We consider the SIRWJS epidemiological model that includes the waning and boosting of immunity via secondary infections. We carry out combined analytical and numerical investigations of the dynamics. The formulae describing the existence and stability of equilibria are derived. Combining this analysis with numerical continuation techniques, we construct global bifurcation diagrams with respect to several epidemiological parameters. The bifurcation analysis reveals a very rich structure of possible global dynamics. We show that backward bifurcation is possible at the critical value of the basic reproduction number, $\mathcal{R}_0 = 1$. Furthermore, we find stability switches and Hopf bifurcations from steady states forming multiple endemic bubbles, and saddle-node bifurcations of periodic orbits. Regions of bistability are also found, where either two stable steady states, or a stable steady state and a stable periodic orbit coexist. This work provides an insight to the rich and complicated infectious disease dynamics that can emerge from the waning and boosting of immunity.
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There has been an explosion in interest in machine learning (ML) in recent years due to its applications to science and engineering. However, as ML techniques have advanced, tools for explaining and visualizing novel ML algorithms have lagged behind. Animation has been shown to be a powerful tool for making engaging visualizations of systems that dynamically change over time, which makes it well suited to the task of communicating ML algorithms. However, the current approach to animating ML algorithms is to handcraft applications that highlight specific algorithms or use complex generalized animation software. We developed ManimML, an open-source Python library for easily generating animations of ML algorithms directly from code. We sought to leverage ML practitioners' preexisting knowledge of programming rather than requiring them to learn complex animation software. ManimML has a familiar syntax for specifying neural networks that mimics popular deep learning frameworks like Pytorch. A user can take a preexisting neural network architecture and easily write a specification for an animation in ManimML, which will then automatically compose animations for different components of the system into a final animation of the entire neural network. ManimML is open source and available at //github.com/helblazer811/ManimML.
Partial orders are a natural model for the social hierarchies that may constrain "queue-like" rank-order data. However, the computational cost of counting the linear extensions of a general partial order on a ground set with more than a few tens of elements is prohibitive. Vertex-series-parallel partial orders (VSPs) are a subclass of partial orders which admit rapid counting and represent the sorts of relations we expect to see in a social hierarchy. However, no Bayesian analysis of VSPs has been given to date. We construct a marginally consistent family of priors over VSPs with a parameter controlling the prior distribution over VSP depth. The prior for VSPs is given in closed form. We extend an existing observation model for queue-like rank-order data to represent noise in our data and carry out Bayesian inference on "Royal Acta" data and Formula 1 race data. Model comparison shows our model is a better fit to the data than Plackett-Luce mixtures, Mallows mixtures, and "bucket order" models and competitive with more complex models fitting general partial orders.
Community detection is a crucial task in network analysis that can be significantly improved by incorporating subject-level information, i.e. covariates. However, current methods often struggle with selecting tuning parameters and analyzing low-degree nodes. In this paper, we introduce a novel method that addresses these challenges by constructing network-adjusted covariates, which leverage the network connections and covariates with a unique weight to each node based on the node's degree. Spectral clustering on network-adjusted covariates yields an exact recovery of community labels under certain conditions, which is tuning-free and computationally efficient. We present novel theoretical results about the strong consistency of our method under degree-corrected stochastic blockmodels with covariates, even in the presence of mis-specification and sparse communities with bounded degrees. Additionally, we establish a general lower bound for the community detection problem when both network and covariates are present, and it shows our method is optimal up to a constant factor. Our method outperforms existing approaches in simulations and a LastFM app user network, and provides interpretable community structures in a statistics publication citation network where $30\%$ of nodes are isolated.
In the study of sparse stochastic block models (SBMs) one often needs to analyze a distributional recursion, known as the belief propagation (BP) recursion. Uniqueness of the fixed point of this recursion implies several results about the SBM, including optimal recovery algorithms for SBM (Mossel et al. (2016)) and SBM with side information (Mossel and Xu (2016)), and a formula for SBM mutual information (Abbe et al. (2021)). The 2-community case corresponds to an Ising model, for which Yu and Polyanskiy (2022) established uniqueness for all cases. In this paper we analyze the $q$-ary Potts model, i.e., broadcasting of $q$-ary spins on a Galton-Watson tree with expected offspring degree $d$ through Potts channels with second-largest eigenvalue $\lambda$. We allow the intermediate vertices to be observed through noisy channels (side information). We prove that BP uniqueness holds with and without side information when $d\lambda^2 \ge 1 + C \max\{\lambda, q^{-1}\}\log q$ for some absolute constant $C>0$ independent of $q,\lambda,d$. For large $q$ and $\lambda = o(1/\log q)$, this is asymptotically achieving the Kesten-Stigum threshold $d\lambda^2=1$. These results imply mutual information formulas and optimal recovery algorithms for the $q$-community SBM in the corresponding ranges. For $q\ge 4$, Sly (2011); Mossel et al. (2022) showed that there exist choices of $q,\lambda,d$ below Kesten-Stigum (i.e. $d\lambda^2 < 1$) but reconstruction is possible. Somewhat surprisingly, we show that in such regimes BP uniqueness does not hold at least in the presence of weak side information. Our technical tool is a theory of $q$-ary symmetric channels, that we initiate here, generalizing the classical and widely-utilized information-theoretic characterization of BMS (binary memoryless symmetric) channels.
