Suffix Tree Characterization of Maximal Motifs in Biological Sequences

Finding motifs in biological sequences is one of the most intriguing problems for string algorithms designers as it is necessary to deal with approximations and this complicates the problem. Existing algorithms run in time linear with the input size. Nevertheless, the output size can be very large due to the approximation. This makes the output often unreadable, next to slowing down the inference itself. Since only a subset of the motifs, i.e. the \emph{maximal} motifs, could be enough to give the information of all of them, in this paper, we aim at removing such redundancy. We define notions of maximality that we characterize in the suffix tree data structure. Given that this is used by a whole class of motifs extraction tools, we show how these tools can be modified to include the maximality requirement on the fly without changing the asymptotical complexity

Inference of Network Expressions

No abstract availabl

Statistical Inspired Parton Distributions and the Violation of QPM Sum Rules

A quantum statistical parametrization of parton distributions has been considered. In this framework, the exclusion Pauli principle connects the violation of the Gottfried sum rule with the Ellis and Jaffe one, and implies a defect in the Bjorken sum rule. However, in terms of standard parametrizations of the polarized distributions a good description of the data is obtained once a large gluon polarization is provided. Interestingly, in this description there is no violation of the Bjorken sum rule.Comment: 10 pages, LateX + 15 figures, Talk given at ``Hadrons 96'' Workshop, Novy Svet (CRIMEA), June 9-1

Even faster elastic-degenerate string matching via fast matrix multiplication

An elastic-degenerate (ED) string is a sequence of n sets of strings of total length N, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of length m in an ED text. The EDSM problem has recently received some attention in the combinatorial pattern matching community, and an O(nm1.5 √(log m) + N)-time algorithm is known [Aoyama et al., CPM 2018]. The standard assumption in the prior work on this question is that N is substantially larger than both n and m, and thus we would like to have a linear dependency on the former. Under this assumption, the natural open problem is whether we can decrease the 1.5 exponent in the time complexity, similarly as in the related (but, to the best of our knowledge, not equivalent) word break problem [Backurs and Indyk, FOCS 2016].Our starting point is a conditional lower bound for the EDSM problem. We use the popular combinatorial Boolean matrix multiplication (BMM) conjecture stating that there is no truly subcubic combinatorial algorithm for BMM [Abboud and Williams, FOCS 2014]. By designing an appropriate reduction we show that a combinatorial algorithm solving the EDSM problem in O(nm1.5−∊ + N) time, for any ∊ > 0, refutes this conjecture. Of course, the notion of combinatorial algorithms is not clearly defined, so our reduction should be understood as an indication that decreasing the exponent requires fast matrix multiplication.Two standard tools used in algorithms on strings are string periodicity and fast Fourier transform. Our main technical contribution is that we successfully combine these tools with fast matrix multiplication to design a non-combinatorial O(nm1.381 + N)-time algorithm for EDSM. To the best of our knowledge, we are the first to do so.</p

A proton-recoil track imaging system for fast neutrons: the RIPTIDE detector

Fast neutron detection is often based on the neutron-proton elastic scattering reaction: the ionization caused by recoil protons in a hydrogenous material constitutes the basic information for the design and development of a class of neutron detectors. Although experimental techniques have continuously improved, proton-recoil track imaging remains still at the frontier of n-detection systems, due to the high photon sensitivity required. Several state-of-the-art approaches for neutron tracking by using n-p single and double scattering - referred to as Recoil Proton Track Imaging (RPTI) - can be found in the literature. So far, they have showed limits in terms of detection efficiency, complexity, cost, and implementation. In order to address some of these deficiencies, we have proposed RIPTIDE a novel recoil-proton track imaging detector in which the light output produced by a fast scintillator is used to perform a complete reconstruction in space and time of the interaction events. The proposed idea is viable thanks to the dramatic advances in low noise and single photon counting achieved in the last decade by new scientific CMOS cameras as well as pixel sensors, like Timepix or MIMOSIS. In this contribution, we report the advances on the RIPTIDE concept: Geant4 Monte Carlo simulations, light collection tests as well as state-of-the-art approach to image readout, processing and fast analysis.Comment: proceeding of the 23rd International Workshop on Radiation Imaging Detectors, IWoRID 2022, 26-30 June 2022, Riva del Garda (TN), Ital

