TopologyNet: Topology based deep convolutional neural networks for biomolecular property predictions

Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional (3D) biomolecular structural data sets have been hindered by the entangled geometric complexity and biological complexity. We introduce topology, i.e., element specific persistent homology (ESPH), to untangle geometric complexity and biological complexity. ESPH represents 3D complex geometry by one-dimensional (1D) topological invariants and retains crucial biological information via a multichannel image representation. It is able to reveal hidden structure-function relationships in biomolecules. We further integrate ESPH and convolutional neural networks to construct a multichannel topological neural network (TopologyNet) for the predictions of protein-ligand binding affinities and protein stability changes upon mutation. To overcome the limitations to deep learning arising from small and noisy training sets, we present a multitask topological convolutional neural network (MT-TCNN). We demonstrate that the present TopologyNet architectures outperform other state-of-the-art methods in the predictions of protein-ligand binding affinities, globular protein mutation impacts, and membrane protein mutation impacts.Comment: 20 pages, 8 figures, 5 table

Baryon Number Non-Conservation and the Topology of Gauge Fields

An introduction to the subject of baryon number non-conservation in the electroweak theory at high temperatures or energies is followed by a summary of our discovery of an infinite surface of sphaleron-like configurations which play a key role in baryon-number non-conserving transitions in a hot electroweak plasma.Comment: Talk given by Ola Tornkvist, to appear in the proceedings of the meeting of the American Physical Society, Division of Particles and Fields (DPF 96) in Minneapolis, Minnesota, August 10-15, 1996. Plain latex, 6 page

Limits on Electroweak Instanton-Induced Processes with Multiple Boson Production

Recently, the CMS collaboration has reported their search for electroweak instanton-like processes with anomalous $B+L$ violation assuming multi-fermion but zero-boson final states. On the other hand, many theoretical studies suggest that anomalous $B+L$ processes may have an observably large production rate only if their final state contains a large number of electroweak gauge bosons. In this paper, we compare collider signatures of zero- and multi-boson events of anomalous $B+L$ violation at the LHC and derive an upper limit on the cross-section for the multi-boson process by recasting the CMS analysis.Comment: 14 pages, 6 figures; JHEP version with typographic errors fixe

Scattering with Baryon Number Violation -- The Case of Higgs Particle Production --

\noindent A formalism based on path-integral expression of time-evolution operator during tunneling at a finite energy proposed by the authors is applied to $SU(2)$ gauge-Higgs system to produce Higgs particles with $\Delta B=1$. Instead of starting from instanton tunneling at the zero energy, a classical bounce solution giving sphaleron (instanton) action at high (low) energies is used as the tunneling configuration. Fourier transform of the bounce configuration in coherent state expression at the entrance and exit of the tunneling plays an important role. Numerical results at various energies for $M_H/M_W=1 \sim 2$ are given. Though the cross section with $\Delta B=1$ results from a severe cancellation of several large quantities in the leading order as occured in the instanton calculus, it seems unlikely that the cross section grows as largely as to reach unitarity bound at energies $E \leq E_{sph}$. It is pointed out that the actual value $g^2=0.418$ of the $SU(2)$ gauge coupling constant may be too large to take the weak coupling limit.}Comment: modified PHYZZX(included), 4 Figures (not included), SAGA-HE-46 : KYUSHU-HET-

Semiclassical Study of Baryon and Lepton Number Violation in High-Energy Electroweak Collisions

We make use of a semiclassical method for calculating the suppression exponent for topology changing transitions in high-energy electroweak collisions. In the Standard Model these processes are accompanied by violation of baryon and lepton number. By using a suitable computational technique we obtain results for s-wave scattering in a large region of initial data. Our results show that baryon and lepton number violation remains exponentially suppressed up to very high energies of at least 30 sphaleron masses (250 TeV). We also conclude that the known analytic approaches inferred from low energy expansion provide reasonably good approximations up to the sphaleron energy (8 TeV) only.Comment: 23 pages, 18 figures. Phys.Rev.D journal version (two references added

Chern-Simons number diffusion in (1+1)-dimensional Higgs theory

We study the Chern-Simons number diffusion rate in the (1+1)-dimensional latticeAbelian Higgs model at temperatures much higher than, as well as comparable to, the sphaleron energy. It is found that in the high-temperature limit the rate is likely to grow as power 2/3 of the temperature. In the intermediate-temperature regime, our numerical simulations show that very weak temperature dependence of the rate, found in previous work, persists at smaller lattice spacings. We discuss possibilities of relating the observed behavior of the rate to static finite-temperature properties of the model.Comment: 9 pages, LATeX + 4 figures included as postscript files, to be encapsulated using epsf. Text + figures uuencoded. Also available as a compressed postscript file by anonymous ftp from maggia.ethz.ch (login ftp, pw ftp; then: cd pub, binary, get ahm.ps.Z). IPS Research Report No. 94-0