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.
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.
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.
33407352
Document image matching and annotation lifting
Two images of the same document could differ significantly due to faxing, scanner distortions, or degradation through multigeneration copying. Additionally, one of the images may have extensive annotations not present in the other. We give a method for registering two such images and separating out annotations. We further present an algorithm for detecting and repairing broken strokes in the annotations. Our methods have been tested on a wide variety of documents with reliable results; for the special case of form dropout our results are better than had been obtained previously with special-purpose algorithms.
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.
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.
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.
8543826
Analog VLSI spiking neural network with address domain probabilistic synapses
We present an analog VLSI address-event transceiver containing an array of integrate-and-fire neurons and a scheme for implementing a reconfigurable neural network with probabilistic synapses. Neural "spikes" are transmitted through address-event representation-the address of the sending neuron is communicated through an asynchronous request and acknowledgment cycle. Continuous-valued synaptic weights are implemented by probabilistically routing address events. Results from a prototype system with 1024 analog VLSI integrate-and-fire neurons, each with up to 128 probabilistic synapses, demonstrate these concepts in an image processing application.
6053956
A low-power correlation-derivative CMOS VLSI circuit for bearing estimation
We present a CMOS integrated circuit (IC) for bearing estimation in the low-audio range that performs a correlation derivative approach in a 0.35-/spl mu/m technology. The IC calculates the bearing angle of a sound source with a mean variance of one degree in a 360/spl deg/ range using four microphones: one pair is used to produce the indication and the other to define the quadrant. An adaptive algorithm decides which pair to use depending on the direction of the incoming signal, in such a way to obtain the best estimate. The IC contains two blocks with 104 stages each. Every stage has a delay unit, a block to reduce the clock speed, and a 10-bit UP/DN counter. The IC measures 2 mm by 2.4 mm, and dissipates 600 /spl mu/W at 3.3 V and 200 kHz. It is purely digital and uses a one-bit quantization of the input signals.
16600244
Heterogeneous integration of biomimetic acoustic microsystems
We discuss biologically inspired devices and architectures for acoustic processing microsystems. We exploit state of the art integrated microsystems technologies to heterogeneously integrate electronics and micromechanical structures for acoustic sensing and signal processing.