The physics of brain network structure, function, and control

The brain is a complex organ characterized by heterogeneous patterns of structural connections supporting unparalleled feats of cognition and a wide range of behaviors. New noninvasive imaging techniques now allow these patterns to be carefully and comprehensively mapped in individual humans and animals. Yet, it remains a fundamental challenge to understand how the brain's structural wiring supports cognitive processes, with major implications for the personalized treatment of mental health disorders. Here, we review recent efforts to meet this challenge that draw on intuitions, models, and theories from physics, spanning the domains of statistical mechanics, information theory, and dynamical systems and control. We begin by considering the organizing principles of brain network architecture instantiated in structural wiring under constraints of symmetry, spatial embedding, and energy minimization. We next consider models of brain network function that stipulate how neural activity propagates along these structural connections, producing the long-range interactions and collective dynamics that support a rich repertoire of system functions. Finally, we consider perturbative experiments and models for brain network control, which leverage the physics of signal transmission along structural wires to infer intrinsic control processes that support goal-directed behavior and to inform stimulation-based therapies for neurological disease and psychiatric disorders. Throughout, we highlight several open questions in the physics of brain network structure, function, and control that will require creative efforts from physicists willing to brave the complexities of living matter

Cognitive computational neuroscience

To learn how cognition is implemented in the brain, we must build computational models that can perform cognitive tasks, and test such models with brain and behavioral experiments. Cognitive science has developed computational models of human cognition, decomposing task performance into computational components. However, its algorithms still fall short of human intelligence and are not grounded in neurobiology. Computational neuroscience has investigated how interacting neurons can implement component functions of brain computation. However, it has yet to explain how those components interact to explain human cognition and behavior. Modern technologies enable us to measure and manipulate brain activity in unprecedentedly rich ways in animals and humans. However, experiments will yield theoretical insight only when employed to test brain-computational models. It is time to assemble the pieces of the puzzle of brain computation. Here we review recent work in the intersection of cognitive science, computational neuroscience, and artificial intelligence. Computational models that mimic brain information processing during perceptual, cognitive, and control tasks are beginning to be developed and tested with brain and behavioral data.Comment: 31 pages, 4 figure

Reverse-engineering biological networks from large data sets

Much of contemporary systems biology owes its success to the abstraction of a network, the idea that diverse kinds of molecular, cellular, and organismal species and interactions can be modeled as relational nodes and edges in a graph of dependencies. Since the advent of high-throughput data acquisition technologies in fields such as genomics, metabolomics, and neuroscience, the automated inference and reconstruction of such interaction networks directly from large sets of activation data, commonly known as reverse-engineering, has become a routine procedure. Whereas early attempts at network reverse-engineering focused predominantly on producing maps of system architectures with minimal predictive modeling, reconstructions now play instrumental roles in answering questions about the statistics and dynamics of the underlying systems they represent. Many of these predictions have clinical relevance, suggesting novel paradigms for drug discovery and disease treatment. While other reviews focus predominantly on the details and effectiveness of individual network inference algorithms, here we examine the emerging field as a whole. We first summarize several key application areas in which inferred networks have made successful predictions. We then outline the two major classes of reverse-engineering methodologies, emphasizing that the type of prediction that one aims to make dictates the algorithms one should employ. We conclude by discussing whether recent breakthroughs justify the computational costs of large-scale reverse-engineering sufficiently to admit it as a mainstay in the quantitative analysis of living systems.Comment: 24 pages, 2 figures. To appear as Chapter 10 of 'Quantitative Biology: Theory, Computational Methods and Examples of Models'. Brian Munsky, Lev Tsimring, William S. Hlavacek, editors. MIT Press, 201

Interpretability Beyond Feature Attribution: Quantitative Testing with Concept Activation Vectors (TCAV)

The interpretation of deep learning models is a challenge due to their size, complexity, and often opaque internal state. In addition, many systems, such as image classifiers, operate on low-level features rather than high-level concepts. To address these challenges, we introduce Concept Activation Vectors (CAVs), which provide an interpretation of a neural net's internal state in terms of human-friendly concepts. The key idea is to view the high-dimensional internal state of a neural net as an aid, not an obstacle. We show how to use CAVs as part of a technique, Testing with CAVs (TCAV), that uses directional derivatives to quantify the degree to which a user-defined concept is important to a classification result--for example, how sensitive a prediction of "zebra" is to the presence of stripes. Using the domain of image classification as a testing ground, we describe how CAVs may be used to explore hypotheses and generate insights for a standard image classification network as well as a medical application

Challenges and Prospects in Vision and Language Research

Language grounded image understanding tasks have often been proposed as a method for evaluating progress in artificial intelligence. Ideally, these tasks should test a plethora of capabilities that integrate computer vision, reasoning, and natural language understanding. However, rather than behaving as visual Turing tests, recent studies have demonstrated state-of-the-art systems are achieving good performance through flaws in datasets and evaluation procedures. We review the current state of affairs and outline a path forward

