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Register a new userHow to Color a French Flag--Biologically Inspired Algorithms for Scale-Invariant Patterning
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Added by
Frederik Mallmann-Trenn
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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In the French flag problem, initially uncolored cells on a grid must differentiate to become blue, white or red. The goal is for the cells to color the grid as a French flag, i.e., a three-colored triband, in a distributed manner. To solve a generalized version of the problem in a distributed computational setting, we consider two models: a biologically-inspired version that relies on morphogens (diffusing proteins acting as chemical signals) and a more abstract version based on reliable message passing between cellular agents. Much of developmental biology research has focused on concentration-based approaches using morphogens, since morphogen gradients are thought to be an underlying mechanism in tissue patterning. We show that both our model types easily achieve a French ribbon - a French flag in the 1D case. However, extending the ribbon to the 2D flag in the concentration model is somewhat difficult unless each agent has additional positional information. Assuming that cells are are identical, it is impossible to achieve a French flag or even a close approximation. In contrast, using a message-based approach in the 2D case only requires assuming that agents can be represented as constant size state machines. We hope that our insights may lay some groundwork for what kind of message passing abstractions or guarantees, if any, may be useful in analogy to cells communicating at long and short distances to solve patterning problems. In addition, we hope that our models and findings may be of interest in the design of nano-robots.
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The Dendritic Cell Algorithm (DCA) is an immune-inspired algorithm, developed for the purpose of anomaly detection. The algorithm performs multi-sensor data fusion and correlation which results in a context aware detection system. Previous applications of the DCA have included the detection of potentially malicious port scanning activity, where it has produced high rates of true positives and low rates of false positives. In this work we aim to compare the performance of the DCA and of a Self-Organizing Map (SOM) when applied to the detection of SYN port scans, through experimental analysis. A SOM is an ideal candidate for comparison as it shares similarities with the DCA in terms of the data fusion method employed. It is shown that the results of the two systems are comparable, and both produce false positives for the same processes. This shows that the DCA can produce anomaly detection results to the same standard as an established technique.
The backpropagation (BP) algorithm is often thought to be biologically implausible in the brain. One of the main reasons is that BP requires symmetric weight matrices in the feedforward and feedback pathways. To address this weight transport problem (Grossberg, 1987), two more biologically plausible algorithms, proposed by Liao et al. (2016) and Lillicrap et al. (2016), relax BPs weight symmetry requirements and demonstrate comparable learning capabilities to that of BP on small datasets. However, a recent study by Bartunov et al. (2018) evaluate variants of target-propagation (TP) and feedback alignment (FA) on MINIST, CIFAR, and ImageNet datasets, and find that although many of the proposed algorithms perform well on MNIST and CIFAR, they perform significantly worse than BP on ImageNet. Here, we additionally evaluate the sign-symmetry algorithm (Liao et al., 2016), which differs from both BP and FA in that the feedback and feedforward weights share signs but not magnitudes. We examine the performance of sign-symmetry and feedback alignment on ImageNet and MS COCO datasets using different network architectures (ResNet-18 and AlexNet for ImageNet, RetinaNet for MS COCO). Surprisingly, networks trained with sign-symmetry can attain classification performance approaching that of BP-trained networks. These results complement the study by Bartunov et al. (2018), and establish a new benchmark for future biologically plausible learning algorithms on more difficult datasets and more complex architectures.
Randomized exponential backoff is a widely deployed technique for coordinating access to a shared resource. A good backoff protocol should, arguably, satisfy three natural properties: (i) it should provide constant throughput, wasting as little time as possible; (ii) it should require few failed access attempts, minimizing the amount of wasted effort; and (iii) it should be robust, continuing to work efficiently even if some of the access attempts fail for spurious reasons. Unfortunately, exponential backoff has some well-known limitations in two of these areas: it provides poor (sub-constant) throughput (in the worst case), and is not robust (to resource acquisition failures). The goal of this paper is to fix exponential backoff by making it scalable, particularly focusing on the case where processes arrive in an on-line, worst-case fashion. We present a relatively simple backoff protocol~Re-Backoff~that has, at its heart, a version of exponential backoff. It guarantees expected constant throughput with dynamic process arrivals and requires only an expected polylogarithmic number of access attempts per process. Re-Backoff is also robust to periods where the shared resource is unavailable for a period of time. If it is unavailable for $D$ time slots, Re-Backoff provides the following guarantees. When the number of packets is a finite $n$, the average expected number of access attempts for successfully sending a packet is $O(log^2( n + D))$. In the infinite case, the average expected number of access attempts for successfully sending a packet is $O( log^2(eta) + log^2(D) )$ where $eta$ is the maximum number of processes that are ever in the system concurrently.
The understanding of the nanoscale physical properties of biomolecules and biomaterials will ultimately promote the research in the biological sciences. In this review, we focused on theory, simulation, and experiments involving nanoscale materials inspired by biological systems. Specifically, self-assembly in living and synthetic materials, bio-functionalized nanomaterials and probing techniques that use nanomaterials are discussed.
A convolutional neural network strongly robust to adversarial perturbations at reasonable computational and performance cost has not yet been demonstrated. The primate visual ventral stream seems to be robust to small perturbations in visual stimuli but the underlying mechanisms that give rise to this robust perception are not understood. In this work, we investigate the role of two biologically plausible mechanisms in adversarial robustness. We demonstrate that the non-uniform sampling performed by the primate retina and the presence of multiple receptive fields with a range of receptive field sizes at each eccentricity improve the robustness of neural networks to small adversarial perturbations. We verify that these two mechanisms do not suffer from gradient obfuscation and study their contribution to adversarial robustness through ablation studies.
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