The role of idiotypic interactions in the adaptive immune system: a belief-propagation approach

In this work we use belief-propagation techniques to study the equilibrium behaviour of a minimal model for the immune system comprising interacting T and B clones. We investigate the effect of the so-called idiotypic interactions among complementary B clones on the system's activation. Our result shows that B-B interactions increase the system's resilience to noise, making clonal activation more stable, while increasing the cross-talk between different clones. We derive analytically the noise level at which a B clone gets activated, in the absence of cross-talk, and find that this increases with the strength of idiotypic interactions and with the number of T cells signalling the B clone. We also derive, analytically and numerically, via population dynamics, the critical line where clonal cross-talk arises. Our approach allows us to derive the B clone size distribution, which can be experimentally measured and gives important information about the adaptive immune system response to antigens and vaccination.Comment: 37 pages, 18 figure

Spin systems on hypercubic Bethe lattices: A Bethe-Peierls approach

We study spin systems on Bethe lattices constructed from d-dimensional hypercubes. Although these lattices are not tree-like, and therefore closer to real cubic lattices than Bethe lattices or regular random graphs, one can still use the Bethe-Peierls method to derive exact equations for the magnetization and other thermodynamic quantities. We compute phase diagrams for ferromagnetic Ising models on hypercubic Bethe lattices with dimension d=2, 3, and 4. Our results are in good agreement with the results of the same models on d-dimensional cubic lattices, for low and high temperatures, and offer an improvement over the conventional Bethe lattice with connectivity k=2d.Comment: Version accepted for publication by the Journal of Physics A: Mathematical and Theoretical with improved list of references and with an additional section on specific hea

Consistent inference of a general model using the pseudo-likelihood method

Recently maximum pseudo-likelihood (MPL) inference method has been successfully applied to statistical physics models with intractable likelihoods. We use information theory to derive a relation between the pseudo-likelihood and likelihood functions. We use this relation to show consistency of the pseudo-likelihood method for a general model.Comment: A new more mathematically rigorous version accepted for publication in Physical Review E: Rapid Communicatio

Transfer matrix analysis of one-dimensional majority cellular automata with thermal noise

Thermal noise in a cellular automaton refers to a random perturbation to its function which eventually leads this automaton to an equilibrium state controlled by a temperature parameter. We study the 1-dimensional majority-3 cellular automaton under this model of noise. Without noise, each cell in this automaton decides its next state by majority voting among itself and its left and right neighbour cells. Transfer matrix analysis shows that the automaton always reaches a state in which every cell is in one of its two states with probability 1/2 and thus cannot remember even one bit of information. Numerical experiments, however, support the possibility of reliable computation for a long but finite time.Comment: 12 pages, 4 figure

On reliable computation by noisy random Boolean formulas

We study noisy computation in randomly generated k-ary Boolean formulas. We establish bounds on the noise level above which the results of computation by random formulas are not reliable. This bound is saturated by formulas constructed from a single majority-like gates. We show that these gates can be used to compute any Boolean function reliably below the noise bound.Comment: A new version with improved presentation accepted for publication in IEEE TRANSACTIONS ON INFORMATION THEOR

Space of Functions Computed by Deep-Layered Machines

We study the space of functions computed by random-layered machines, including deep neural networks and Boolean circuits. Investigating the distribution of Boolean functions computed on the recurrent and layer-dependent architectures, we find that it is the same in both models. Depending on the initial conditions and computing elements used, we characterize the space of functions computed at the large depth limit and show that the macroscopic entropy of Boolean functions is either monotonically increasing or decreasing with the growing depth

On the robustness of random Boolean formulae

Random Boolean formulae, generated by a growth process of noisy logical gates are analyzed using the generating functional methodology of statistical physics. We study the type of functions generated for different input distributions, their robustness for a given level of gate error and its dependence on the formulae depth and complexity and the gates used. Bounds on their performance, derived in the information theory literature for specific gates, are straightforwardly retrieved, generalized and identified as the corresponding typical-case phase transitions. Results for error-rates, function-depth and sensitivity of the generated functions are obtained for various gate-type and noise models