Generating Focussed Molecule Libraries for Drug Discovery with Recurrent Neural Networks

In de novo drug design, computational strategies are used to generate novel molecules with good affinity to the desired biological target. In this work, we show that recurrent neural networks can be trained as generative models for molecular structures, similar to statistical language models in natural language processing. We demonstrate that the properties of the generated molecules correlate very well with the properties of the molecules used to train the model. In order to enrich libraries with molecules active towards a given biological target, we propose to fine-tune the model with small sets of molecules, which are known to be active against that target. Against Staphylococcus aureus, the model reproduced 14% of 6051 hold-out test molecules that medicinal chemists designed, whereas against Plasmodium falciparum (Malaria) it reproduced 28% of 1240 test molecules. When coupled with a scoring function, our model can perform the complete de novo drug design cycle to generate large sets of novel molecules for drug discovery.Comment: 17 pages, 17 figure

A fundamental test of the Higgs Yukawa coupling at RHIC in A+A collisions

Searches for the intermediate boson, $W^{\pm}$, the heavy quantum of the Weak Interaction, via its semi-leptonic decay, $W\to e +\nu$, in the 1970's instead discovered unexpectedly large hadron production at high $p_T$, notably $\pi^0$, which provided a huge background of $e^{\pm}$ from internal and external conversions. Methods developed at the CERN ISR which led to the discovery of direct-single-$e^{\pm}$ in 1974, later determined to be from the semi-leptonic decay of charm which had not yet been discovered, were used by PHENIX at RHIC to make precision measurements of heavy quark production in p-p and Au+Au collisions, leading to the puzzle of apparent equal suppression of light and heavy quarks in the QGP. If the Higgs mechanism gives mass to gauge bosons but not to fermions, then a proposal that all 6 quarks are nearly massless in a QGP, which would resolve the puzzle, can not be excluded. This proposal can be tested with future measurements of heavy quark correlations in A+A collisionsComment: 12 pages, 16 figures, 26th Winter Workshop on Nuclear Dynamics, Ocho Rios, Jamaica WI, January 2-9, 2010. Corrected citation of 1974 direct single lepton discover

Automorphism Properties and Classification of Adinkras

Adinkras are graphical tools for studying off-shell representations of supersymmetry. In this paper we efficiently classify the automorphism groups of Adinkras relative to a set of local parameters. Using this, we classify Adinkras according to their equivalence and isomorphism classes. We extend previous results dealing with characterization of Adinkra degeneracy via matrix products and present algorithms for calculating the automorphism groups of Adinkras and partitioning Adinkras into their isomorphism classes

Measurement of total cross sections on hydrogen and deuterium

Total cross sections of {pi}{sup {+-}}, K{sup {+-}}, p and {bar p} on hydrogen and deuterium are to be measured at about eight energies between 20 GeV and the maximum available energy. An accuracy of about one part in one thousand will yield the energy dependence of cross sections, comparisons of cross sections within SU(3) supermultiplets, and stringent tests of high energy limiting theorems

Observation of Hadronic W Decays in t-tbar Events with the Collider Detector at Fermilab

We observe hadronic W decays in t-tbar -> W (-> l nu) + >= 4 jet events using a 109 pb-1 data sample of p-pbar collisions at sqrt{s} = 1.8 TeV collected with the Collider Detector at Fermilab (CDF). A peak in the dijet invariant mass distribution is obtained that is consistent with W decay and inconsistent with the background prediction by 3.3 standard deviations. From this peak we measure the W mass to be 77.2 +- 4.6 (stat+syst) GeV/c^2. This result demonstrates the presence of two W bosons in t-tbar candidates in the W (-> l nu) + >= 4 jet channel.Comment: 20 pages, 4 figures, submitted to PR

Search for a Fourth-Generation Quark More Massive than the Z0 Boson in ppbar Collisions at sqrt(s) = 1.8 TeV

We present the results of a search for pair production of a fourth-generation charge -1/3 quark (b') in sqrt(s)=1.8 TeV ppbar collisions using 88 pb^(-1) of data obtained with the Collider Detector at Fermilab. We assume that both quarks decay via the flavor-changing neutral current process b' -> bZ and that the b' mass is greater than m_Z + m_b. We studied the decay mode b'b'bar -> ZZ b bbar where one Z0 decays into e^+e^- or mu^+ mu^- and the other decays hadronically, giving a signature of two leptons plus jets. An upper limit on the cross section of ppbar -> b'b'bar times [BR (b' -> bZ)]^2 is established as a function of the b' mass. We exclude at 95% confidence level a b' quark with mass between 100 and 199 GeV/c^2 for BR(b' -> bZ) = 100%.Comment: 12 pages, 2 figures, submitted to Phys. Rev. Letters on 9/12/9