Biomaker CA: a Biome Maker project using Cellular Automata

We introduce Biomaker CA: a Biome Maker project using Cellular Automata (CA). In Biomaker CA, morphogenesis is a first class citizen and small seeds need to grow into plant-like organisms to survive in a nutrient starved environment and eventually reproduce with variation so that a biome survives for long timelines. We simulate complex biomes by means of CA rules in 2D grids and parallelize all of its computation on GPUs through the Python JAX framework. We show how this project allows for several different kinds of environments and laws of 'physics', alongside different model architectures and mutation strategies. We further analyze some configurations to show how plant agents can grow, survive, reproduce, and evolve, forming stable and unstable biomes. We then demonstrate how one can meta-evolve models to survive in a harsh environment either through end-to-end meta-evolution or by a more surgical and efficient approach, called Petri dish meta-evolution. Finally, we show how to perform interactive evolution, where the user decides how to evolve a plant model interactively and then deploys it in a larger environment. We open source Biomaker CA at: https://tinyurl.com/2x8yu34s .

Growing Steerable Neural Cellular Automata

Neural Cellular Automata (NCA) models have shown remarkable capacity for pattern formation and complex global behaviors stemming from local coordination. However, in the original implementation of NCA, cells are incapable of adjusting their own orientation, and it is the responsibility of the model designer to orient them externally. A recent isotropic variant of NCA (Growing Isotropic Neural Cellular Automata) makes the model orientation-independent - cells can no longer tell up from down, nor left from right - by removing its dependency on perceiving the gradient of spatial states in its neighborhood. In this work, we revisit NCA with a different approach: we make each cell responsible for its own orientation by allowing it to "turn" as determined by an adjustable internal state. The resulting Steerable NCA contains cells of varying orientation embedded in the same pattern. We observe how, while Isotropic NCA are orientation-agnostic, Steerable NCA have chirality: they have a predetermined left-right symmetry. We therefore show that we can train Steerable NCA in similar but simpler ways than their Isotropic variant by: (1) breaking symmetries using only two seeds, or (2) introducing a rotation-invariant training objective and relying on asynchronous cell updates to break the up-down symmetry of the system.

Differentiable Programming of Chemical Reaction Networks

We present a differentiable formulation of abstract chemical reaction networks (CRNs) that can be trained to solve a variety of computational tasks. Chemical reaction networks are one of the most fundamental computational substrates used by nature. We study well-mixed single-chamber systems, as well as systems with multiple chambers separated by membranes, under mass-action kinetics. We demonstrate that differentiable optimisation, combined with proper regularisation, can discover non-trivial sparse reaction networks that can implement various sorts of oscillators and other chemical computing devices.

Transformers learn in-context by gradient descent

Transformers have become the state-of-the-art neural network architecture across numerous domains of machine learning. This is partly due to their celebrated ability to transfer and to learn in-context based on few examples. Nevertheless, the mechanisms by which Transformers become in-context learners are not well understood and remain mostly an intuition. Here, we argue that training Transformers on auto-regressive tasks can be closely related to well-known gradient-based meta-learning formulations. We start by providing a simple weight construction that shows the equivalence of data transformations induced by 1) a single linear self-attention layer and by 2) gradient-descent (GD) on a regression loss. Motivated by that construction, we show empirically that when training self-attention-only Transformers on simple regression tasks either the models learned by GD and Transformers show great similarity or, remarkably, the weights found by optimization match the construction. Thus we show how trained Transformers implement gradient descent in their forward pass. This allows us, at least in the domain of regression problems, to mechanistically understand the inner workings of optimized Transformers that learn in-context. Furthermore, we identify how Transformers surpass plain gradient descent by an iterative curvature correction and learn linear models on deep data representations to solve non-linear regression tasks. Finally, we discuss intriguing parallels to a mechanism identified to be crucial for in-context learning termed induction-head (Olsson et al., 2022) and show how it could be understood as a specific case of in-context learning by gradient descent learning within Transformers.