Riptide: a proton-recoil track imaging detector for fast neutrons

Riptide is a detector concept aiming to track fast neutrons. It is based on neutron--proton elastic collisions inside a plastic scintillator, where the neutron momentum can be measured by imaging the scintillation light. More specifically, by stereoscopically imaging the recoil proton tracks, the proposed apparatus provides neutron spectrometry capability and enable the online analysis of the specific energy loss along the track. In principle, the spatial and topological event reconstruction enables particle discrimination, which is a crucial property for neutron detectors. In this contribution, we report the advances on the Riptide detector concept. In particular, we have developed a Geant4 optical simulation to demonstrate the possibility of reconstructing with sufficient precision the tracks and the vertices of neutron interactions inside a plastic scintillator. To realistically model the optics of the scintillation detector, mono-energetic protons were generated inside a $6\times6\times6$ cm$^3$ cubic BC-408 scintillator, and the produced optical photons were propagated and then recorded on a scoring plane corresponding to the surfaces of the cube. The photons were then transported through an optical system to a $2\times2$ cm$^2$ photo sensitive area with 1 Megapixel. Moreover, we have developed two different analysis procedures to reconstruct 3D tracks: one based on data fitting and one on Principal Component Analysis. The main results of this study will be presented with a particular focus on the role of the optical system and the attainable spatial and energy resolution.Comment: Prepared for submission to JINS

Riptide: a proton-recoil track imaging detector for fast neutrons

Abstract: Riptide is a detector concept aiming to track fast neutrons. It is based on neutron-proton elastic collisions inside a plastic scintillator, where the neutron momentum can be measured by imaging the scintillation light. More specifically, by stereoscopically imaging the recoil proton tracks, the proposed apparatus provides neutron spectrometry capability and enable the online analysis of the specific energy loss along the track. In principle, the spatial and topological event reconstruction enables particle discrimination, which is a crucial property for neutron detectors. In this contribution, we report the advances on the Riptide detector concept. In particular, we have developed a Geant4 optical simulation to demonstrate the possibility of reconstructing with sufficient precision the tracks and the vertices of neutron interactions inside a plastic scintillator. To realistically model the optics of the scintillation detector, mono-energetic protons were generated inside a 6 × 6 × 6 cm3 cubic BC-408 scintillator, and the produced optical photons were propagated and then recorded on a scoring plane corresponding to the surfaces of the cube. The photons were then transported through an optical system to a 2 × 2 cm2 photo sensitive area with 1 Megapixel. Moreover, we have developed two different analysis procedures to reconstruct 3D tracks: one based on data fitting and one on Principal Component Analysis. The main results of this study will be presented with a particular focus on the role of the optical system and the attainable spatial and energy resolution

Neutrino masses and mixings in a seesaw framework

Assuming the seesaw mechanism for hierarchical neutrino masses, we calculate the heavy neutrino masses under the hypotheses that the mixing in the Dirac leptonic sector is similar to the quark mixing ($V_D \sim V_{CKM}$) and that $M_{\nu} \sim M_u$ or $M_e$, where $M_{\nu}$ is the Dirac mass matrix of neutrinos. As a result we find that for $M_{\nu} \sim M_u$ the vacuum oscillation solution of the solar neutrino problem leads to a scale for the heavy neutrino mass well above the unification scale, while for the MSW solutions there is agreement with this scale. For $M_{\nu} \sim M_e$ the vacuum solution is consistent with the unification scale, and the MSW solutions with an intermediate scale. The mass of the lightest heavy neutrino can be as small as $10^5$ GeV.Comment: 13 pages RevTex, no figures. Revised versio

Upper Bounds on the Neutrino-Nucleon Inelastic Cross Section

Extraterrestrial neutrinos can initiate deeply developing air showers, and those that traverse the atmosphere unscathed may produce cascades in the ice or water. Up to now, no such events have been observed. This can be translated into upper limits on the diffuse neutrino flux. On the other hand, the observation of cosmic rays with primary energies > 10^{10} GeV suggests that there is a guaranteed flux of cosmogenic neutrinos, arising from the decay of charged pions (and their muon daughters) produced in proton interactions with the cosmic microwave background. In this work, armed with these cosmogenic neutrinos and the increased exposure of neutrino telescopes we bring up-to-date model-independent upper bounds on the neutrino-nucleon inelastic cross section. Uncertainties in the cosmogenic neutrino flux are discussed and taken into account in our analysis. The prospects for improving these bounds with the Pierre Auger Observatory are also estimated. The unprecedented statistics to be collected by this experiment in 6 yr of operation will probe the neutrino-nucleon inelastic cross section at the level of Standard Model predictions.Comment: To be published in JCA