Descriptive Simulation: Combining Symbolic and Numerical Methods in the Analysis of Chemical Reaction Mechanisms

The Kineticist's Workbench is a computer program currently under development whose purpose is to help chemists understand, analyze, and simplify complex chemical reaction mechanisms. This paper discusses one module of the program that numerically simulates mechanisms and constructs qualitative descriptions of the simulation results. These descriptions are given in terms that are meaningful to the working chemist (e.g., steady states, stable oscillations, and so on); and the descriptions (as well as the data structures used to construct them) are accessible as input to other programs.

The Role of Chemical Mechanisms in Neural Computation and Learning

Most computational models of neurons assume that their electrical characteristics are of paramount importance. However, all long-term changes in synaptic efficacy, as well as many short-term effects, are mediated by chemical mechanisms. This technical report explores the interaction between electrical and chemical mechanisms in neural learning and development. Two neural systems that exemplify this interaction are described and modelled. The first is the mechanisms underlying habituation, sensitization, and associative learning in the gill withdrawal reflex circuit in Aplysia, a marine snail. The second is the formation of retinotopic projections in the early visual pathway during embryonic development.

Hypothesizing Device Mechanisms: Opening Up the Black Box

I describe an approach to forming hypotheses about hidden mechanism configurations within devices given external observations and a vocabulary of primitive mechanisms. An implemented causal modelling system called JACK constructs explanations for why a second piece of toast comes out lighter, why the slide in a tire gauge does not slip back inside when the gauge is removed from the tire, and how in a refrigerator a single substance can serve as a heat sink for the interior and a heat source for the exterior. I report the number of hypotheses admitted for each device example, and provide empirical results which isolate the pruning power due to different constraint sources.

Thread Scheduling Mechanisms for Multiple-Context Parallel Processors

Scheduling tasks to efficiently use the available processor resources is crucial to minimizing the runtime of applications on shared-memory parallel processors. One factor that contributes to poor processor utilization is the idle time caused by long latency operations, such as remote memory references or processor synchronization operations. One way of tolerating this latency is to use a processor with multiple hardware contexts that can rapidly switch to executing another thread of computation whenever a long latency operation occurs, thus increasing processor utilization by overlapping computation with communication. Although multiple contexts are effective for tolerating latency, this effectiveness can be limited by memory and network bandwidth, by cache interference effects among the multiple contexts, and by critical tasks sharing processor resources with less critical tasks. This thesis presents techniques that increase the effectiveness of multiple contexts by intelligently scheduling threads to make more efficient use of processor pipeline, bandwidth, and cache resources. This thesis proposes thread prioritization as a fundamental mechanism for directing the thread schedule on a multiple-context processor. A priority is assigned to each thread either statically or dynamically and is used by the thread scheduler to decide which threads to load in the contexts, and to decide which context to switch to on a context switch. We develop a multiple-context model that integrates both cache and network effects, and shows how thread prioritization can both maintain high processor utilization, and limit increases in critical path runtime caused by multithreading. The model also shows that in order to be effective in bandwidth limited applications, thread prioritization must be extended to prioritize memory requests. We show how simple hardware can prioritize the running of threads in the multiple contexts, and the issuing of requests to both the local memory and the network. Simulation experiments show how thread prioritization is used in a variety of applications. Thread prioritization can improve the performance of synchronization primitives by minimizing the number of processor cycles wasted in spinning and devoting more cycles to critical threads. Thread prioritization can be used in combination with other techniques to improve cache performance and minimize cache interference between different working sets in the cache. For applications that are critical path limited, thread prioritization can improve performance by allowing processor resources to be devoted preferentially to critical threads. These experimental results show that thread prioritization is a mechanism that can be used to implement a wide range of scheduling policies.

Observations on Cortical Mechanisms for Object Recognition andsLearning

This paper sketches a hypothetical cortical architecture for visual 3D object recognition based on a recent computational model. The view-centered scheme relies on modules for learning from examples, such as Hyperbf-like networks. Such models capture a class of explanations we call Memory-Based Models (MBM) that contains sparse population coding, memory-based recognition, and codebooks of prototypes. Unlike the sigmoidal units of some artificial neural networks, the units of MBMs are consistent with the description of cortical neurons. We describe how an example of MBM may be realized in terms of cortical circuitry and biophysical mechanisms, consistent with psychophysical and physiological data.

Role of Low-level Mechanisms in Brightness Perception

Brightness judgments are a key part of the primate brain's visual analysis of the environment. There is general consensus that the perceived brightness of an image region is based not only on its actual luminance, but also on the photometric structure of its neighborhood. However, it is unclear precisely how a region's context influences its perceived brightness. Recent research has suggested that brightness estimation may be based on a sophisticated analysis of scene layout in terms of transparency, illumination and shadows. This work has called into question the role of low-level mechanisms, such as lateral inhibition, as explanations for brightness phenomena. Here we describe experiments with displays for which low-level and high-level analyses make qualitatively different predictions, and with which we can quantitatively assess the trade-offs between low-level and high-level factors. We find that brightness percepts in these displays are governed by low-level stimulus properties, even when these percepts are inconsistent with higher-level interpretations of scene layout. These results point to the important role of low-level mechanisms in determining brightness percepts.

Exact Solution of the Nonlinear Dynamics of Recurrent Neural Mechanisms for Direction Selectivity

Different theoretical models have tried to investigate the feasibility of recurrent neural mechanisms for achieving direction selectivity in the visual cortex. The mathematical analysis of such models has been restricted so far to the case of purely linear networks. We present an exact analytical solution of the nonlinear dynamics of a class of direction selective recurrent neural models with threshold nonlinearity. Our mathematical analysis shows that such networks have form-stable stimulus-locked traveling pulse solutions that are appropriate for modeling the responses of direction selective cortical neurons. Our analysis shows also that the stability of such solutions can break down giving raise to a different class of solutions ("lurching activity waves") that are characterized by a specific spatio-temporal periodicity. These solutions cannot arise in models for direction selectivity with purely linear spatio-temporal filtering.

The Kineticist's Workbench: Combining Symbolic and Numerical Methods in the Simulation of Chemical Reaction Mechanisms

The Kineticist's Workbench is a program that simulates chemical reaction mechanisms by predicting, generating, and interpreting numerical data. Prior to simulation, it analyzes a given mechanism to predict that mechanism's behavior; it then simulates the mechanism numerically; and afterward, it interprets and summarizes the data it has generated. In performing these tasks, the Workbench uses a variety of techniques: graph- theoretic algorithms (for analyzing mechanisms), traditional numerical simulation methods, and algorithms that examine simulation results and reinterpret them in qualitative terms. The Workbench thus serves as a prototype for a new class of scientific computational tools---tools that provide symbiotic collaborations between qualitative and quantitative methods.