Extracting a stable and compact representation of the environment is crucial for efficient reinforcement learning in high-dimensional, noisy, and non-stationary environments. Different categories of information coexist in such environments -- how to effectively extract and disentangle these information remains a challenging problem. In this paper, we propose IFactor, a general framework to model four distinct categories of latent state variables that capture various aspects of information within the RL system, based on their interactions with actions and rewards. Our analysis establishes block-wise identifiability of these latent variables, which not only provides a stable and compact representation but also discloses that all reward-relevant factors are significant for policy learning. We further present a practical approach to learning the world model with identifiable blocks, ensuring the removal of redundants but retaining minimal and sufficient information for policy optimization. Experiments in synthetic worlds demonstrate that our method accurately identifies the ground-truth latent variables, substantiating our theoretical findings. Moreover, experiments in variants of the DeepMind Control Suite and RoboDesk showcase the superior performance of our approach over baselines.
As advancements in artificial intelligence propel progress in the life sciences, they may also enable the weaponisation and misuse of biological agents. This article differentiates two classes of AI tools that pose such biosecurity risks: large language models (LLMs) and biological design tools (BDTs). LLMs, such as GPT-4, are already able to provide dual-use information that could have enabled historical biological weapons efforts to succeed. As LLMs are turned into lab assistants and autonomous science tools, this will further increase their ability to support research. Thus, LLMs will in particular lower barriers to biological misuse. In contrast, BDTs will expand the capabilities of sophisticated actors. Concretely, BDTs may enable the creation of pandemic pathogens substantially worse than anything seen to date and could enable forms of more predictable and targeted biological weapons. In combination, LLMs and BDTs could raise the ceiling of harm from biological agents and could make them broadly accessible. The differing risk profiles of LLMs and BDTs have important implications for risk mitigation. LLM risks require urgent action and might be effectively mitigated by controlling access to dangerous capabilities. Mandatory pre-release evaluations could be critical to ensure that developers eliminate dangerous capabilities. Science-specific AI tools demand differentiated strategies to allow access to legitimate users while preventing misuse. Meanwhile, risks from BDTs are less defined and require monitoring by developers and policymakers. Key to reducing these risks will be enhanced screening of gene synthesis, interventions to deter biological misuse by sophisticated actors, and exploration of specific controls of BDTs.
In this paper, we present a toolbox for interval analysis in numpy, with an application to formal verification of neural network controlled systems. Using the notion of natural inclusion functions, we systematically construct interval bounds for a general class of mappings. The toolbox offers efficient computation of natural inclusion functions using compiled C code, as well as a familiar interface in numpy with its canonical features, such as n-dimensional arrays, matrix/vector operations, and vectorization. We then use this toolbox in formal verification of dynamical systems with neural network controllers, through the composition of their inclusion functions.
Theoretical studies on transfer learning or domain adaptation have so far focused on situations with a known hypothesis class or model; however in practice, some amount of model selection is usually involved, often appearing under the umbrella term of hyperparameter-tuning: for example, one may think of the problem of tuning for the right neural network architecture towards a target task, while leveraging data from a related source task. Now, in addition to the usual tradeoffs on approximation vs estimation errors involved in model selection, this problem brings in a new complexity term, namely, the transfer distance between source and target distributions, which is known to vary with the choice of hypothesis class. We present a first study of this problem, focusing on classification; in particular, the analysis reveals some remarkable phenomena: adaptive rates, i.e., those achievable with no distributional information, can be arbitrarily slower than oracle rates, i.e., when given knowledge on distances.
The conjoining of dynamical systems and deep learning has become a topic of great interest. In particular, neural differential equations (NDEs) demonstrate that neural networks and differential equation are two sides of the same coin. Traditional parameterised differential equations are a special case. Many popular neural network architectures, such as residual networks and recurrent networks, are discretisations. NDEs are suitable for tackling generative problems, dynamical systems, and time series (particularly in physics, finance, ...) and are thus of interest to both modern machine learning and traditional mathematical modelling. NDEs offer high-capacity function approximation, strong priors on model space, the ability to handle irregular data, memory efficiency, and a wealth of available theory on both sides. This doctoral thesis provides an in-depth survey of the field. Topics include: neural ordinary differential equations (e.g. for hybrid neural/mechanistic modelling of physical systems); neural controlled differential equations (e.g. for learning functions of irregular time series); and neural stochastic differential equations (e.g. to produce generative models capable of representing complex stochastic dynamics, or sampling from complex high-dimensional distributions). Further topics include: numerical methods for NDEs (e.g. reversible differential equations solvers, backpropagation through differential equations, Brownian reconstruction); symbolic regression for dynamical systems (e.g. via regularised evolution); and deep implicit models (e.g. deep equilibrium models, differentiable optimisation). We anticipate this thesis will be of interest to anyone interested in the marriage of deep learning with dynamical systems, and hope it will provide a useful reference for the current state of the art.
We consider the problem of discovering $K$ related Gaussian directed acyclic graphs (DAGs), where the involved graph structures share a consistent causal order and sparse unions of supports. Under the multi-task learning setting, we propose a $l_1/l_2$-regularized maximum likelihood estimator (MLE) for learning $K$ linear structural equation models. We theoretically show that the joint estimator, by leveraging data across related tasks, can achieve a better sample complexity for recovering the causal order (or topological order) than separate estimations. Moreover, the joint estimator is able to recover non-identifiable DAGs, by estimating them together with some identifiable DAGs. Lastly, our analysis also shows the consistency of union support recovery of the structures. To allow practical implementation, we design a continuous optimization problem whose optimizer is the same as the joint estimator and can be approximated efficiently by an iterative algorithm. We validate the theoretical analysis and the effectiveness of the joint estimator in experiments.
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