Data Augmentation Strategy to help probabilistic models adaptively fit samples with different ranges of uncertainty. We have evaluated each of them on both the publicly available lung nodule dataset and our in-house Liver Tumor dataset. Results show that our proposed methods achieves the overall best performance on both accuracy and efficiency, demonstrating its great potential in lesion segmentations and more downstream tasks in real clinical scenarios.

Hierarchical path planning from speech instructions with spatial concept-based topometric semantic mapping.

Assisting individuals in their daily activities through autonomous mobile robots is a significant concern, especially for users without specialized knowledge. Specifically, the capability of a robot to navigate to destinations based on human speech instructions is crucial. Although robots can take different paths toward the same objective, the shortest path is not always the most suitable. A preferred approach would be to accommodate waypoint specifications flexibly for planning an improved alternative path even with detours. Furthermore, robots require real-time inference capabilities. In this sense, spatial representations include semantic, topological, and metric-level representations, each capturing different aspects of the environment. This study aimed to realize a hierarchical spatial representation using a topometric semantic map and path planning with speech instructions by including waypoints. Thus, we present a hierarchical path planning method called spatial concept-based topometric semantic mapping for hierarchical path planning (SpCoTMHP), which integrates place connectivity. This approach provides a novel integrated probabilistic generative model and fast approximate inferences with interactions among the hierarchy levels. A formulation based on "control as probabilistic inference" theoretically supports the proposed path planning algorithm. We conducted experiments in a home environment using the Toyota human support robot on the SIGVerse simulator and in a lab-office environment with the real robot Albert. Here, the user issues speech commands that specify the waypoint and goal, such as "Go to the bedroom via the corridor." Navigation experiments were performed using speech instructions with a waypoint to demonstrate the performance improvement of the SpCoTMHP over the baseline hierarchical path planning method with heuristic path costs (HPP-I) in terms of the weighted success rate at which the robot reaches the closest target (0.590) and passes the correct waypoints. The computation time was significantly improved by 7.14 s with the SpCoTMHP than the baseline HPP-I in advanced tasks. Thus, hierarchical spatial representations provide mutually understandable instruction forms for both humans and robots, thus enabling language-based navigation.

Emotion prediction as computation over a generative theory of mind.

From sparse descriptions of events, observers can make systematic and nuanced predictions of what emotions the people involved will experience. We propose a formal model of emotion prediction in the context of a public high-stakes social dilemma. This model uses inverse planning to infer a person's beliefs and preferences, including social preferences for equity and for maintaining a good reputation. The model then combines these inferred mental contents with the event to compute 'appraisals': whether the situation conformed to the expectations and fulfilled the preferences. We learn functions mapping computed appraisals to emotion labels, allowing the model to match human observers' quantitative predictions of 20 emotions, including joy, relief, guilt and envy. Model comparison indicates that inferred monetary preferences are not sufficient to explain observers' emotion predictions; inferred social preferences are factored into predictions for nearly every emotion. Human observers and the model both use minimal individualizing information to adjust predictions of how different people will respond to the same event. Thus, our framework integrates inverse planning, event appraisals and emotion concepts in a single computational model to reverse-engineer people's intuitive theory of emotions. This article is part of a discussion meeting issue 'Cognitive artificial intelligence'.

Learning the progression patterns of treatments using a probabilistic generative model.

Modeling a disease or the treatment of a patient has drawn much attention in recent years due to the vast amount of information that Electronic Health Records contain. This paper presents a probabilistic generative model of treatments that are described in terms of sequences of medical activities of variable length. The main objective is to identify distinct subtypes of treatments for a given disease, and discover their development and progression. To this end, the model considers that a sequence of actions has an associated hierarchical structure of latent variables that both classifies the sequences based on their evolution over time, and segments the sequences into different progression stages. The learning procedure of the model is performed with the Expectation-Maximization algorithm which considers the exponential number of configurations of the latent variables and is efficiently solved with a method based on dynamic programming. The evaluation of the model is twofold: first, we use synthetic data to demonstrate that the learning procedure allows the generative model underlying the data to be recovered; we then further assess the potential of our model to provide treatment classification and staging information in real-world data. Our model can be seen as a tool for classification, simulation, data augmentation and missing data imputation.

Using an optimized generative model to infer the progression of complications in type 2 diabetes patients.

