Analysis of dogs’ sleep patterns using convolutional neural networks

Video-based analysis is one of the most important tools of animal behavior and animal welfare scientists. While automatic analysis systems exist for many species, this problem has not yet been adequately addressed for one of the most studied species in animal science—dogs. In this paper we describe a system developed for analyzing sleeping patterns of kenneled dogs, which may serve as indicator of their welfare. The system combines convolutional neural networks with classical data processing methods, and works with very low quality video from cameras installed in dogs shelters

Convolutional Neural Networks for Epileptic Seizure Prediction

Epilepsy is the most common neurological disorder and an accurate forecast of seizures would help to overcome the patient's uncertainty and helplessness. In this contribution, we present and discuss a novel methodology for the classification of intracranial electroencephalography (iEEG) for seizure prediction. Contrary to previous approaches, we categorically refrain from an extraction of hand-crafted features and use a convolutional neural network (CNN) topology instead for both the determination of suitable signal characteristics and the binary classification of preictal and interictal segments. Three different models have been evaluated on public datasets with long-term recordings from four dogs and three patients. Overall, our findings demonstrate the general applicability. In this work we discuss the strengths and limitations of our methodology.Comment: accepted for MLESP 201

Distributed brain co-processor for tracking spikes, seizures and behaviour during electrical brain stimulation

Early implantable epilepsy therapy devices provided open-loop electrical stimulation without brain sensing, computing, or an interface for synchronized behavioural inputs from patients. Recent epilepsy stimulation devices provide brain sensing but have not yet developed analytics for accurately tracking and quantifying behaviour and seizures. Here we describe a distributed brain co-processor providing an intuitive bi-directional interface between patient, implanted neural stimulation and sensing device, and local and distributed computing resources. Automated analysis of continuous streaming electrophysiology is synchronized with patient reports using a handheld device and integrated with distributed cloud computing resources for quantifying seizures, interictal epileptiform spikes and patient symptoms during therapeutic electrical brain stimulation. The classification algorithms for interictal epileptiform spikes and seizures were developed and parameterized using long-term ambulatory data from nine humans and eight canines with epilepsy, and then implemented prospectively in out-of-sample testing in two pet canines and four humans with drug-resistant epilepsy living in their natural environments. Accurate seizure diaries are needed as the primary clinical outcome measure of epilepsy therapy and to guide brain-stimulation optimization. The brain co-processor system described here enables tracking interictal epileptiform spikes, seizures and correlation with patient behavioural reports. In the future, correlation of spikes and seizures with behaviour will allow more detailed investigation of the clinical impact of spikes and seizures on patients

Video-based estimation of pain indicators in dogs

Dog owners are typically capable of recognizing behavioral cues that reveal subjective states of their dogs, such as pain. But automatic recognition of the pain state is very challenging. This paper proposes a novel video-based, two-stream deep neural network approach for this problem. We extract and preprocess body keypoints, and compute features from both keypoints and the RGB representation over the video. We propose an approach to deal with self-occlusions and missing keypoints. We also present a unique video-based dog behavior dataset, collected by veterinary professionals, and annotated for presence of pain, and report good classification results with the proposed approach. This study is one of the first works on machine learning based estimation of dog pain state.Comment: 20 pages, 7 figure

Learning cortical representations through perturbed and adversarial dreaming.

Humans and other animals learn to extract general concepts from sensory experience without extensive teaching. This ability is thought to be facilitated by offline states like sleep where previous experiences are systemically replayed. However, the characteristic creative nature of dreams suggests that learning semantic representations may go beyond merely replaying previous experiences. We support this hypothesis by implementing a cortical architecture inspired by generative adversarial networks (GANs). Learning in our model is organized across three different global brain states mimicking wakefulness, NREM and REM sleep, optimizing different, but complementary objective functions. We train the model on standard datasets of natural images and evaluate the quality of the learned representations. Our results suggest that generating new, virtual sensory inputs via adversarial dreaming during REM sleep is essential for extracting semantic concepts, while replaying episodic memories via perturbed dreaming during NREM sleep improves the robustness of latent representations. The model provides a new computational perspective on sleep states, memory replay and dreams and suggests a cortical implementation of GANs

Explainable automated recognition of emotional states from canine facial expressions: the case of positive anticipation and frustration.

In animal research, automation of affective states recognition has so far mainly addressed pain in a few species. Emotional states remain uncharted territories, especially in dogs, due to the complexity of their facial morphology and expressions. This study contributes to fill this gap in two aspects. First, it is the first to address dog emotional states using a dataset obtained in a controlled experimental setting, including videos from (n = 29) Labrador Retrievers assumed to be in two experimentally induced emotional states: negative (frustration) and positive (anticipation). The dogs' facial expressions were measured using the Dogs Facial Action Coding System (DogFACS). Two different approaches are compared in relation to our aim: (1) a DogFACS-based approach with a two-step pipeline consisting of (i) a DogFACS variable detector and (ii) a positive/negative state Decision Tree classifier; (2) An approach using deep learning techniques with no intermediate representation. The approaches reach accuracy of above 71% and 89%, respectively, with the deep learning approach performing better. Secondly, this study is also the first to study explainability of AI models in the context of emotion in animals. The DogFACS-based approach provides decision trees, that is a mathematical representation which reflects previous findings by human experts in relation to certain facial expressions (DogFACS variables) being correlates of specific emotional states. The deep learning approach offers a different, visual form of explainability in the form of heatmaps reflecting regions of focus of the network's attention, which in some cases show focus clearly related to the nature of particular DogFACS variables. These heatmaps may hold the key to novel insights on the sensitivity of the network to nuanced pixel patterns reflecting information invisible to the human eye

Count data time series models and their applications

“Due to fast developments of advanced sensors, count data sets have become ubiquitous in many fields. Modeling and forecasting such time series have generated great interest. Modeling can shed light on the behavior of the count series and to see how they are related to other factors such as the environmental conditions under which the data are generated. In this research, three approaches to modeling such count data are proposed. First, a periodic autoregressive conditional Poisson (PACP) model is proposed as a natural generalization of the autoregressive conditional Poisson (ACP) model. By allowing for cyclical variations in the parameters of the model, it provides a way to explain the periodicity inherent in many count data series. For example, in epidemiology the prevalence of a disease may depend on the season. The autoregressive conditional Poisson hidden Markov model (ACP-HMM) is developed to deal with count data time series whose mean, conditional on the past, is a function of previous observations, with this relationship possibly determined by an unobserved process that switches its state or regime as time progresses. This model, in a sense, is the combination of the discrete version of the autoregressive conditional heteroscedastic (ARCH) formulation and the Poisson hidden Markov model. Both the above models address the frequently present serial correlation and the clustering of high or low counts observed in time series of count data, while at the same time allowing the underlying data generating mechanism to change cyclically or according to a hidden Markov process. Applications to empirical data sets show that these models provide a better fit than the standard ACP models. In addition to the above models, a modification of a zero-inflated Poisson model is used to analyze activity counts of the fruit fly. The model captures the dynamic structure of activity patterns and the fly\u27s propensity to sleep. The obtained results when fed to a convolutional neural network provides the possibility of building a predictive model to identify fruit flies with short and long lifespans”--Abstract, page iv