SUMMARY: ChromaX is a Python library that enables the simulation of genetic recombination, genomic estimated breeding value calculations, and selection processes. By utilizing GPU processing, it can perform these simulations up to two orders of magnitude faster than existing tools with standard hardware. This offers breeders and scientists new opportunities to simulate genetic gain and optimize breeding schemes. AVAILABILITY AND IMPLEMENTATION: The documentation is available at https://chromax.readthedocs.io. The code is available at https://github.com/kora-labs/chromax.

In this work, we consider the problem of recovery a planted k-densest sub-hypergraph on d-uniform hypergraphs. This fundamental problem appears in different contexts, e.g., community detection, average-case complexity, and neuroscience applications as a structural variant of tensor-PCA problem. We provide tight information-theoretic upper and lower bounds for the exact recovery threshold by the maximum-likelihood estimator, as well as algorithmic bounds based on approximate message passing algorithms. The problem exhibits a typical statistical-to-computational gap observed in analogous sparse settings that widen with increasing sparsity of the problem. The bounds show that the signal structure impacts the location of the statistical and computational phase transition that the known existing bounds for the tensor-PCA model do not capture. This effect is due to the generic planted signal prior that this latter model addresses.

To improve the sustainability and resilience of modern food systems, designing improved crop management strategies is crucial. The increasing abundance of data on agricultural systems suggests that future strategies could benefit from adapting to environmental conditions, but how to design these adaptive policies poses a new frontier. A natural technique for learning policies in these kinds of sequential decision-making problems is reinforcement learning (RL). To obtain the large number of samples required to learn effective RL policies, existing work has used mechanistic crop growth models (CGMs) as simulators. These solutions focus on single-year, single-crop simulations for learning strategies for a single agricultural management practice. However, to learn sustainable long-term policies we must be able to train in multi-year environments, with multiple crops, and consider a wider array of management techniques. We introduce CYCLESGYM, an RL environment based on the multi-year, multi-crop CGM Cycles. CYCLESGYM allows for long-term planning in agroecosystems, provides modular state space and reward constructors and weather generators, and allows for complex actions. For RL researchers, this is a novel benchmark to investigate issues arising in real-world applications. For agronomists, we demonstrate the potential of RL as a powerful optimization tool for agricultural systems management in multi-year case studies on nitrogen (N) fertilization and crop planning scenarios.

We study the problem of estimating a rank-1additive deformation of a Gaussian tensor according to the maximum-likelihood estimator (MLE). The analysis is carried out in the sparse setting, where the underlying signal has a support that scales sublinearly with the total number of dimensions. We show that for Bernoulli distributed signals, the MLE undergoes an all-or-nothing (AoN) phase transition, already established for the minimum mean-square-error estimator (MMSE) in the same problem. The result follows from two main technical points: (i) the connection established between the MLE and the MMSE, using the first and second-moment methods in the constrained signal space, (ii) a recovery regime for the MMSE stricter than the simple error vanishing characterization given in the standard AoN, that is here proved as a general result. A full version of this paper is accessible at: https://arxiv.org/pdf/2101.09994.pdf

A myriad of access control policy languages have been and continue to be proposed. The design of policy miners for each such language is a challenging task that has required specialized machine learning and combinatorial algorithms. We present an alternative method, universal access control policy mining (Unicorn). We show how this method streamlines the design of policy miners for a wide variety of policy languages including ABAC, RBAC, RBAC with user-attribute constraints, RBAC with spatio-temporal constraints, and an expressive fragment of XACML. For the latter two, there were no known policy miners until now. To design a policy miner using Unicorn, one needs a policy language and a metric quantifying how well a policy fits an assignment of permissions to users. From these, one builds the policy miner as a search algorithm that computes a policy that best fits the given permission assignment. We experimentally evaluate the policy miners built with Unicorn on logs from Amazon and access control matrices from other companies. Despite the genericity of our method, our policy miners are competitive with and sometimes even better than specialized state-of-the-art policy miners. The true positive rates of policies we mined differ by only 5% from the policies mined by the state of the art and the false positive rates are always below 5%. In the case of ABAC, it even outperforms the state of the art.

Generative models for networks with communities have been studied extensively for being a fertile ground to establish information-theoretic and computational thresholds. In this paper we propose a new toy model for planted generative models called planted Random Energy Model (REM), inspired by Derrida's REM. For this model we provide the asymptotic behaviour of the probability of error for the maximum likelihood estimator and hence the exact recovery threshold. As an application, we further consider the 2 non-equally sized community Weighted Stochastic Block Model (2-WSBM) on h uniform hypergraphs, that is equivalent to the P-REM on both sides of the spectrum, for high and low edge cardinality h. We provide upper and lower bounds for the exact recoverability for any h, mapping these problems to the aforementioned P-REM. To the best of our knowledge these are the first consistency results for the 2-WSBM on graphs and on hypergraphs with non-equally sized community.