A Novel Semantics and Feature Preserving Perspective for Content Aware Image Retargeting

There is an increasing requirement for efficient image retargeting techniques to adapt the content to various forms of digital media. With rapid growth of mobile communications and dynamic web page layouts, one often needs to resize the media content to adapt to the desired display sizes. For various layouts of web pages and typically small sizes of handheld portable devices, the importance in the original image content gets obfuscated after resizing it with the approach of uniform scaling. Thus, there occurs a need for resizing the images in a content aware manner which can automatically discard irrelevant information from the image and present the salient features with more magnitude. There have been proposed some image retargeting techniques keeping in mind the content awareness of the input image. However, these techniques fail to prove globally effective for various kinds of images and desired sizes. The major problem is the inefficiency of these algorithms to process these images with minimal visual distortion while also retaining the meaning conveyed from the image. In this dissertation, we present a novel perspective for content aware image retargeting, which is well implementable in real time. We introduce a novel method of analysing semantic information within the input image while also maintaining the important and visually significant features. We present the various nuances of our algorithm mathematically and logically, and show that the results prove better than the state-of-the-art techniques.Comment: 74 Pages, 46 Figures, Masters Thesi

Network Analysis of Particles and Grains

The arrangements of particles and forces in granular materials have a complex organization on multiple spatial scales that ranges from local structures to mesoscale and system-wide ones. This multiscale organization can affect how a material responds or reconfigures when exposed to external perturbations or loading. The theoretical study of particle-level, force-chain, domain, and bulk properties requires the development and application of appropriate physical, mathematical, statistical, and computational frameworks. Traditionally, granular materials have been investigated using particulate or continuum models, each of which tends to be implicitly agnostic to multiscale organization. Recently, tools from network science have emerged as powerful approaches for probing and characterizing heterogeneous architectures across different scales in complex systems, and a diverse set of methods have yielded fascinating insights into granular materials. In this paper, we review work on network-based approaches to studying granular matter and explore the potential of such frameworks to provide a useful description of these systems and to enhance understanding of their underlying physics. We also outline a few open questions and highlight particularly promising future directions in the analysis and design of granular matter and other kinds of material networks

Case studies in network community detection

Community structure describes the organization of a network into subgraphs that contain a prevalence of edges within each subgraph and relatively few edges across boundaries between subgraphs. The development of community-detection methods has occurred across disciplines, with numerous and varied algorithms proposed to find communities. As we present in this Chapter via several case studies, community detection is not just an "end game" unto itself, but rather a step in the analysis of network data which is then useful for furthering research in the disciplinary domain of interest. These case-study examples arise from diverse applications, ranging from social and political science to neuroscience and genetics, and we have chosen them to demonstrate key aspects of community detection and to highlight that community detection, in practice, should be directed by the application at hand.Comment: 21 pages, 5 figure

Radiological images and machine learning: trends, perspectives, and prospects

The application of machine learning to radiological images is an increasingly active research area that is expected to grow in the next five to ten years. Recent advances in machine learning have the potential to recognize and classify complex patterns from different radiological imaging modalities such as x-rays, computed tomography, magnetic resonance imaging and positron emission tomography imaging. In many applications, machine learning based systems have shown comparable performance to human decision-making. The applications of machine learning are the key ingredients of future clinical decision making and monitoring systems. This review covers the fundamental concepts behind various machine learning techniques and their applications in several radiological imaging areas, such as medical image segmentation, brain function studies and neurological disease diagnosis, as well as computer-aided systems, image registration, and content-based image retrieval systems. Synchronistically, we will briefly discuss current challenges and future directions regarding the application of machine learning in radiological imaging. By giving insight on how take advantage of machine learning powered applications, we expect that clinicians can prevent and diagnose diseases more accurately and efficiently.Comment: 13 figure

Learning crystal plasticity using digital image correlation: Examples from discrete dislocation dynamics

Digital image correlation (DIC) is a well-established, non-invasive technique for tracking and quantifying the deformation of mechanical samples under strain. While it provides an obvious way to observe incremental and aggregate displacement information, it seems likely that DIC data sets, which after all reflect the spatially-resolved response of a microstructure to loads, contain much richer information than has generally been extracted from them. In this paper, we demonstrate a machine-learning approach to quantifying the prior deformation history of a crystalline sample based on its response to a subsequent DIC test. This prior deformation history is encoded in the microstructure through the inhomogeneity of the dislocation microstructure, and in the spatial correlations of the dislocation patterns, which mediate the system's response to the DIC test load. Our domain consists of deformed crystalline thin films generated by a discrete dislocation plasticity simulation. We explore the range of applicability of machine learning (ML) for typical experimental protocols, and as a function of possible size effects and stochasticity. Plasticity size effects may directly influence the data, rendering unsupervised techniques unable to distinguish different plasticity regimes.Comment: 35 pages, 31 figure