BACKGROUND: People live a long time in pre-diabetes/early diabetes without a formal diagnosis or management. Heterogeneity of progression coupled with deficiencies in electronic health records related to incomplete data, discrete events, and irregular event intervals make identification of pre-diabetes and critical points of diabetes progression challenging. METHODS: We utilized longitudinal electronic health records of 9298 patients with type 2 diabetes or prediabetes from 2005 to 2016 from a large regional healthcare delivery network in China. We optimized a generative Markov-Bayesian-based model to generate 5000 synthetic illness trajectories. The synthetic data were manually reviewed by endocrinologists. RESULTS: We build an optimized generative progression model for type 2 diabetes using anchor information to reduce the number of parameters learning in the third layer of the model from [Formula: see text] to [Formula: see text], where [Formula: see text] is the number of clinical findings, [Formula: see text] is the number of complications, [Formula: see text] is the number of anchors. Based on this model, we infer the relationships between progression stages, the onset of complication categories, and the associated diagnoses during the whole progression of type 2 diabetes using electronic health records. DISCUSSION: Our findings indicate that 55.3% of single complications and 31.8% of complication patterns could be predicted early and managed appropriately to potentially delay (as it is a progressive disease) or prevented (by lifestyle modifications that keep patient from developing/triggering diabetes in the first place). CONCLUSIONS: The full type 2 diabetes patient trajectories generated by the chronic disease progression model can counter a lack of real-world evidence of desired longitudinal timeframe while facilitating population health management.

Hippocampal formation-inspired probabilistic generative model.

In building artificial intelligence (AI) agents, referring to how brains function in real environments can accelerate development by reducing the design space. In this study, we propose a probabilistic generative model (PGM) for navigation in uncertain environments by integrating the neuroscientific knowledge of hippocampal formation (HF) and the engineering knowledge in robotics and AI, namely, simultaneous localization and mapping (SLAM). We follow the approach of brain reference architecture (BRA) (Yamakawa, 2021) to compose the PGM and outline how to verify the model. To this end, we survey and discuss the relationship between the HF findings and SLAM models. The proposed hippocampal formation-inspired probabilistic generative model (HF-PGM) is designed to be highly consistent with the anatomical structure and functions of the HF. By referencing the brain, we elaborate on the importance of integration of egocentric/allocentric information from the entorhinal cortex to the hippocampus and the use of discrete-event queues.

A whole brain probabilistic generative model: Toward realizing cognitive architectures for developmental robots.

Building a human-like integrative artificial cognitive system, that is, an artificial general intelligence (AGI), is the holy grail of the artificial intelligence (AI) field. Furthermore, a computational model that enables an artificial system to achieve cognitive development will be an excellent reference for brain and cognitive science. This paper describes an approach to develop a cognitive architecture by integrating elemental cognitive modules to enable the training of the modules as a whole. This approach is based on two ideas: (1) brain-inspired AI, learning human brain architecture to build human-level intelligence, and (2) a probabilistic generative model (PGM)-based cognitive architecture to develop a cognitive system for developmental robots by integrating PGMs. The proposed development framework is called a whole brain PGM (WB-PGM), which differs fundamentally from existing cognitive architectures in that it can learn continuously through a system based on sensory-motor information. In this paper, we describe the rationale for WB-PGM, the current status of PGM-based elemental cognitive modules, their relationship with the human brain, the approach to the integration of the cognitive modules, and future challenges. Our findings can serve as a reference for brain studies. As PGMs describe explicit informational relationships between variables, WB-PGM provides interpretable guidance from computational sciences to brain science. By providing such information, researchers in neuroscience can provide feedback to researchers in AI and robotics on what the current models lack with reference to the brain. Further, it can facilitate collaboration among researchers in neuro-cognitive sciences as well as AI and robotics.

Probabilistic generative modeling and reinforcement learning extract the intrinsic features of animal behavior.

It is one of the ultimate goals of ethology to understand the generative process of animal behavior, and the ability to reproduce and control behavior is an important step in this field. However, it is not easy to achieve this goal in systems with complex and stochastic dynamics such as animal behavior. In this study, we have shown that MDN-RNN,a type of probabilistic deep generative model, is able to reproduce stochastic animal behavior with high accuracy by modeling the behavior of C. elegans. Furthermore, we found that the model learns different dynamics in a disentangled representation as a time-evolving Gaussian mixture. Finally, by combining the model and reinforcement learning, we were able to extract a behavioral policy of goal-directed behavior in silico, and showed that it can be used for regulating the behavior of real animals. This set of methods will be applicable not only to animal behavior but also to broader areas such as neuroscience and robotics.

Necessary conditions for STDP-based pattern recognition learning in a memristive spiking neural network.

This work is aimed to study experimental and theoretical approaches for searching effective local training rules for unsupervised pattern recognition by high-performance memristor-based Spiking Neural Networks (SNNs). First, the possibility of weight change using Spike-Timing-Dependent Plasticity (STDP) is demonstrated with a pair of hardware analog neurons connected through a (CoFeB)x(LiNbO3)1-x nanocomposite memristor. Next, the learning convergence to a solution of binary clusterization task is analyzed in a wide range of memristive STDP parameters for a single-layer fully connected feedforward SNN. The memristive STDP behavior supplying convergence in this simple task is shown also to provide it in the handwritten digit recognition domain by the more complex SNN architecture with a Winner-Take-All competition between neurons. To investigate basic conditions necessary for training convergence, an original probabilistic generative model of a rate-based single-layer network with independent or competing neurons is built and thoroughly analyzed. The main result is a statement of "correlation growth-anticorrelation decay" principle which prompts near-optimal policy to configure model parameters. This principle is in line with requiring the binary clusterization convergence which can be defined as the necessary condition for optimal learning and used as the simple benchmark for tuning parameters of various neural network realizations with population-rate information coding. At last, a heuristic algorithm is described to experimentally find out the convergence conditions in a memristive SNN, including robustness to a device variability. Due to the generality of the proposed approach, it can be applied to a wide range of memristors and neurons of software- or hardware-based rate-coding single-layer SNNs when searching for local rules that ensure their unsupervised learning convergence in a pattern recognition task domain.