Growing Isotropic Neural Cellular Automata

Modeling the ability of multicellular organisms to build and maintain their bodies through local interactions between individual cells (morphogenesis) is a long-standing challenge of developmental biology. Recently, the Neural Cellular Automata (NCA) model was proposed as a way to find local system rules that produce a desired global behaviour, such as growing and persisting a predefined pattern, by repeatedly applying the same rule over a grid starting from a single cell. In this work we argue that the original Growing NCA model has an important limitation: anisotropy of the learned update rule. This implies the presence of an external factor that orients the cells in a particular direction. In other words, 'physical' rules of the underlying system are not invariant to rotation, thus prohibiting the existence of differently oriented instances of the target pattern on the same grid. We propose a modified Isotropic NCA model that does not have this limitation. We demonstrate that cell systems can be trained to grow accurate asymmetrical patterns through either of two methods: by breaking symmetries using structured seeds; or by introducing a rotation-reflection invariant training objective and relying on symmetry breaking caused by asynchronous cell updates.

Differentiable Programming of Reaction-Diffusion Patterns

Reaction-Diffusion (RD) systems provide a computational framework that governs many pattern formation processes in nature. Current RD system design practices boil down to trial-and-error parameter search. We propose a differentiable optimization method for learning the RD system parameters to perform example-based texture synthesis on a 2D plane. We do this by representing the RD system as a variant of Neural Cellular Automata and using task-specific differentiable loss functions. RD systems generated by our method exhibit robust, non-trivial 'life-like' behavior.

Texture Generation with Neural Cellular Automata

Neural Cellular Automata (NCA) have shown a remarkable ability to learn the required rules to "grow" images, classify morphologies, segment images, as well as to do general computation such as path-finding. We believe the inductive prior they introduce lends itself to the generation of textures. Textures in the natural world are often generated by variants of locally interacting reaction-diffusion systems. Human-made textures are likewise often generated in a local manner (textile weaving, for instance) or using rules with local dependencies (regular grids or geometric patterns). We demonstrate learning a texture generator from a single template image, with the generation method being embarrassingly parallel, exhibiting quick convergence and high fidelity of output, and requiring only some minimal assumptions around the underlying state manifold. Furthermore, we investigate properties of the learned models that are both useful and interesting, such as non-stationary dynamics and an inherent robustness to damage. Finally, we make qualitative claims that the behaviour exhibited by the NCA model is a learned, distributed, local algorithm to generate a texture, setting our method apart from existing work on texture generation. We discuss the advantages of such a paradigm.

Image segmentation via Cellular Automata

In this paper, we propose a new approach for building cellular automata to solve real-world segmentation problems. We design and train a cellular automaton that can successfully segment high-resolution images. We consider a colony that densely inhabits the pixel grid, and all cells are governed by a randomized update that uses the current state, the color, and the state of the $3\times 3$ neighborhood. The space of possible rules is defined by a small neural network. The update rule is applied repeatedly in parallel to a large random subset of cells and after convergence is used to produce segmentation masks that are then back-propagated to learn the optimal update rules using standard gradient descent methods. We demonstrate that such models can be learned efficiently with only limited trajectory length and that they show remarkable ability to organize the information to produce a globally consistent segmentation result, using only local information exchange. From a practical perspective, our approach allows us to build very efficient models -- our smallest automaton uses less than 10,000 parameters to solve complex segmentation tasks.

MPLP: Learning a Message Passing Learning Protocol

We present a novel method for learning the weights of an artificial neural network - a Message Passing Learning Protocol (MPLP). In MPLP, we abstract every operations occurring in ANNs as independent agents. Each agent is responsible for ingesting incoming multidimensional messages from other agents, updating its internal state, and generating multidimensional messages to be passed on to neighbouring agents. We demonstrate the viability of MPLP as opposed to traditional gradient-based approaches on simple feed-forward neural networks, and present a framework capable of generalizing to non-traditional neural network architectures. MPLP is meta learned using end-to-end gradient-based meta-optimisation. We further discuss the observed properties of MPLP and hypothesize its applicability on various fields of deep learning.