900 research outputs found
WordRank: Learning Word Embeddings via Robust Ranking
Embedding words in a vector space has gained a lot of attention in recent
years. While state-of-the-art methods provide efficient computation of word
similarities via a low-dimensional matrix embedding, their motivation is often
left unclear. In this paper, we argue that word embedding can be naturally
viewed as a ranking problem due to the ranking nature of the evaluation
metrics. Then, based on this insight, we propose a novel framework WordRank
that efficiently estimates word representations via robust ranking, in which
the attention mechanism and robustness to noise are readily achieved via the
DCG-like ranking losses. The performance of WordRank is measured in word
similarity and word analogy benchmarks, and the results are compared to the
state-of-the-art word embedding techniques. Our algorithm is very competitive
to the state-of-the- arts on large corpora, while outperforms them by a
significant margin when the training set is limited (i.e., sparse and noisy).
With 17 million tokens, WordRank performs almost as well as existing methods
using 7.2 billion tokens on a popular word similarity benchmark. Our multi-node
distributed implementation of WordRank is publicly available for general usage.Comment: Conference on Empirical Methods in Natural Language Processing
(EMNLP), November 1-5, 2016, Austin, Texas, US
Partitioning a graph into degenerate subgraphs
Let be a connected graph with maximum degree distinct
from . Given integers and , is
said to be -partitionable if there exists a partition of
into sets~ such that is -degenerate for
. In this paper, we prove that we can find a -partition of in -time whenever and . This generalizes a result of Bonamy
et al. (MFCS, 2017) and can be viewed as an algorithmic extension of Brooks'
theorem and several results on vertex arboricity of graphs of bounded maximum
degree.
We also prove that deciding whether is -partitionable is
-complete for every and pairs of non-negative integers
such that and . This resolves an
open problem of Bonamy et al. (manuscript, 2017). Combined with results of
Borodin, Kostochka and Toft (\emph{Discrete Mathematics}, 2000), Yang and Yuan
(\emph{Discrete Mathematics}, 2006) and Wu, Yuan and Zhao (\emph{Journal of
Mathematical Study}, 1996), it also settles the complexity of deciding whether
a graph with bounded maximum degree can be partitioned into two subgraphs of
prescribed degeneracy.Comment: 16 pages; minor revisio
Connecting the Cytoskeleton to the Endoplasmic Reticulum and Golgi
A tendency in cell biology is to divide and conquer. For example, decades of painstaking work have led to an understanding of endoplasmic reticulum (ER) and Golgi structure, dynamics, and transport. In parallel, cytoskeletal researchers have revealed a fantastic diversity of structure and cellular function in both actin and microtubules. Increasingly, these areas overlap, necessitating an understanding of both organelle and cytoskeletal biology. This review addresses connections between the actin/microtubule cytoskeletons and organelles in animal cells, focusing on three key areas: ER structure and function; ER-to-Golgi transport; and Golgi structure and function. Making these connections has been challenging for several reasons: the small sizes and dynamic characteristics of some components; the fact that organelle-specific cytoskeletal elements can easily be obscured by more abundant cytoskeletal structures; and the difficulties in imaging membranes and cytoskeleton simultaneously, especially at the ultrastructural level. One major concept is that the cytoskeleton is frequently used to generate force for membrane movement, with two potential consequences: translocation of the organelle, or deformation of the organelle membrane. While initially discussing issues common to metazoan cells in general, we subsequently highlight specific features of neurons, since these highly polarized cells present unique challenges for organellar distribution and dynamics
Novel Roles for Actin in Mitochondrial Fission
Mitochondrial dynamics, including fusion, fission and translocation, are crucial to cellular homeostasis, with roles in cellular polarity, stress response and apoptosis. Mitochondrial fission has received particular attention, owing to links with several neurodegenerative diseases. A central player in fission is the cytoplasmic dynamin-related GTPase Drp1, which oligomerizes at the fission site and hydrolyzes GTP to drive membrane ingression. Drp1 recruitment to the outer mitochondrial membrane (OMM) is a key regulatory event, which appears to require a pre-constriction step in which the endoplasmic reticulum (ER) and mitochondrion interact extensively, a process termed ERMD (ER-associated mitochondrial division). It is unclear how ER-mitochondrial contact generates the force required for pre-constriction or why pre-constriction leads to Drp1 recruitment. Recent results, however, show that ERMD might be an actin-based process in mammals that requires the ER-associated formin INF2 upstream of Drp1, and that myosin II and other actin-binding proteins might be involved. In this Commentary, we present a mechanistic model for mitochondrial fission in which actin and myosin contribute in two ways; firstly, by supplying the force for pre-constriction and secondly, by serving as a coincidence detector for Drp1 binding. In addition, we discuss the possibility that multiple fission mechanisms exist in mammals
Bayesian Forecasting of US Growth using Basic Time Varying Parameter Models and Expectations Data
