@inproceedings{2272,
abstract = {We consider Conditional Random Fields (CRFs) with pattern-based potentials defined on a chain. In this model the energy of a string (labeling) x1...xn is the sum of terms over intervals [i,j] where each term is non-zero only if the substring xi...xj equals a prespecified pattern α. Such CRFs can be naturally applied to many sequence tagging problems.
We present efficient algorithms for the three standard inference tasks in a CRF, namely computing (i) the partition function, (ii) marginals, and (iii) computing the MAP. Their complexities are respectively O(nL), O(nLℓmax) and O(nLmin{|D|,log(ℓmax+1)}) where L is the combined length of input patterns, ℓmax is the maximum length of a pattern, and D is the input alphabet. This improves on the previous algorithms of (Ye et al., 2009) whose complexities are respectively O(nL|D|), O(n|Γ|L2ℓ2max) and O(nL|D|), where |Γ| is the number of input patterns.
In addition, we give an efficient algorithm for sampling. Finally, we consider the case of non-positive weights. (Komodakis & Paragios, 2009) gave an O(nL) algorithm for computing the MAP. We present a modification that has the same worst-case complexity but can beat it in the best case. },
author = {Takhanov, Rustem and Kolmogorov, Vladimir},
booktitle = {ICML'13 Proceedings of the 30th International Conference on International},
location = {Atlanta, GA, USA},
number = {3},
pages = {145 -- 153},
publisher = {International Machine Learning Society},
title = {{Inference algorithms for pattern-based CRFs on sequence data}},
volume = {28},
year = {2013},
}
@article{2277,
abstract = {Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible.},
author = {Simmons, Kristina and Prentice, Jason and Tkacik, Gasper and Homann, Jan and Yee, Heather and Palmer, Stephanie and Nelson, Philip and Balasubramanian, Vijay},
journal = {PLoS Computational Biology},
number = {12},
publisher = {Public Library of Science},
title = {{Transformation of stimulus correlations by the retina}},
doi = {10.1371/journal.pcbi.1003344},
volume = {9},
year = {2013},
}
@inproceedings{2518,
abstract = {A class of valued constraint satisfaction problems (VCSPs) is characterised by a valued constraint language, a fixed set of cost functions on a finite domain. An instance of the problem is specified by a sum of cost functions from the language with the goal to minimise the sum. We study which classes of finite-valued languages can be solved exactly by the basic linear programming relaxation (BLP). Thapper and Živný showed [20] that if BLP solves the language then the language admits a binary commutative fractional polymorphism. We prove that the converse is also true. This leads to a necessary and a sufficient condition which can be checked in polynomial time for a given language. In contrast, the previous necessary and sufficient condition due to [20] involved infinitely many inequalities. More recently, Thapper and Živný [21] showed (using, in particular, a technique introduced in this paper) that core languages that do not satisfy our condition are NP-hard. Taken together, these results imply that a finite-valued language can either be solved using Linear Programming or is NP-hard.},
author = {Kolmogorov, Vladimir},
location = {Riga, Latvia},
number = {1},
pages = {625 -- 636},
publisher = {Springer},
title = {{The power of linear programming for finite-valued CSPs: A constructive characterization}},
doi = {10.1007/978-3-642-39206-1_53},
volume = {7965},
year = {2013},
}
@inproceedings{2520,
abstract = {We propose a probabilistic model to infer supervised latent variables in
the Hamming space from observed data. Our model allows simultaneous
inference of the number of binary latent variables, and their values. The
latent variables preserve neighbourhood structure of the data in a sense
that objects in the same semantic concept have similar latent values, and
objects in different concepts have dissimilar latent values. We formulate
the supervised infinite latent variable problem based on an intuitive
principle of pulling objects together if they are of the same type, and
pushing them apart if they are not. We then combine this principle with a
flexible Indian Buffet Process prior on the latent variables. We show that
the inferred supervised latent variables can be directly used to perform a
nearest neighbour search for the purpose of retrieval. We introduce a new
application of dynamically extending hash codes, and show how to
effectively couple the structure of the hash codes with continuously
growing structure of the neighbourhood preserving infinite latent feature
space.},
author = {Quadrianto, Novi and Sharmanska, Viktoriia and Knowles, David and Ghahramani, Zoubin},
booktitle = {Proceedings of the 29th conference uncertainty in Artificial Intelligence},
isbn = {9780974903996},
location = {Bellevue, WA, United States},
pages = {527 -- 536},
publisher = {AUAI Press},
title = {{The supervised IBP: Neighbourhood preserving infinite latent feature models}},
year = {2013},
}
@article{2448,
abstract = {Cell-to-cell directional flow of the phytohormone auxin is primarily established by polar localization of the PIN auxin transporters, a process tightly regulated at multiple levels by auxin itself. We recently reported that, in the context of strong auxin flows, activity of the vacuolar ZIFL1.1 transporter is required for fine-tuning of polar auxin transport rates in the Arabidopsis root. In particular, ZIFL1.1 function protects plasma-membrane stability of the PIN2 carrier in epidermal root tip cells under conditions normally triggering PIN2 degradation. Here, we show that ZIFL1.1 activity at the root tip also promotes PIN1 plasma-membrane abundance in central cylinder cells, thus supporting the notion that ZIFL1.1 acts as a general positive modulator of polar auxin transport in roots.},
author = {Remy, Estelle and Baster, Pawel and Friml, Jirí and Duque, Paula},
journal = {Plant Signaling & Behavior},
number = {10},
publisher = {Landes Bioscience},
title = {{ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip}},
doi = {10.4161/psb.25688},
volume = {8},
year = {2013},
}