684 research outputs found
Randomized benchmarking of single and multi-qubit control in liquid-state NMR quantum information processing
Being able to quantify the level of coherent control in a proposed device
implementing a quantum information processor (QIP) is an important task for
both comparing different devices and assessing a device's prospects with
regards to achieving fault-tolerant quantum control. We implement in a
liquid-state nuclear magnetic resonance QIP the randomized benchmarking
protocol presented by Knill et al (PRA 77: 012307 (2008)). We report an error
per randomized pulse of with a
single qubit QIP and show an experimentally relevant error model where the
randomized benchmarking gives a signature fidelity decay which is not possible
to interpret as a single error per gate. We explore and experimentally
investigate multi-qubit extensions of this protocol and report an average error
rate for one and two qubit gates of for a three
qubit QIP. We estimate that these error rates are still not decoherence limited
and thus can be improved with modifications to the control hardware and
software.Comment: 10 pages, 6 figures, submitted versio
13 Genotype, disease severity, and healthcare resource use by patients with CF in the UK National Health Service
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Systematic evaluation of spliced alignment programs for RNA-seq data
High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence. To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets. In total, we compared 26 mapping protocols based on 11 programs and pipelines and found major performance differences between methods on numerous benchmarks, including alignment yield, basewise accuracy, mismatch and gap placement, exon junction discovery and suitability of alignments for transcript reconstruction. We observed concordant results on real and simulated RNA-seq data, confirming the relevance of the metrics employed. Future developments in RNA-seq alignment methods would benefit from improved placement of multimapped reads, balanced utilization of existing gene annotation and a reduced false discovery rate for splice junctions
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment
BACKGROUND: This study analyzes the predictions of a number of promoter predictors on the ENCODE regions of the human genome as part of the ENCODE Genome Annotation Assessment Project (EGASP). The systems analyzed operate on various principles and we assessed the effectiveness of different conceptual strategies used to correlate produced promoter predictions with the manually annotated 5' gene ends. RESULTS: The predictions were assessed relative to the manual HAVANA annotation of the 5' gene ends. These 5' gene ends were used as the estimated reference transcription start sites. With the maximum allowed distance for predictions of 1,000 nucleotides from the reference transcription start sites, the sensitivity of predictors was in the range 32% to 56%, while the positive predictive value was in the range 79% to 93%. The average distance mismatch of predictions from the reference transcription start sites was in the range 259 to 305 nucleotides. At the same time, using transcription start site estimates from DBTSS and H-Invitational databases as promoter predictions, we obtained a sensitivity of 58%, a positive predictive value of 92%, and an average distance from the annotated transcription start sites of 117 nucleotides. In this experiment, the best performing promoter predictors were those that combined promoter prediction with gene prediction. The main reason for this is the reduced promoter search space that resulted in smaller numbers of false positive predictions. CONCLUSION: The main finding, now supported by comprehensive data, is that the accuracy of human promoter predictors for high-throughput annotation purposes can be significantly improved if promoter prediction is combined with gene prediction. Based on the lessons learned in this experiment, we propose a framework for the preparation of the next similar promoter prediction assessment
Tema Con Variazioni: Quantum Channel Capacity
Channel capacity describes the size of the nearly ideal channels, which can
be obtained from many uses of a given channel, using an optimal error
correcting code. In this paper we collect and compare minor and major
variations in the mathematically precise statements of this idea which have
been put forward in the literature. We show that all the variations considered
lead to equivalent capacity definitions. In particular, it makes no difference
whether one requires mean or maximal errors to go to zero, and it makes no
difference whether errors are required to vanish for any sequence of block
sizes compatible with the rate, or only for one infinite sequence.Comment: 32 pages, uses iopart.cl
Quantum state merging and negative information
We consider a quantum state shared between many distant locations, and define
a quantum information processing primitive, state merging, that optimally
merges the state into one location. As announced in [Horodecki, Oppenheim,
Winter, Nature 436, 673 (2005)], the optimal entanglement cost of this task is