__Abstract__
Time varying patterns in US growth are analyzed using various univariate model structures, starting from a naive model structure where all features change every period to a model where the slow variation in the conditional mean and changes in the conditional variance are specified together with their interaction, including survey data on expected growth in order to strengthen the information in the model. Use is made of a simulation based Bayesian inferential method to determine the forecasting performance of the various model specifications. The extension of a basic growth model with a constant mean to models including time variation in the mean and variance requires careful investigation of possible identification issues of the parameters and existence conditions of the posterior under a diffuse prior. The use of diffuse priors leads to a focus on the likelihood fu nction and it enables a researcher and policy adviser to evaluate the scientific information contained in model and data. Empirical results indicate that incorporating time variation in mean growth rates as well as in volatility are important in order to improve for the predictive performances of growth models. Furthermore, using data information on growth expectations is important for forecasting growth in specific periods, such as the the recession periods around 2000s and around 2008
Incorporation of a sequential BMP-2/BMP-7 delivery system into chitosan-based scaffolds for bone tissue engineering
The aim of this study was to develop a 3-D construct carrying an inherent sequential growth factor
delivery system. Poly(lactic acid-co-glycolic acid) (PLGA) nanocapsules loaded with bone morphogenetic
protein BMP-2 and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) nanocapsules loaded with
BMP-7 made the early release of BMP-2 and longer term release of BMP-7 possible. 3-D fiber mesh
scaffolds were prepared from chitosan and from chitosan–PEO by wet spinning. Chitosan of 4%
concentration in 2% acetic acid (CHI4–HAc2) and chitosan (4%) and PEO (2%) in 5% acetic acid (CHI4–
PEO2–HAc5) yielded scaffolds with smooth and rough fiber surfaces, respectively. These scaffolds were
seeded with rat bone marrow mesenchymal stem cells (MSCs). When there were no nanoparticles the
initial differentiation rate was higher on (CHI4–HAc2) scaffolds but by three weeks both the scaffolds had
similar alkaline phosphatase (ALP) levels. The cell numbers were also comparable by the end of the third
week. Incorporation of nanoparticles into the scaffolds was achieved by two different methods: incorporation
within the scaffold fibers (NP–IN) and on the fibers (NP–ON). It was shown that incorporation
on the CHI4–HAc2 fibers (NP–ON) prevented the burst release observed with the free nanoparticles, but
this did not influence the total amount released in 25 days. However NP–IN for the same fibers revealed
a much slower rate of release; ca. 70% released at the end of incubation period. The effect of single,
simultaneous and sequential delivery of BMP-2 and BMP-7 from the CHI4–HAc2 scaffolds was studied in
vitro using samples prepared with both incorporation methods. The effect of delivered agents was higher
with the NP–ON samples. Delivery of BMP-2 alone suppressed cell proliferation while providing higher
ALP activity compared to BMP-7. Simultaneous delivery was not particularly effective on cell numbers
and ALP activity. The sequential delivery of BMP-2 and BMP-7, on the other hand, led to the highest ALP
activity per cell (while suppressing proliferation) indicating the synergistic effect of using both growth
factors holds promise for the production of tissue engineered bone.This project was conducted within the scope of the EU FP6 NoE Project Expertissues (NMP3-CT-2004-500283). We acknowledge the support to PY through the same project in the form of an integrated PhD grant. We also would like to acknowledge the support from Scientific and Technical Research Council of Turkey (TUBITAK) through project METUNANOBIOMAT (TBAG 105T508)
Effect of scaffold architecture and BMP-2/BMP-7 delivery on in vitro bone regeneration
The aim of this study was to develop 3-D tissue engineered constructs that mimic the in vivo conditions through a self-contained growth factor delivery system. A set of nanoparticles providing the release of BMP-2 initially followed by the release of BMP-7 were incorporated in poly(ε-caprolactone) scaffolds with different 3-D architectures produced by 3-D plotting and wet spinning. The release patterns were: each growth factor alone, simultaneous, and sequential. The orientation of the fibers did not have a significant effect on the kinetics of release of the model protein BSA; but affected proliferation of bone marrow mesenchymal stem cells. Cell proliferation on random scaffolds was significantly higher compared to the oriented ones. Delivery of BMP-2 alone suppressed MSC proliferation and increased the ALP activity to a higher level than that with BMP-7 delivery. Proliferation rate was suppressed the most by the sequential delivery of the two growth factors from the random scaffold on which the ALP activity was the highest. Results indicated the distinct effect of scaffold architecture and the mode of growth factor delivery on the proliferation and osteogenic differentiation of MSCs, enabling us to design multifunctional scaffolds capable of controlling bone healing.This project was conducted within the scope of the EU FP6 NoE Project Expertissues (NMP3-CT-2004-500283). We acknowledge the support to PY through the same project in the form of an integrated PhD grant. We also would like to acknowledge the support from Scientific and Technical Research Council of Turkey (TUBITAK) through project METUNANOBIOMAT (TBAG 105T508)
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