Classifying and scoring of molecules with the NGN: new datasets, significance tests, and generalization

<p>Abstract</p> <p/> <p>This paper demonstrates how a Neural Grammar Network learns to classify and score molecules for a variety of tasks in chemistry and toxicology. In addition to a more detailed analysis on datasets previously studied, we introduce three new datasets (BBB, FXa, and toxicology) to show the generality of the approach. A new experimental methodology is developed and applied to both the new datasets as well as previously studied datasets. This methodology is rigorous and statistically grounded, and ultimately culminates in a Wilcoxon significance test that proves the effectiveness of the system. We further include a complete generalization of the specific technique to arbitrary grammars and datasets using a mathematical abstraction that allows researchers in different domains to apply the method to their own work.</p> <p>Background</p> <p>Our work can be viewed as an alternative to existing methods to solve the quantitative structure-activity relationship (QSAR) problem. To this end, we review a number approaches both from a methodological and also a performance perspective. In addition to these approaches, we also examined a number of chemical properties that can be used by generic classifier systems, such as feed-forward artificial neural networks. In studying these approaches, we identified a set of interesting benchmark problem sets to which many of the above approaches had been applied. These included: ACE, AChE, AR, BBB, BZR, Cox2, DHFR, ER, FXa, GPB, Therm, and Thr. Finally, we developed our own benchmark set by collecting data on toxicology.</p> <p>Results</p> <p>Our results show that our system performs better than, or comparatively to, the existing methods over a broad range of problem types. Our method does not require the expert knowledge that is necessary to apply the other methods to novel problems.</p> <p>Conclusions</p> <p>We conclude that our success is due to the ability of our system to: 1) encode molecules losslessly before presentation to the learning system, and 2) leverage the design of molecular description languages to facilitate the identification of relevant structural attributes of the molecules over different problem domains.</p

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Toward A Photonic Arbitrary Waveform Generator Using A Modelocked External Cavity Semiconductor Laser

We propose an architecture for photonic arbitrary waveform generation where the phase-locked longitudinal modes of a 12.4-GHz fundamentally modelocked external cavity semiconductor laser are individually modulated. We report photonic synthesis of microwave tones at 37.2 GHz (limited by photodetector bandwidth) with linewidth \u3c100 Hz and dynamic range 50 dB at 100-Hz resolution bandwidth. We show photonically synthesized 12.4-GHz sine waves with superimposed sinusoidal and pulsed RF modulations, demonstrating the potential for photonic arbitrary waveform generation with the proposed architecture

Noise In Fundamental And Harmonic Modelocked Semiconductor Lasers: Experiments And Simulations

Electric-field correlation measurements of fundamental and harmonic modelocked external cavity semiconductor lasers are presented. Based on these results, an empirical model of a harmonic modelocked pulsetrain is constructed. Using this model, the equivalence between the time-interleaved pulsetrains picture and the supermode picture of a harmonic modelocked pulsetrain is shown. Simulations based on the model are presented showing the key characteristics of modelocked pulsetrains in radio frequency (RF) and optical domains. The fundamental relationship between longitudinal mode linewidth and RF phase-noise corner frequency is delineated. The generated results point to fundamental limitations in timing jitter in modelocked lasers

High-Quality Photonic Sampling Streams From A Semiconductor Diode Ring Laser

We report on the development of an ultralow-noise, external-cavity, actively mode-locked semiconductor diode laser for application in next-generation photonic sampling systems. A summary of harmonically mode-locked noise characteristics in a 65-MHz ring cavity is presented through the range of pulse repetition frequencies between 130 MHz and 8.3 GHz (2nd-128th harmonic). Important implications regarding the use of gain-versus-loss modulation as the active modelocking mechanisms are discussed. We also report what are, to our knowledge, the lowest noise characteristics achieved to date for a semiconductor diode laser operating at 10 GHz. Individually optimized results of 0.12% rms amplitude noise (10 Hz-10 MHz), and 43 fs rms residual phase jitter (10 Hz-10 MHz) provide a theoretical resolution of 8.6 bits in a 10-GSPS optical analog-to-digital converter. We have also achieved dispersion-compensated pulsewidths as short as 1.2 ps, and shown successful operation of a novel phase-locked-loop capable of reducing the rms residual phase noise by as much as 91% within its response bandwidth. Finally, the first measurements of residual phase noise out to the Nyquist frequency (5 GHz) are presented, providing an upper bound on the rms residual phase jitter of 121 fs (10 Hz-5 GHz)

Noise Reduction And Control In Modelocked Semiconductor Diode Lasers For Use In Next-Generation All-Optical Analog-To-Digital Converters

External-cavity, actively-modelocked semiconductor diode lasers (SDLs) have proven to be attractive candidates for forming the backbone of next-generation analog-to-digital converters (ADCs), which are currently being developed to sample signals at repetition rates exceeding several GHz with up to 12 bits of digital resolution. Modelocked SDLs are capable of producing waveform-sampling pulse trains with very low temporal jitter (phase noise) and very small fluctuations in pulse height (amplitude noise) - two basic conditions that must be met in order for high-speed ADCs to achieve projected design goals. Single-wavelength modelocked operation (at nominal repetition frequencies of 400 MHz) has produced pulse trains with very low amplitude noise (approx. 0.08%), and the implementation of a phase-locked-loop (PLL) has been effective in reducing the system\u27s low-frequency phase noise (RMS timing jitter for offset frequencies between 10 Hz and 10 KHz has been reduced from 240 fs to 27 fs)

Modelocked External Cavity Semiconductor Laser For Applications In Photonic Arbitrary Waveform Generation And Photonic Synthesis

A photonic arbitrary waveform generator (PAWG) that has potential for photonic arbitrary waveform generation through modulation of individual channels before recombining them is proposed. The concept of this scheme relies on the fact that modelocked lasers produce a periodic comb of phase-locked longitudinal modes

Low Timing Jitter Mode-Locked Semiconductor Diode Lasers

Low timing jitter mode-locked semiconductor diode lasers was discussed. Optical linewidth of the individual comb components within the mode-locked laser optical spectrum was measured using heterodyne method. Results showed that the longitudinal mode linewidth determines the phase noise corner frequency

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least 4 m. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the 6.5 m James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 yr, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit