Simulation Intelligence: Towards a New Generation of Scientific Methods

The original "Seven Motifs" set forth a roadmap of essential methods for the field of scientific computing, where a motif is an algorithmic method that captures a pattern of computation and data movement. We present the "Nine Motifs of Simulation Intelligence", a roadmap for the development and integration of the essential algorithms necessary for a merger of scientific computing, scientific simulation, and artificial intelligence. We call this merger simulation intelligence (SI), for short. We argue the motifs of simulation intelligence are interconnected and interdependent, much like the components within the layers of an operating system. Using this metaphor, we explore the nature of each layer of the simulation intelligence operating system stack (SI-stack) and the motifs therein: (1) Multi-physics and multi-scale modeling; (2) Surrogate modeling and emulation; (3) Simulation-based inference; (4) Causal modeling and inference; (5) Agent-based modeling; (6) Probabilistic programming; (7) Differentiable programming; (8) Open-ended optimization; (9) Machine programming. We believe coordinated efforts between motifs offers immense opportunity to accelerate scientific discovery, from solving inverse problems in synthetic biology and climate science, to directing nuclear energy experiments and predicting emergent behavior in socioeconomic settings. We elaborate on each layer of the SI-stack, detailing the state-of-art methods, presenting examples to highlight challenges and opportunities, and advocating for specific ways to advance the motifs and the synergies from their combinations. Advancing and integrating these technologies can enable a robust and efficient hypothesis-simulation-analysis type of scientific method, which we introduce with several use-cases for human-machine teaming and automated science

Converging Intracranial Markers of Conscious Access

We compared conscious and nonconscious processing of briefly flashed words using a visual masking procedure while recording intracranial electroencephalogram (iEEG) in ten patients. Nonconscious processing of masked words was observed in multiple cortical areas, mostly within an early time window (<300 ms), accompanied by induced gamma-band activity, but without coherent long-distance neural activity, suggesting a quickly dissipating feedforward wave. In contrast, conscious processing of unmasked words was characterized by the convergence of four distinct neurophysiological markers: sustained voltage changes, particularly in prefrontal cortex, large increases in spectral power in the gamma band, increases in long-distance phase synchrony in the beta range, and increases in long-range Granger causality. We argue that all of those measures provide distinct windows into the same distributed state of conscious processing. These results have a direct impact on current theoretical discussions concerning the neural correlates of conscious access

Information Processing in the Orbitofrontal Cortex and the Ventral Striatum in Rats Performing an Economic Decision-Making Task

University of Minnesota Ph.D. dissertation. August 2015. Major: Neuroscience. Advisor: David Redish. 1 computer file (PDF); vi, 144 pages.The orbitofrontal cortex (OFC) and ventral striatum (vStr) are key brain structures that represent information about value during decision-making tasks. Despite their very different anatomical properties, numerous studies have found similar patterns of value-related signaling in these structures. In particular, both structures are intimately involved in delay-discounting tasks, which involve a tradeoff between reward magnitude and delay to reward. However, the overlapping activity profiles of these brain regions makes it difficult to tease apart their specific contributions to delay-discounting behavior, and to economic decision-making more generally. In order to better understand the contributions of these two regions to value-based choice, we made simultaneous recordings in the OFC and vStr in rats performing a spatial variant of a traditional delay-discounting task. This allowed us to compare OFC and vStr activity directly in the same subjects while they engaged in a prototypical economic decision-making task, and additionally it allowed us to leverage the tools of spatial decoding analysis to measure non-local reward signaling. Chapter 1 provides an introduction to current theories of OFC and vStr function within the decision-making literature, in particular contrasting the concepts of neuroeconomics with the multiple decision-making systems framework. Chapter 2 describes the methods used in this thesis, including the design of the spatial delay-discounting task and the analysis of the neural data. Chapter 3 presents the results of single-unit and Bayesian decoding analyses from this dataset. We found that activity in the OFC and vStr was quite similar at the single-unit level, and inconsistent with the neuroeconomic account of value signaling in a common currency. Instead, when we looked specifically at moments of deliberative decision-making (as emphasized by the multiple systems account), we found important differences between the OFC and vStr. Both the OFC and the vStr showed covert reward signaling during deliberative, vicarious trial-and-error (VTE) behaviors. But vStr signals emerged earlier, before the moment of choice, while covert reward coding in the OFC appeared after the rats had committed to their decision. These analyses were extended to the level of local field potentials (LFPs), recorded from the same dataset. Local field potentials are a useful tool for studying local processing and interactions between brain regions. Chapter 4 describes the LFP results. Important among these was the finding that the vStr led the OFC at the LFP level (again showing temporal precedence), and furthermore, that the vStr was a stronger driver of OFC activity than vice versa, particularly during VTE. The implications of these results, along with those from the single-unit and Bayesian decoding analyses, are discussed in Chapter 5. Emphasis is placed on our emerging understanding of the role of the vStr in flexible behavior, and how the OFC and the vStr might cooperate to influence value-based choice

