9,859 research outputs found
Structured Prediction of Sequences and Trees using Infinite Contexts
Linguistic structures exhibit a rich array of global phenomena, however
commonly used Markov models are unable to adequately describe these phenomena
due to their strong locality assumptions. We propose a novel hierarchical model
for structured prediction over sequences and trees which exploits global
context by conditioning each generation decision on an unbounded context of
prior decisions. This builds on the success of Markov models but without
imposing a fixed bound in order to better represent global phenomena. To
facilitate learning of this large and unbounded model, we use a hierarchical
Pitman-Yor process prior which provides a recursive form of smoothing. We
propose prediction algorithms based on A* and Markov Chain Monte Carlo
sampling. Empirical results demonstrate the potential of our model compared to
baseline finite-context Markov models on part-of-speech tagging and syntactic
parsing
Machine learning-guided directed evolution for protein engineering
Machine learning (ML)-guided directed evolution is a new paradigm for
biological design that enables optimization of complex functions. ML methods
use data to predict how sequence maps to function without requiring a detailed
model of the underlying physics or biological pathways. To demonstrate
ML-guided directed evolution, we introduce the steps required to build ML
sequence-function models and use them to guide engineering, making
recommendations at each stage. This review covers basic concepts relevant to
using ML for protein engineering as well as the current literature and
applications of this new engineering paradigm. ML methods accelerate directed
evolution by learning from information contained in all measured variants and
using that information to select sequences that are likely to be improved. We
then provide two case studies that demonstrate the ML-guided directed evolution
process. We also look to future opportunities where ML will enable discovery of
new protein functions and uncover the relationship between protein sequence and
function.Comment: Made significant revisions to focus on aspects most relevant to
applying machine learning to speed up directed evolutio
Socially Constrained Structural Learning for Groups Detection in Crowd
Modern crowd theories agree that collective behavior is the result of the
underlying interactions among small groups of individuals. In this work, we
propose a novel algorithm for detecting social groups in crowds by means of a
Correlation Clustering procedure on people trajectories. The affinity between
crowd members is learned through an online formulation of the Structural SVM
framework and a set of specifically designed features characterizing both their
physical and social identity, inspired by Proxemic theory, Granger causality,
DTW and Heat-maps. To adhere to sociological observations, we introduce a loss
function (G-MITRE) able to deal with the complexity of evaluating group
detection performances. We show our algorithm achieves state-of-the-art results
when relying on both ground truth trajectories and tracklets previously
extracted by available detector/tracker systems
Retrieving the structure of probabilistic sequences of auditory stimuli from EEG data
Using a new probabilistic approach we model the relationship between
sequences of auditory stimuli generated by stochastic chains and the
electroencephalographic (EEG) data acquired while 19 participants were exposed
to those stimuli. The structure of the chains generating the stimuli are
characterized by rooted and labeled trees whose leaves, henceforth called
contexts, represent the sequences of past stimuli governing the choice of the
next stimulus. A classical conjecture claims that the brain assigns
probabilistic models to samples of stimuli. If this is true, then the context
tree generating the sequence of stimuli should be encoded in the brain
activity. Using an innovative statistical procedure we show that this context
tree can effectively be extracted from the EEG data, thus giving support to the
classical conjecture.Comment: 16 pages, 7 figure
The Origins of Computational Mechanics: A Brief Intellectual History and Several Clarifications
The principle goal of computational mechanics is to define pattern and
structure so that the organization of complex systems can be detected and
quantified. Computational mechanics developed from efforts in the 1970s and
early 1980s to identify strange attractors as the mechanism driving weak fluid
turbulence via the method of reconstructing attractor geometry from measurement
time series and in the mid-1980s to estimate equations of motion directly from
complex time series. In providing a mathematical and operational definition of
structure it addressed weaknesses of these early approaches to discovering
patterns in natural systems.
Since then, computational mechanics has led to a range of results from
theoretical physics and nonlinear mathematics to diverse applications---from
closed-form analysis of Markov and non-Markov stochastic processes that are
ergodic or nonergodic and their measures of information and intrinsic
computation to complex materials and deterministic chaos and intelligence in
Maxwellian demons to quantum compression of classical processes and the
evolution of computation and language.
This brief review clarifies several misunderstandings and addresses concerns
recently raised regarding early works in the field (1980s). We show that
misguided evaluations of the contributions of computational mechanics are
groundless and stem from a lack of familiarity with its basic goals and from a
failure to consider its historical context. For all practical purposes, its
modern methods and results largely supersede the early works. This not only
renders recent criticism moot and shows the solid ground on which computational
mechanics stands but, most importantly, shows the significant progress achieved
over three decades and points to the many intriguing and outstanding challenges
in understanding the computational nature of complex dynamic systems.Comment: 11 pages, 123 citations;
http://csc.ucdavis.edu/~cmg/compmech/pubs/cmr.ht
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