How a well-adapted immune system is organized Mayer, Andreas; Balasubramanian, Vijay; Mora, Thierry ...
Proceedings of the National Academy of Sciences - PNAS,
05/2015, Letnik:
112, Številka:
19
Journal Article
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The repertoire of lymphocyte receptors in the adaptive immune system protects organisms from diverse pathogens. A well-adapted repertoire should be tuned to the pathogenic environment to reduce the ...cost of infections. We develop a general framework for predicting the optimal repertoire that minimizes the cost of infections contracted from a given distribution of pathogens. The theory predicts that the immune system will have more receptors for rare antigens than expected from the frequency of encounters; individuals exposed to the same infections will have sparse repertoires that are largely different, but nevertheless exploit cross-reactivity to provide the same coverage of antigens; and the optimal repertoires can be reached via the dynamics of competitive binding of antigens by receptors and selective amplification of stimulated receptors. Our results follow from a tension between the statistics of pathogen detection, which favor a broader receptor distribution, and the effects of cross-reactivity, which tend to concentrate the optimal repertoire onto a few highly abundant clones. Our predictions can be tested in high-throughput surveys of receptor and pathogen diversity.
Significance The adaptive immune system uses the experience of past infections to prepare its limited repertoire of specialized receptors to protect organisms from future threats. What is the best way of doing this? Building a theoretical framework from first principles, we predict the composition of receptor repertoires that are optimally adapted to minimize the cost of infections from a given pathogenic environment. A naive repertoire can reach these optima through a biologically plausible competitive mechanism. Our findings explain how limited populations of immune receptors can self-organize to provide effective immunity against highly diverse pathogens. Our results also inform the design and interpretation of experiments surveying immune repertoires.
GaussianSource Coding Based on P-LDPC Code Song, Dan; Ren, Jinkai; Wang, Lin ...
IEEE transactions on communications,
2023-April, 2023-4-00, Letnik:
71, Številka:
4
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A lossy source coding system based on the protograph low-density parity-check (P-LDPC) code is proposed for Gaussian source compression. In the proposed system, the conventional belief propagation ...(BP) algorithm is modified to be a concatenated BP-inverse BP (BP-<inline-formula> <tex-math notation="LaTeX">i </tex-math></inline-formula>BP) for encoding and decoding, where the <inline-formula> <tex-math notation="LaTeX">i </tex-math></inline-formula>BP is constructed by a fully-connected layer of a neural network. Compared to the existing approximate message passing algorithm, the proposed BP-<inline-formula> <tex-math notation="LaTeX">i </tex-math></inline-formula>BP realizes a float-to-bit compression with low complexity for arbitrary Gaussian sources. The BP-<inline-formula> <tex-math notation="LaTeX">i </tex-math></inline-formula>BP is implemented based on the linking relation of the protograph; therefore, it is necessary to optimally design the protograph to obtain better rate-distortion function (RDF) performance. Regarding the coding optimal procedure, a mutual information iteration convergence (MIIC) algorithm is designed as the optimal criterion to determine the source P-LDPC code with minimum distortion. Inspired by the plane construction of quantum stabilizer code, a lattice topological splicing (LTS) algorithm is proposed for regularly building the protograph to reduce the code searching complexity. By using the MIIC and the LTS algorithms, the BP-<inline-formula> <tex-math notation="LaTeX">i </tex-math></inline-formula>BP based on the designed P-LDPC code maintains good distortion performance close to the RDF limit.