Information Processing in the Orbitofrontal Cortex and the Ventral Striatum in Rats Performing an Economic Decision-Making Task

University of Minnesota Ph.D. dissertation. August 2015. Major: Neuroscience. Advisor: David Redish. 1 computer file (PDF); vi, 144 pages.The orbitofrontal cortex (OFC) and ventral striatum (vStr) are key brain structures that represent information about value during decision-making tasks. Despite their very different anatomical properties, numerous studies have found similar patterns of value-related signaling in these structures. In particular, both structures are intimately involved in delay-discounting tasks, which involve a tradeoff between reward magnitude and delay to reward. However, the overlapping activity profiles of these brain regions makes it difficult to tease apart their specific contributions to delay-discounting behavior, and to economic decision-making more generally. In order to better understand the contributions of these two regions to value-based choice, we made simultaneous recordings in the OFC and vStr in rats performing a spatial variant of a traditional delay-discounting task. This allowed us to compare OFC and vStr activity directly in the same subjects while they engaged in a prototypical economic decision-making task, and additionally it allowed us to leverage the tools of spatial decoding analysis to measure non-local reward signaling. Chapter 1 provides an introduction to current theories of OFC and vStr function within the decision-making literature, in particular contrasting the concepts of neuroeconomics with the multiple decision-making systems framework. Chapter 2 describes the methods used in this thesis, including the design of the spatial delay-discounting task and the analysis of the neural data. Chapter 3 presents the results of single-unit and Bayesian decoding analyses from this dataset. We found that activity in the OFC and vStr was quite similar at the single-unit level, and inconsistent with the neuroeconomic account of value signaling in a common currency. Instead, when we looked specifically at moments of deliberative decision-making (as emphasized by the multiple systems account), we found important differences between the OFC and vStr. Both the OFC and the vStr showed covert reward signaling during deliberative, vicarious trial-and-error (VTE) behaviors. But vStr signals emerged earlier, before the moment of choice, while covert reward coding in the OFC appeared after the rats had committed to their decision. These analyses were extended to the level of local field potentials (LFPs), recorded from the same dataset. Local field potentials are a useful tool for studying local processing and interactions between brain regions. Chapter 4 describes the LFP results. Important among these was the finding that the vStr led the OFC at the LFP level (again showing temporal precedence), and furthermore, that the vStr was a stronger driver of OFC activity than vice versa, particularly during VTE. The implications of these results, along with those from the single-unit and Bayesian decoding analyses, are discussed in Chapter 5. Emphasis is placed on our emerging understanding of the role of the vStr in flexible behavior, and how the OFC and the vStr might cooperate to influence value-based choice