Symbol Emergence as an Interpersonal Multimodal Categorization.

This study focuses on category formation for individual agents and the dynamics of symbol emergence in a multi-agent system through semiotic communication. In this study, the semiotic communication refers to exchanging signs composed of the signifier (i.e., words) and the signified (i.e., categories). We define the generation and interpretation of signs associated with the categories formed through the agent's own sensory experience or by exchanging signs with other agents as basic functions of the semiotic communication. From the viewpoint of language evolution and symbol emergence, organization of a symbol system in a multi-agent system (i.e., agent society) is considered as a bottom-up and dynamic process, where individual agents share the meaning of signs and categorize sensory experience. A constructive computational model can explain the mutual dependency of the two processes and has mathematical support that guarantees a symbol system's emergence and sharing within the multi-agent system. In this paper, we describe a new computational model that represents symbol emergence in a two-agent system based on a probabilistic generative model for multimodal categorization. It models semiotic communication via a probabilistic rejection based on the receiver's own belief. We have found that the dynamics by which cognitively independent agents create a symbol system through their semiotic communication can be regarded as the inference process of a hidden variable in an interpersonal multimodal categorizer, i.e., the complete system can be regarded as a single agent performing multimodal categorization using the sensors of all agents, if we define the rejection probability based on the Metropolis-Hastings algorithm. The validity of the proposed model and algorithm for symbol emergence, i.e., forming and sharing signs and categories, is also verified in an experiment with two agents observing daily objects in the real-world environment. In the experiment, we compared three communication algorithms: no communication, no rejection, and the proposed algorithm. The experimental results demonstrate that our model reproduces the phenomena of symbol emergence, which does not require a teacher who would know a pre-existing symbol system. Instead, the multi-agent system can form and use a symbol system without having pre-existing categories.

NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis.

BACKGROUND: High-throughput experimental techniques have been dramatically improved and widely applied in the past decades. However, biological interpretation of the high-throughput experimental results, such as differential expression gene sets derived from microarray or RNA-seq experiments, is still a challenging task. Gene Ontology (GO) is commonly used in the functional enrichment studies. The GO terms identified via current functional enrichment analysis tools often contain direct parent or descendant terms in the GO hierarchical structure. Highly redundant terms make users difficult to analyze the underlying biological processes. RESULTS: In this paper, a novel network-based probabilistic generative model, NetGen, was proposed to perform the functional enrichment analysis. An additional protein-protein interaction (PPI) network was explicitly used to assist the identification of significantly enriched GO terms. NetGen achieved a superior performance than the existing methods in the simulation studies. The effectiveness of NetGen was explored further on four real datasets. Notably, several GO terms which were not directly linked with the active gene list for each disease were identified. These terms were closely related to the corresponding diseases when accessed to the curated literatures. NetGen has been implemented in the R package CopTea publicly available at GitHub ( http://github.com/wulingyun/CopTea/ ). CONCLUSION: Our procedure leads to a more reasonable and interpretable result of the functional enrichment analysis. As a novel term combination-based functional enrichment analysis method, NetGen is complementary to current individual term-based methods, and can help to explore the underlying pathogenesis of complex diseases.

An overview of topic modeling and its current applications in bioinformatics.

BACKGROUND: With the rapid accumulation of biological datasets, machine learning methods designed to automate data analysis are urgently needed. In recent years, so-called topic models that originated from the field of natural language processing have been receiving much attention in bioinformatics because of their interpretability. Our aim was to review the application and development of topic models for bioinformatics. DESCRIPTION: This paper starts with the description of a topic model, with a focus on the understanding of topic modeling. A general outline is provided on how to build an application in a topic model and how to develop a topic model. Meanwhile, the literature on application of topic models to biological data was searched and analyzed in depth. According to the types of models and the analogy between the concept of document-topic-word and a biological object (as well as the tasks of a topic model), we categorized the related studies and provided an outlook on the use of topic models for the development of bioinformatics applications. CONCLUSION: Topic modeling is a useful method (in contrast to the traditional means of data reduction in bioinformatics) and enhances researchers' ability to interpret biological information. Nevertheless, due to the lack of topic models optimized for specific biological data, the studies on topic modeling in biological data still have a long and challenging road ahead. We believe that topic models are a promising method for various applications in bioinformatics research.