654791
An image signature for any kind of image
We describe an algorithm for computing an image signature, suitable for first-stage screening for duplicate images. Our signature relies on the relative brightness of image regions, and is generally applicable to photographs, text documents, and line art. We give experimental results on the sensitivity and robustness of signatures for actual image collections, and also results on the robustness of signatures under transformations such as resizing, rescanning, and compression.
2216158
Automatic Quality Assessment of Peptide Tandem Mass Spectra
MOTIVATION
A powerful proteomics methodology couples high-performance liquid chromatography (HPLC) with tandem mass spectrometry and database-search software, such as SEQUEST. Such a set-up, however, produces a large number of spectra, many of which are of too poor quality to be useful. Hence a filter that eliminates poor spectra before the database search can significantly improve throughput and robustness. Moreover, spectra judged to be of high quality, but that cannot be identified by database search, are prime candidates for still more computationally intensive methods, such as de novo sequencing or wider database searches including post-translational modifications.


RESULTS
We report on two different approaches to assessing spectral quality prior to identification: binary classification, which predicts whether or not SEQUEST will be able to make an identification, and statistical regression, which predicts a more universal quality metric involving the number of b- and y-ion peaks. The best of our binary classifiers can eliminate over 75% of the unidentifiable spectra while losing only 10% of the identifiable spectra. Statistical regression can pick out spectra of modified peptides that can be identified by a de novo program but not by SEQUEST. In a section of independent interest, we discuss intensity normalization of mass spectra.
46268673
EigenMS: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning
We report on a new de novo peptide sequencing algorithm that uses spectral graph partitioning. In this approach, relationships between m/z peaks are represented by attractive and repulsive springs, and the vibrational modes of the spring system are used to infer information about the peaks (such as “likely b-ion” or “likely y-ion”). We demonstrate the effectiveness of this approach by comparison with other de novo sequencers on test sets of ion-trap and QTOF spectra, including spectra of mixtures of peptides. On all data sets we outperform the other sequencers. Along with spectral graph theory techniques, EigenMS incorporates another improvement of independent interest: robust statistical methods for recalibration of time-of-flight mass measurements. Robust recalibration greatly outperforms simple least-squares recalibration, achieving about three times the accuracy for one QTOF data set.
9584467
Improved Ranking Functions for Protein and Modification-Site Identifications
There are a number of computational tools for assigning identifications to peptide tandem mass spectra, but many fewer tools for the crucial next step of integrating spectral identifications into higher-level identifications, such as proteins or modification sites. Here we describe a new program called ComByne for scoring and ranking higher-level identifications. We compare ComByne to existing algorithms on several complex biological samples, including a sample of mouse blood plasma spiked with known concentrations of human proteins. A Web interface to our software is at http://bio.parc.xerox.com.
26906105
Trustworthy Paper Documents
In the first part of this paper, we propose a watermarking method for text documents that is less vulnerable to attacks than previous methods. In the second part, we propose a method for protecting the actual content of the document. In a section of independent interest, we discuss the interplay between error-correcting codes and steganography.
4796791
A global approach to automatic solution of jigsaw puzzles
We present a new algorithm for automatically solving jigsaw puzzles by shape alone. The algorithm can solve more difficult puzzles than could be solved before, without the use of backtracking or branch-and-bound. The algorithm can handle puzzles in which pieces border more than four neighbors, and puzzles with as many as 200 pieces. Our overall strategy follows that of previous algorithms but applies a number of new ideas, such as robust fiducial points, "highest- confidence-first" search, and frequent global reoptimization of partial solutions.
8685428
Continuous queries over append-only databases
In a database to which data is continually added, users may wish to issue a permanent query and be notified whenever data matches the query. If such continuous queries examine only single records, this can be implemented by examining each record as it arrives. This is very efficient because only the incoming record needs to be scanned. This simple approach does not work for queries involving joins or time. The Tapestry system allows users to issue such queries over a database of mail and bulletin board messages. The user issues a static query, such as “show me all messages that have been replied to by Jones,” as though the database were fixed and unchanging. Tapestry converts the query into an incremental query that efficiently finds new matches to the original query as new messages are added to the database. This paper describes the techniques used in Tapestry, which do not depend on triggers and thus be implemented on any commercial database that supports SQL. Although Tapestry is designed for filtering mail and news messages, its techniques are applicable to any append-only database.
30699245
A low-power CMOS integrated circuit for bearing estimation
We present the design and testing of a micropower integrated circuit for the estimation of the bearing angle of a sound source with respect to a pair of microphones. The algorithm is based on a modified binary cross-correlation approach suitable for low-power operation. The circuit has been tested and operates at 600 /spl mu/W at performance levels matching theoretical simulations.
36729490
Energy efficiency in a channel model for the spiking axon
Abstract We examine the spiking axon as a communication channel. We develop a first principles channel model that encompasses the noise in the axon, which manifests itself as spike jitter, and the power consumption, which arises from the activity of the Na + –K + pump. This model enables us to examine the trade-off between the information rate and power consumption. Using parameters from the frog myelinated axon, we determine the spike rate that corresponds to the maximum energy efficiency. This spike rate is consistent with experimental observations, which suggests that neural communication may have developed to maximize energy efficiency rather than information rate alone.
15116838
Lateral connectivity as a scaffold for developing orientation preference maps
Abstract In the visual cortex of the cat and ferret, it is established that orientation selectivity is the consequence of experience-dependent plasticity. Recent experiments, however, indicate that the layout of orientation maps is remarkably stable and experience-independent. We present a model to account for these seemingly paradoxical results. In this model, a scaffold consisting of anisotropic lateral connections is laid down in horizontal circuitry prior to visual experience. These lateral connections provide an experience-independent framework for the developing orientation map by inducing broad orientation tuning. Adult-like, sharp orientation tuning emerges as the result of experience-dependent plasticity of the feedforward connections. This plasticity is modeled by the BCM synaptic plasticity rule in a natural scene environment. This model simultaneously satisfies the requirements of plasticity and stability that are seen in experiment. In addition, this model provides an explanation of the phenomenon where two eyes without common visual experience develop similar orientation maps.
14474778
Spike Timing-Dependent Plasticity in the Address Domain
Address-event representation (AER), originally proposed as a means to communicate sparse neural events between neuromorphic chips, has proven efficient in implementing large-scale networks with arbitrary, configurable synaptic connectivity. In this work, we further extend the functionality of AER to implement arbitrary, configurable synaptic plasticity in the address domain. As proof of concept, we implement a biologically inspired form of spike timing-dependent plasticity (STDP) based on relative timing of events in an AER framework. Experimental results from an analog VLSI integrate-and-fire network demonstrate address domain learning in a task that requires neurons to group correlated inputs.