Perceptual video quality and quality of experience for adaptive video streaming

We live in a world where images and videos dominate our everyday lives. Every day, an enormous amount of video data is being shared in social media and consumer applications, while video streaming is becoming a new form of digital entertainment. Large-scale video streaming on demand has become possible thanks to numerous engineering achievements in fields such as video compression, high-speed computation and display technologies. Nevertheless, the skyrocketing needs for bandwidth and network resources consumed by video applications challenges modern video content delivery. Since the available bandwidth resources are limited, streaming service providers have to mediate between operation costs, bandwidth efficiency and maximizing user quality of experience. However, these goals are inherently conflicting and require knowledge of how user quality of experience is affected by the network-induced changes in video quality. Being able to understand and predict user quality of experience and perceptually optimize rate allocation, can have significant effects in better network utilization, reduced costs for service providers and improved user satisfaction. The goal of this dissertation is to study and predict user quality of experience in video streaming applications, by exploiting perceptual video quality and human behavioral responses to streaming-related video impairments. To this end, I present the details of three large-scale video subjective studies which target video streaming under multiple viewing conditions, such as display device, session duration, content characteristics and network/buffer conditions. By analyzing how humans react to changes in visual quality and streaming video impairments, I also design numerous video quality and quality of experience prediction models that can be used to evaluate the overall and the continuous-time perceived video quality. Throughout this dissertation, my goal is to perceptually optimize various stages of the video streaming pipeline, such as video encoding and video quality control as well as client-based rate adaptation. Ultimately, I envision that the outcome of this dissertation can be useful for video streaming applications at global scaleElectrical and Computer Engineerin

Will the Conscious–Subconscious Pacing Quagmire Help Elucidate the Mechanisms of Self-Paced Exercise? New Opportunities in Dual Process Theory and Process Tracing Methods

The extent to which athletic pacing decisions are made consciously or subconsciously is a prevailing issue. In this article we discuss why the one-dimensional conscious–subconscious debate that has reigned in the pacing literature has suppressed our understanding of the multidimensional processes that occur in pacing decisions. How do we make our decisions in real-life competitive situations? What information do we use and how do we respond to opponents? These are questions that need to be explored and better understood, using smartly designed experiments. The paper provides clarity about key conscious, preconscious, subconscious and unconscious concepts, terms that have previously been used in conflicting and confusing ways. The potential of dual process theory in articulating multidimensional aspects of intuitive and deliberative decision-making processes is discussed in the context of athletic pacing along with associated process-tracing research methods. In attempting to refine pacing models and improve training strategies and psychological skills for athletes, the dual-process framework could be used to gain a clearer understanding of (1) the situational conditions for which either intuitive or deliberative decisions are optimal; (2) how intuitive and deliberative decisions are biased by things such as perception, emotion and experience; and (3) the underlying cognitive mechanisms such as memory, attention allocation, problem solving and hypothetical thought

SLEEPING WHILE AWAKE: A NEUROPHYSIOLOGICAL INVESTIGATION ON SLEEP DURING WAKEFULNESS.