Values available for choice in different behavioral contexts can vary immensely. To compensate for this variability, neuronal circuits underlying economic decisions undergo adaptation. In ...orbitofrontal cortex (OFC), neurons encode the subjective value of offered and chosen goods in a quasilinear way. Previous experiments found that the gain of the encoding is lower when the value range is wider. However, the parameters OFC neurons adapted to remained unclear. Furthermore, previous studies did not examine additive changes in neuronal responses. Computational considerations indicate that these factors can directly impact choice behavior. Here we investigated how OFC neurons adapt to changes in the value range. We recorded from two male rhesus monkeys during a juice choice task. Each session was divided into two blocks of trials. In each block, juices were offered within a set range of values, and ranges changed between blocks. Across blocks, neuronal responses adapted to both the maximum and the minimum value, but only partially. As a result, the minimum neural activity was elevated in some value ranges relative to others. Through simulation of a linear decision model, we showed that increasing the minimum response increases choice variability, lowering the expected payoff. This effect is modulated by the balance between cells with positive and negative encoding. The presence of these two populations induces a non-monotonic relationship between the value range and choice efficacy, such that the expected payoff is highest for decisions in an intermediate value range.
Economic decisions are thought to rely on the orbitofrontal cortex (OFC). The values available for choice vary enormously in different contexts. Previous work showed that neurons in OFC encode values in a linear way, and that the gain of encoding is inversely related to the range of available values. However, the specific parameters driving adaptation remained unclear. Here we show that OFC neurons adapt to both the maximum and minimum value in the current context. However, adaptation is partial, leading to contextual changes in the response offset. Interestingly, increasing the activity offset negatively affects choices in a simulated network. Partial adaptation may allow the circuit to maintain information about context value at the cost of slightly reduced payoff.
The joint source channel coding (JSCC) system is sensitive to the changing channel characteristics, because the optimally designed source-channel code pair always needs to be redesigned when the ...transmission environment is updated. A solution is to seek a common code pair for variable channels. Channel model 3 (CM3) is a variable on-body channel following the Weibull distribution, which is analyzed in four conditions due to varying shape factors, namely with exponential, Rayleigh, log-normal and normal distributions. The JSCC system is considered in this paper based on double protograph low-density parity-check (DP-LDPC) code pair over the variable CM3 channel. Firstly, four DP-LDPC code pairs are searched by the conventional differential evolution (DE) algorithm with four distributions of the Weibull model, respectively. However, these four code pairs only present good bit-error ratio performance in their own distribution, and have error floors in the other three. To resolve the problem, an artificial intelligence method based on principle component analysis (PCA) algorithm is designed to extract the common code pair. It is demonstrated that the common code pair performs well in noise-varying and practical-parameter transmissions. Instead of four DE code pairs, the designed one PCA code pair provides a strong technical support to low-complexity manufacturing such as eHealthcare.
As a side-effect-free method, meter coding can successfully detect stealthy false data injection (FDI) attacks without significantly affecting physical plants by encoding the sensor outputs with an ...invertible matrix. However, since the relationship between the detection of stealthy FDI attacks and the cost of meter coding was not clearly analyzed in existing works, the optimal design of coding schemes has not been well studied. This paper investigates the optimal design of coding schemes based on the analysis of detection conditions for stealthy FDI attacks in power system state estimation. Specifically, detection conditions for stealthy FDI attacks are derived in both general and special coding schemes, which reveal the requirements on the encoded measurements, the coding scheme and the meters in power systems. Utilizing the constraints determined by the detection conditions, the optimization of the special coding scheme is formulated and equivalently simplified, which decouples the design of coding matrix with the other decision variables. Finally, simulation results are carried out on the alternating current (AC) state estimation in the IEEE 14-bus and 57-bus test systems to validate theoretical results on the conditions and cost of detecting stealthy FDI attacks in meter coding.
