24,085 research outputs found
SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.
We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is an extension of the SATCHMO algorithm, and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all HMM-HMM scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the PREFAB benchmark dataset show that SATCHMO-JS provides a statistically significant improvement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT), ClustalW and the original SATCHMO algorithm. The SATCHMO-JS webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/
TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences
Abstract Background The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function of an RNA sequence. The most accurate computational methods predict conserved structures for a set of homologous RNA sequences. These methods usually suffer from high computational complexity. In this paper, TurboFold, a novel and efficient method for secondary structure prediction for multiple RNA sequences, is presented. Results TurboFold takes, as input, a set of homologous RNA sequences and outputs estimates of the base pairing probabilities for each sequence. The base pairing probabilities for a sequence are estimated by combining intrinsic information, derived from the sequence itself via the nearest neighbor thermodynamic model, with extrinsic information, derived from the other sequences in the input set. For a given sequence, the extrinsic information is computed by using pairwise-sequence-alignment-based probabilities for co-incidence with each of the other sequences, along with estimated base pairing probabilities, from the previous iteration, for the other sequences. The extrinsic information is introduced as free energy modifications for base pairing in a partition function computation based on the nearest neighbor thermodynamic model. This process yields updated estimates of base pairing probability. The updated base pairing probabilities in turn are used to recompute extrinsic information, resulting in the overall iterative estimation procedure that defines TurboFold. TurboFold is benchmarked on a number of ncRNA datasets and compared against alternative secondary structure prediction methods. The iterative procedure in TurboFold is shown to improve estimates of base pairing probability with each iteration, though only small gains are obtained beyond three iterations. Secondary structures composed of base pairs with estimated probabilities higher than a significance threshold are shown to be more accurate for TurboFold than for alternative methods that estimate base pairing probabilities. TurboFold-MEA, which uses base pairing probabilities from TurboFold in a maximum expected accuracy algorithm for secondary structure prediction, has accuracy comparable to the best performing secondary structure prediction methods. The computational and memory requirements for TurboFold are modest and, in terms of sequence length and number of sequences, scale much more favorably than joint alignment and folding algorithms. Conclusions TurboFold is an iterative probabilistic method for predicting secondary structures for multiple RNA sequences that efficiently and accurately combines the information from the comparative analysis between sequences with the thermodynamic folding model. Unlike most other multi-sequence structure prediction methods, TurboFold does not enforce strict commonality of structures and is therefore useful for predicting structures for homologous sequences that have diverged significantly. TurboFold can be downloaded as part of the RNAstructure package at http://rna.urmc.rochester.edu.</p
Fine-To-Coarse Global Registration of RGB-D Scans
RGB-D scanning of indoor environments is important for many applications,
including real estate, interior design, and virtual reality. However, it is
still challenging to register RGB-D images from a hand-held camera over a long
video sequence into a globally consistent 3D model. Current methods often can
lose tracking or drift and thus fail to reconstruct salient structures in large
environments (e.g., parallel walls in different rooms). To address this
problem, we propose a "fine-to-coarse" global registration algorithm that
leverages robust registrations at finer scales to seed detection and
enforcement of new correspondence and structural constraints at coarser scales.
To test global registration algorithms, we provide a benchmark with 10,401
manually-clicked point correspondences in 25 scenes from the SUN3D dataset.
During experiments with this benchmark, we find that our fine-to-coarse
algorithm registers long RGB-D sequences better than previous methods
Deep Learning Techniques for Music Generation -- A Survey
This paper is a survey and an analysis of different ways of using deep
learning (deep artificial neural networks) to generate musical content. We
propose a methodology based on five dimensions for our analysis:
Objective - What musical content is to be generated? Examples are: melody,
polyphony, accompaniment or counterpoint. - For what destination and for what
use? To be performed by a human(s) (in the case of a musical score), or by a
machine (in the case of an audio file).
Representation - What are the concepts to be manipulated? Examples are:
waveform, spectrogram, note, chord, meter and beat. - What format is to be
used? Examples are: MIDI, piano roll or text. - How will the representation be
encoded? Examples are: scalar, one-hot or many-hot.
Architecture - What type(s) of deep neural network is (are) to be used?
Examples are: feedforward network, recurrent network, autoencoder or generative
adversarial networks.
Challenge - What are the limitations and open challenges? Examples are:
variability, interactivity and creativity.
Strategy - How do we model and control the process of generation? Examples
are: single-step feedforward, iterative feedforward, sampling or input
manipulation.
For each dimension, we conduct a comparative analysis of various models and
techniques and we propose some tentative multidimensional typology. This
typology is bottom-up, based on the analysis of many existing deep-learning
based systems for music generation selected from the relevant literature. These
systems are described and are used to exemplify the various choices of
objective, representation, architecture, challenge and strategy. The last
section includes some discussion and some prospects.Comment: 209 pages. This paper is a simplified version of the book: J.-P.
Briot, G. Hadjeres and F.-D. Pachet, Deep Learning Techniques for Music
Generation, Computational Synthesis and Creative Systems, Springer, 201
Dynamics of the solar chromosphere. V. High-frequency modulation in ultraviolet image sequences from TRACE
We search for signatures of high-frequency oscillations in the upper solar
photosphere and low chromosphere in the context of acoustic heating of outer
stellar atmospheres. We use ultraviolet image sequences of a quiet center-disk
area from the Transition Region and Coronal Explorer (TRACE) mission which were
taken with strict cadence regularity. The latter permits more reliable
high-frequency diagnosis than in earlier work. Spatial Fourier power maps,
spatially averaged coherence and phase-difference spectra, and spatio-temporal
k-f decompositions all contain high-frequency features that at first sight seem
of considerable intrinsic interest but actually are more likely to represent
artifacts of different nature. Spatially averaged phase difference measurement
provides the most sensitive diagnostic and indicates the presence of acoustic
modulation up to f=20 mHz (periods down to 50 seconds) in internetwork areas.Comment: 9 pages, 8 figure
Recent trends, technical concepts and components of computer-assisted orthopedic surgery systems: A comprehensive review
Computer-assisted orthopedic surgery (CAOS) systems have become one of the most important and challenging types of system in clinical orthopedics, as they enable precise treatment of musculoskeletal diseases, employing modern clinical navigation systems and surgical tools. This paper brings a comprehensive review of recent trends and possibilities of CAOS systems. There are three types of the surgical planning systems, including: systems based on the volumetric images (computer tomography (CT), magnetic resonance imaging (MRI) or ultrasound images), further systems utilize either 2D or 3D fluoroscopic images, and the last one utilizes the kinetic information about the joints and morphological information about the target bones. This complex review is focused on three fundamental aspects of CAOS systems: their essential components, types of CAOS systems, and mechanical tools used in CAOS systems. In this review, we also outline the possibilities for using ultrasound computer-assisted orthopedic surgery (UCAOS) systems as an alternative to conventionally used CAOS systems.Web of Science1923art. no. 519
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