Il sonno e la veglia vengono comunemente considerati come due stati distinti. L\u2019alternanza tra essi, la cui presenza \ue8 stata dimostrata in ogni specie animale studiata fino ad oggi, sembra essere una delle caratteristiche che definisce la nostra vita. Allo stesso tempo, per\uf2, le scoperte portate alla luce negli ultimi decenni hanno offuscato i confini tra questi due stati. I meccanismi del sonno hanno sempre affascinato i neurofisiologi, che infatti, nell\u2019ultimo secolo, li hanno caratterizzati in dettaglio: ora sappiamo che all\u2019attivit\ue0 del sonno sottost\ue0 una specifica attivit\ue0 neuronale chiamata slow oscillation. La slow oscillation, che \ue8 costituita da (ancora una volta) un\u2019alternanza tra periodi di attivit\ue0 e periodi di iperpolarizzazione e silenzio neuronale (OFF-periods), \ue8 la modalit\ue0 base di attivazione del cervello dormiente. Questa alternanza \ue8 dovuta alla tendenza dei neuroni surante lo stato di sonno, di passare ad un periodo silente dopo un\u2019attivazione iniziale, una tendenza a cui viene dato il nome di bistabilit\ue0 neuronale. Molti studi hanno dimostrato come la bistabilit\ue0 neuronale tipica del sonno ed i relativi OFF-periods, possano accadere anche durante la veglia in particolari condizioni patologiche, nelle transizioni del sonno e durante le deprivazioni di sonno. Per questo motivo, se accettassimo che la bistabilit\ue0 neuronale e gli OFF-periods rappresentino una caratteristica fondamentale del sonno, allora dovremmo ammettere che stiamo assistendo ad un cambio di paradigma: da una prospettiva neurofisiologica il sonno pu\uf2 intrudere nella veglia. In questa tesi ho analizzato i nuovi -fluidi- confini tra sonno e veglia e le possibili implicazioni di questi nel problema della persistenza personale attraverso il tempo. Inoltre, ho studiato le implicazioni cliniche dell\u2019intrusione di sonno nella veglia in pazienti con lesioni cerebrali focali di natura ischemica. In particolare, i miei obiettivi sono stati: 1) Dimostrare come la bistabilit\ue0 neuronale possa essere responsabile della perdita di funzione nei pazienti affetti da ischemia cerebrale e come questo potrebbe avere implicazioni nello studio della patofisiologia dell\u2019ischemia cerebrale e nella sua terapia; 2) Stabilire le basi per un modello di sonno locale presente nella vita di tutti i giorni: la sensazione di sonnolenza. Infatti, essa potrebbe riflettere la presenza di porzioni di corteccia in stato di sonno, ma durante lo stato di veglia; 3) Difendere il criterio biologico di identit\ue0, che troverebbe nell\u2019attivit\ue0 cerebrale la continuit\ue0 necessaria al mantenimento della nostra identit\ue0 nel tempo.Sleep and wakefulness are considered two mutually exclusive states. The alternation between those two states seems to be a defining characteristic of our life, a ubiquitous phenomenon demonstrated in every animal species investigated so far. However, during the last decade, advances in neurophysiology have blurred the boundaries between those states. The mechanisms of sleep have always intrigued neurophysiologists and great advances have been made over the last century in understanding them: we now know that the defining characteristic underlying sleep activity is a specific pattern of neuronal activity, namely the slow oscillation. The slow oscillation, which is characterized by the periodic alternation between periods of activity (ON-periods) and periods of hyperpolarization and neuronal silence (OFF-periods) is the default mode of activity of the sleeping cortex. This alternation is due to the tendency of neurons to fall into a silent period after an initial activation; such tendency is known as \u201cbistability\u201d. There is accumulating evidence that sleep-like bistability, and the ensuing OFF-periods, may occur locally in the awake human brain in some pathological conditions, in sleep transition, as well as after sleep deprivation. Therefore, to the extent that bistability and OFF periods represents the basic neuronal features of sleep, a paradigm shift is in place: from a neurophysiological perspective sleep can intrude into wakefulness. In this thesis, I explore the fluid boundaries between sleep and wakefulness and investigate their possible implications on the problem of personal persistence over time. Moreover, I study the clinical implications of the intrusion of sleep into wakefulness in patients with focal brain injury due to stroke. Specifically, I aim to: 1) show how the sleep-like bistability can be responsible for the loss of function in stroke patients. This may have implications for understanding the pathophysiology of stroke and helping to foster recovery; 2) establish the basis for a model of local sleep that might be present in the everyday life, id est the sensation of sleepiness. Indeed, sleepiness could reflect islands of sleep during wakefulness; 3) advocate the biological criterion of identity, in which the continuity necessary for maintaining ourselves over time could be represented by never resting activity in the brain

A psychophysical study of the neural representation of time by striatal populations

Time is a fundamental dimension of the environment. The ability to estimate the passage of time is essential for both learning and performance of adaptive behavior in natural situations. Yet, how this ability is implemented in the brain is poorly understoo