Clustering files of chemical structures using the Szekely-Rizzo generalization of Ward's method

Ward's method is extensively used for clustering chemical structures represented by 2D fingerprints. This paper compares Ward clusterings of 14 datasets (containing between 278 and 4332 molecules) with those obtained using the Szekely–Rizzo clustering method, a generalization of Ward's method. The clusters resulting from these two methods were evaluated by the extent to which the various classifications were able to group active molecules together, using a novel criterion of clustering effectiveness. Analysis of a total of 1400 classifications (Ward and Székely–Rizzo clustering methods, 14 different datasets, 5 different fingerprints and 10 different distance coefficients) demonstrated the general superiority of the Székely–Rizzo method. The distance coefficient first described by Soergel performed extremely well in these experiments, and this was also the case when it was used in simulated virtual screening experiments

Do Teacher Absences Impact Student Achievement? Longitudinal Evidence from One Urban School District

Rates of employee absences and the effects of absences on productivity are topics of conversation in many organizations in many countries. One reason is that high rates of employee absence may signal weak management and poor labor-management relations. A second reason is that reducing rates of employee absence may be an effective way to improve productivity. This paper reports the results of a study of employee absences in education, a large, labor-intensive industry. Policymakers' concern with teacher absence rests on three premises: (1) that a significant portion of teachers' absences is discretionary, (2) that teachers' absences have a nontrivial impact on productivity, and (3) that feasible policy changes could reduce rates of absence among teachers. This paper presents the results of an empirical investigation of the first two of these premises; it discusses the third premise. We employ a methodology that accounts for time-invariant differences among teachers in skill and motivation. We find large variation in adjusted teacher absence rates among schools. We estimate that each 10 days of teacher absences reduce students' mathematics achievement by 3.3 percent of a standard deviation.

Mark Hepworth: In memoriam

Purpose – To honour the contributions of Mark Hepworth to library and information science. Design/methodology/approach – The personal views of the two authors, both of whom knew Hepworth for many years. Findings – The significance of Hepworth’s research in library and information science, in particular to studies of information behaviour and information literacy. Originality/value – Demonstrates the community’s appreciation of Hepworth’s contributions to the discipline

Compressed sensing performance bounds under Poisson noise

This paper describes performance bounds for compressed sensing (CS) where the underlying sparse or compressible (sparsely approximable) signal is a vector of nonnegative intensities whose measurements are corrupted by Poisson noise. In this setting, standard CS techniques cannot be applied directly for several reasons. First, the usual signal-independent and/or bounded noise models do not apply to Poisson noise, which is non-additive and signal-dependent. Second, the CS matrices typically considered are not feasible in real optical systems because they do not adhere to important constraints, such as nonnegativity and photon flux preservation. Third, the typical $\ell_2$--$\ell_1$ minimization leads to overfitting in the high-intensity regions and oversmoothing in the low-intensity areas. In this paper, we describe how a feasible positivity- and flux-preserving sensing matrix can be constructed, and then analyze the performance of a CS reconstruction approach for Poisson data that minimizes an objective function consisting of a negative Poisson log likelihood term and a penalty term which measures signal sparsity. We show that, as the overall intensity of the underlying signal increases, an upper bound on the reconstruction error decays at an appropriate rate (depending on the compressibility of the signal), but that for a fixed signal intensity, the signal-dependent part of the error bound actually grows with the number of measurements or sensors. This surprising fact is both proved theoretically and justified based on physical intuition.Comment: 12 pages, 3 pdf figures; accepted for publication in IEEE Transactions on Signal Processin

A Fermi Fluid Description of the Half-Filled Landau Level

We present a many-body approach to calculate the ground state properties of a system of electrons in a half-filled Landau level. Our starting point is a simplified version of the recently proposed trial wave function where one includes the antisymmetrization operator to the bosonic Laughlin state. Using the classical plasma analogy, we calculate the pair-correlation function, the static structure function and the ground state energy in the thermodynamic limit. These results are in good agreement with the expected behavior at $\nu=\frac12$.Comment: 4 pages, REVTEX, and 4 .ps file

Scaffold searching: automated identification of similar ring systems for the design of combinatorial libraries

Rigid ring systems can be used to position receptor-binding functional groups in 3D space and they thus play an increasingly important role in the design of combinatorial libraries. This paper discusses the use of shape-similarity methods to identify ring systems that are structurally similar to, and aligned with, a user-defined target ring system. These systems can be used as alternative scaffolds for the construction of a combinatorial library