12319077
Paper position sensing
We describe position sensing algorithms used in an airjet paper moving system built at Xerox PARC. The algorithms combine inputs from optical sensors and compute the rectangle best fitting the data. We consider two different types of sensors: fax scan bars and disk-shaped area sensors. Our algorithms proved to be quite effective both in simulation and in actual use.
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.
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.
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.
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.
10633458
Field test results for low power bearing estimator sensor nodes
The paper describes experimental results of low power sensor nodes designed to perform bearing estimation. The nodes are intended to form a wireless sensor network able to locate an audio source. Two different nodes are tested: one is based on a cross-correlation derivative integrated circuit (IC), and the other on a gradient flow IC. Implementation details and experimental results of both systems working in a natural environment are presented.
6736227
VLSI implementation of an energy-aware wake-up detector for an acoustic surveillance sensor network
We present a low-power VLSI wake-up detector for a sensor network that uses acoustic signals to localize ground-based vehicles. The detection criterion is the degree of low-frequency periodicity in the acoustic signal, and the periodicity is computed from the “bumpiness” of the autocorrelation of a one-bit version of the signal. We then describe a CMOS ASIC that implements the periodicity estimation algorithm. The ASIC is fully functional and its core consumes 835 nanowatts. It was integrated into an acoustic enclosure and deployed in field tests with synthesized sounds and ground-based vehicles.
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.
7913359
Probabilistic synaptic weighting in a reconfigurable network of VLSI integrate-and-fire neurons
We present a scheme for implementing highly-connected, reconfigurable networks of integrate-and-fire neurons in VLSI. Neural activity is encoded by spikes, where the address of an active neuron is communicated through an asynchronous request and acknowledgement cycle. We employ probabilistic transmission of spikes to implement continuous-valued synaptic weights, and memory-based look-up tables to implement arbitrary interconnection topologies. The scheme is modular and scalable, and lends itself to the implementation of multi-chip network architectures. 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 task.
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.