Efficient processing of incoming sensory input is essential for an organism's survival. A growing body of evidence suggests that sensory systems have developed coding strategies that are constrained ...by the statistics of the natural environment. Consequently, it is necessary to first characterize neural responses to natural stimuli to uncover the coding strategies used by a given sensory system. Here we report for the first time the statistics of vestibular rotational and translational stimuli experienced by rhesus monkeys during natural (e.g., walking, grooming) behaviors. We find that these stimuli can reach intensities as high as 1500 deg/s and 8 G. Recordings from afferents during naturalistic rotational and linear motion further revealed strongly nonlinear responses in the form of rectification and saturation, which could not be accurately predicted by traditional linear models of vestibular processing. Accordingly, we used linear-nonlinear cascade models and found that these could accurately predict responses to naturalistic stimuli. Finally, we tested whether the statistics of natural vestibular signals constrain the neural coding strategies used by peripheral afferents. We found that both irregular otolith and semicircular canal afferents, because of their higher sensitivities, were more optimized for processing natural vestibular stimuli as compared with their regular counterparts. Our results therefore provide the first evidence supporting the hypothesis that the neural coding strategies used by the vestibular system are matched to the statistics of natural stimuli.
Accumulating evidence across multiple sensory modalities suggests that the thalamus does not simply relay information from the periphery to the cortex. Here we review recent findings showing that ...vestibular neurons within the ventral posteriolateral area of the thalamus perform nonlinear transformations on their afferent input that determine our subjective awareness of motion. Specifically, these neurons provide a substrate for previous psychophysical observations that perceptual discrimination thresholds are much better than predictions from Weber's law. This is because neural discrimination thresholds, which are determined from both variability and sensitivity, initially increase but then saturate with increasing stimulus amplitude, thereby matching the previously observed dependency of perceptual self-motion discrimination thresholds. Moreover, neural response dynamics give rise to unambiguous and optimized encoding of natural but not artificial stimuli. Finally, vestibular thalamic neurons selectively encode passively applied motion when occurring concurrently with voluntary (i.e., active) movements. Taken together, these results show that the vestibular thalamus plays an essential role towards generating motion perception as well as shaping our vestibular sense of agency that is not simply inherited from afferent input.
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•Vestibular thalamocortical neurons do not merely relay information from the periphery to the cortex.•Nonlinear response properties provide a substrate for observed deviations from Weber's law in motion perception.•These nonlinearities allow for optimal and unambiguous encoding of natural but not artificial stimuli.•Vestibular thalamocortical neurons mediate our sense of agency by selectively encoding passive motion over voluntary movements.•Nonlinear operations performed byhe vestibular thalamus play an essential role towards shaping our generating motion perception of self-motion.
•Kucera–Gacs theorem.•Optimal redundancy.•Logarithmic redundancy.•New coding method.•Compressing streams into random streams.
It is a classic result in algorithmic information theory that every ...infinite binary sequence is computable from an infinite binary sequence which is random in the sense of Martin-Löf. If the computation of the first n bits of a sequence requires n+g(n) bits of the random oracle, then g is the redundancy of the computation. We devise a new coding method that achieves optimal logarithmic redundancy. For any computable non-decreasing function g such that ∑i2−g(i) is bounded we show that there is a coding process that codes any given infinite binary sequence into a Martin-Löf random infinite binary sequence with redundancy g. This redundancy bound is known to be the best possible.
The rth relative generalised Hamming weight (RGHW) of an $n,k$n,k linear code C and an $n,k_1$n,k1 subcode $C^1$C1, a generalisation of generalised Hamming weight (GHW), characterises code ...performances of wiretap channel of type II, secure network coding, linear ramp secret sharing scheme, trellis complexity etc. In this study, the authors investigate non-asymptotic and asymptotic bounds on RGHW. In the non-asymptotic setting, they present a new proof of the Griesmer bound on RGHW by residue code and introduce the new concept of relative chain condition. They show that code pairs meeting the Griesmer, Singleton, and weak Plotkin bounds satisfy this condition. The notion of relative chain condition and these results provide a new perspective on researches including evaluating trellis complexity and determining the weight hierarchy of code pairs etc. In the asymptotic setting, they improve previous work by introducing two new metrics, respectively, for the cases r is fixed and r is proportionally increasing with n. They show the asymptotic Singleton, Plotkin, and Gilbert–Varshamov bounds on the first metric and determine the value of the second metric, which is helpful for characterising the optimal asymptotic performances of applications and constructing the optimal coding schemes.
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