the conditional entropy if classical communication is free. Since this quantity
can be negative, and the state merging rate measures partial quantum
information, we find that quantum information can be negative. The classical
communication rate also has a minimum rate: a certain quantum mutual
information. State merging enabled one to solve a number of open problems:
distributed quantum data compression, quantum coding with side information at
the decoder and sender, multi-party entanglement of assistance, and the
capacity of the quantum multiple access channel. It also provides an
operational proof of strong subadditivity. Here, we give precise definitions
and prove these results rigorously.Comment: 23 pages, 3 figure
Efficient and feasible state tomography of quantum many-body systems
We present a novel method to perform quantum state tomography for
many-particle systems which are particularly suitable for estimating states in
lattice systems such as of ultra-cold atoms in optical lattices. We show that
the need for measuring a tomographically complete set of observables can be
overcome by letting the state evolve under some suitably chosen random circuits
followed by the measurement of a single observable. We generalize known results
about the approximation of unitary 2-designs, i.e., certain classes of random
unitary matrices, by random quantum circuits and connect our findings to the
theory of quantum compressed sensing. We show that for ultra-cold atoms in
optical lattices established techniques like optical super-lattices, laser
speckles, and time-of-flight measurements are sufficient to perform fully
certified, assumption-free tomography. Combining our approach with tensor
network methods - in particular the theory of matrix-product states - we
identify situations where the effort of reconstruction is even constant in the
number of lattice sites, allowing in principle to perform tomography on
large-scale systems readily available in present experiments.Comment: 10 pages, 3 figures, minor corrections, discussion added, emphasizing
that no single-site addressing is needed at any stage of the scheme when
implemented in optical lattice system
Quantum heuristic algorithm for traveling salesman problem
We propose a quantum heuristic algorithm to solve a traveling salesman
problem by generalizing Grover search. Sufficient conditions are derived to
greatly enhance the probability of finding the tours with extremal costs,
reaching almost to unity and they are shown characterized by statistical
properties of tour costs. In particular for a Gaussian distribution of the
tours along the cost we show that the quantum algorithm exhibits the quadratic
speedup of its classical counterpart, similarly to Grover search.Comment: Published versio
Counterexamples to additivity of minimum output p-Renyi entropy for p close to 0
Complementing recent progress on the additivity conjecture of quantum
information theory, showing that the minimum output p-Renyi entropies of
channels are not generally additive for p>1, we demonstrate here by a careful
random selection argument that also at p=0, and consequently for sufficiently
small p, there exist counterexamples.
An explicit construction of two channels from 4 to 3 dimensions is given,
which have non-multiplicative minimum output rank; for this pair of channels,
numerics strongly suggest that the p-Renyi entropy is non-additive for all p <
0.11. We conjecture however that violations of additivity exist for all p<1.Comment: 7 pages, revtex4; v2 added correct ref. [15]; v3 has more information
on the numerical violation as well as 1 figure (2 graphs) - note that the
explicit example was changed and the more conservative estimate of the bound
up to which violations occur, additionally some other small issues are
straightened ou
A Generalization of Quantum Stein's Lemma
We present a generalization of quantum Stein's Lemma to the situation in
which the alternative hypothesis is formed by a family of states, which can
moreover be non-i.i.d.. We consider sets of states which satisfy a few natural
properties, the most important being the closedness under permutations of the
copies. We then determine the error rate function in a very similar fashion to
quantum Stein's Lemma, in terms of the quantum relative entropy.
Our result has two applications to entanglement theory. First it gives an
operational meaning to an entanglement measure known as regularized relative
entropy of entanglement. Second, it shows that this measure is faithful, being
strictly positive on every entangled state. This implies, in particular, that
whenever a multipartite state can be asymptotically converted into another
entangled state by local operations and classical communication, the rate of
conversion must be non-zero. Therefore, the operational definition of
multipartite entanglement is equivalent to its mathematical definition.Comment: 30 pages. (see posting by M. Piani arXiv:0904.2705 for a different
proof of the strict positiveness of the regularized relative entropy of
entanglement on every entangled state). published version
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