Disentangling causal webs in the brain using functional Magnetic Resonance Imaging: A review of current approaches

In the past two decades, functional Magnetic Resonance Imaging has been used to relate neuronal network activity to cognitive processing and behaviour. Recently this approach has been augmented by algorithms that allow us to infer causal links between component populations of neuronal networks. Multiple inference procedures have been proposed to approach this research question but so far, each method has limitations when it comes to establishing whole-brain connectivity patterns. In this work, we discuss eight ways to infer causality in fMRI research: Bayesian Nets, Dynamical Causal Modelling, Granger Causality, Likelihood Ratios, LiNGAM, Patel's Tau, Structural Equation Modelling, and Transfer Entropy. We finish with formulating some recommendations for the future directions in this area

Leaning Robust Sequence Features via Dynamic Temporal Pattern Discovery

As a major type of data, time series possess invaluable latent knowledge for describing the real world and human society. In order to improve the ability of intelligent systems for understanding the world and people, it is critical to design sophisticated machine learning algorithms for extracting robust time series features from such latent knowledge. Motivated by the successful applications of deep learning in computer vision, more and more machine learning researchers put their attentions on the topic of applying deep learning techniques to time series data. However, directly employing current deep models in most time series domains could be problematic. A major reason is that temporal pattern types that current deep models are aiming at are very limited, which cannot meet the requirement of modeling different underlying patterns of data coming from various sources. In this study we address this problem by designing different network structures explicitly based on specific domain knowledge such that we can extract features via most salient temporal patterns. More specifically, we mainly focus on two types of temporal patterns: order patterns and frequency patterns. For order patterns, which are usually related to brain and human activities, we design a hashing-based neural network layer to globally encode the ordinal pattern information into the resultant features. It is further generalized into a specially designed Recurrent Neural Networks (RNN) cell which can learn order patterns in an online fashion. On the other hand, we believe audio-related data such as music and speech can benefit from modeling frequency patterns. Thus, we do so by developing two types of RNN cells. The first type tries to directly learn the long-term dependencies on frequency domain rather than time domain. The second one aims to dynamically filter out the noise frequencies based on temporal contexts. By proposing various deep models based on different domain knowledge and evaluating them on extensive time series tasks, we hope this work can provide inspirations for others and increase the community\u27s interests on the problem of applying deep learning techniques to more time series tasks

Medical imaging analysis with artificial neural networks

Given that neural networks have been widely reported in the research community of medical imaging, we provide a focused literature survey on recent neural network developments in computer-aided diagnosis, medical image segmentation and edge detection towards visual content analysis, and medical image registration for its pre-processing and post-processing, with the aims of increasing awareness of how neural networks can be applied to these areas and to provide a foundation for further research and practical development. Representative techniques and algorithms are explained in detail to provide inspiring examples illustrating: (i) how a known neural network with fixed structure and training procedure could be applied to resolve a medical imaging problem; (ii) how medical images could be analysed, processed, and characterised by neural networks; and (iii) how neural networks could be expanded further to resolve problems relevant to medical imaging. In the concluding section, a highlight of comparisons among many neural network applications is included to provide a global view on computational intelligence with neural networks in medical imaging

Graph Neural Network for spatiotemporal data: methods and applications

In the era of big data, there has been a surge in the availability of data containing rich spatial and temporal information, offering valuable insights into dynamic systems and processes for applications such as weather forecasting, natural disaster management, intelligent transport systems, and precision agriculture. Graph neural networks (GNNs) have emerged as a powerful tool for modeling and understanding data with dependencies to each other such as spatial and temporal dependencies. There is a large amount of existing work that focuses on addressing the complex spatial and temporal dependencies in spatiotemporal data using GNNs. However, the strong interdisciplinary nature of spatiotemporal data has created numerous GNNs variants specifically designed for distinct application domains. Although the techniques are generally applicable across various domains, cross-referencing these methods remains essential yet challenging due to the absence of a comprehensive literature review on GNNs for spatiotemporal data. This article aims to provide a systematic and comprehensive overview of the technologies and applications of GNNs in the spatiotemporal domain. First, the ways of constructing graphs from spatiotemporal data are summarized to help domain experts understand how to generate graphs from various types of spatiotemporal data. Then, a systematic categorization and summary of existing spatiotemporal GNNs are presented to enable domain experts to identify suitable techniques and to support model developers in advancing their research. Moreover, a comprehensive overview of significant applications in the spatiotemporal domain is offered to introduce a broader range of applications to model developers and domain experts, assisting them in exploring potential research topics and enhancing the impact of their work. Finally, open challenges and future directions are discussed

Visual perception of liquids: Insights from deep neural networks

Visually inferring material properties is crucial for many tasks, yet poses significant computational challenges for biological vision. Liquids and gels are particularly challenging due to their extreme variability and complex behaviour. We reasoned that measuring and modelling viscosity perception is a useful case study for identifying general principles of complex visual inferences. In recent years, artificial Deep Neural Networks (DNNs) have yielded breakthroughs in challenging real-world vision tasks. However, to model human vision, the emphasis lies not on best possible performance, but on mimicking the specific pattern of successes and errors humans make. We trained a DNN to estimate the viscosity of liquids using 100.000 simulations depicting liquids with sixteen different viscosities interacting in ten different scenes (stirring, pouring, splashing, etc). We find that a shallow feedforward network trained for only 30 epochs predicts mean observer performance better than most individual observers. This is the first successful image-computable model of human viscosity perception. Further training improved accuracy, but predicted human perception less well. We analysed the network’s features using representational similarity analysis (RSA) and a range of image descriptors (e.g. optic flow, colour saturation, GIST). This revealed clusters of units sensitive to specific classes of feature. We also find a distinct population of units that are poorly explained by hand-engineered features, but which are particularly important both for physical viscosity estimation, and for the specific pattern of human responses. The final layers represent many distinct stimulus characteristics—not just viscosity, which the network was trained on. Retraining the fully-connected layer with a reduced number of units achieves practically identical performance, but results in representations focused on viscosity, suggesting that network capacity is a crucial parameter determining whether artificial or biological neural networks use distributed vs. localized representations