Modeling the time evolution of discrete sets of items (e.g., genetic mutations) is a fundamental problem in many biomedical applications. We approach this problem through the lens of continuous-time Markov chains, and show that the resulting learning task is generally underspecified in the usual setting of cross-sectional data. We explore a perhaps surprising remedy: including a number of additional independent items can help determine time order, and hence resolve underspecification. This is in sharp contrast to the common practice of limiting the analysis to a small subset of relevant items, which is followed largely due to poor scaling of existing methods. To put our theoretical insight into practice, we develop an approximate likelihood maximization method for learning continuous-time Markov chains, which can scale to hundreds of items and is orders of magnitude faster than previous methods. We demonstrate the effectiveness of our approach on synthetic and real cancer data.

Modeling the time evolution of discrete sets of items (e.g., genetic mutations) is a fundamental problem in many biomedical applications. We approach this problem through the lens of continuous-time Markov chains, and show that the resulting learning task is generally underspecified in the usual setting of cross-sectional data. We explore a perhaps surprising remedy: including a number of additional independent items can help determine time order, and hence resolve underspecifi-cation. This is in sharp contrast to the common practice of limiting the analysis to a small subset of relevant items, which is followed largely due to poor scaling of existing methods. To put our theoretical insight into practice, we develop an approximate likelihood maximization method for learning continuous-time Markov chains, which can scale to hundreds of items and is orders of magnitude faster than previous methods. We demonstrate the effectiveness of our approach on synthetic and real cancer data.

This paper proposes a novel method for analyzing food retail processes with a focus on reducing food waste. The approach integrates object-centric process mining (OCPM) with stochastic process discovery and analysis. First, a stochastic process in the form of a continuous-time Markov chain is discovered from grocery store sales data. This model is then extended with supply activities. Finally, a what-if analysis is conducted to evaluate how the quantity of products in the store evolves over time. This enables the identification of an optimal balance between customer purchasing behavior and supply strategies, helping to prevent both food waste due to oversupply and product shortages.

Early diffusion models were formulated as continuous-time Markov chains over continuous spaces with Gaussian transition kernels (Sohl-Dickstein et al., 2015; Ho et al., 2020), and were later connected to continuous-time formulations via stochastic differential equations, offering a unifying perspective on score-based generative modeling (Song et al., 2020). In parallel, discrete diffusion has been developed from the viewpoint of Markov chains over discrete space (Hoogeboom et al., 2021). Notably, Austin et al. (2021) introduced D3PM with several families of discrete transition kernels, and Lou et al. (2023) proposed SEDD, which adopts score-based training objectives. A complementary line of work studies discrete flows (Campbell et al., 2024; Gat et al., 2024), aiming to understand continuous-time Markov chains (CTMCs) that interpolate between data and base distributions; this perspective aligns with ours. Subsequent extensions consider token-wise paths and path-wise structure within such flows (Shaul et al., 2024).

We make two closely related theoretical contributions to the use of importance sampling schemes. First, for independent sampling, we prove that the minimax optimal trial distribution coincides with the target if and only if the target distribution has no atom with probability greater than $1/2$, where "minimax" means that the worst-case asymptotic variance of the self-normalized importance sampling estimator is minimized. When a large atom exists, it should be downweighted by the trial distribution. A similar phenomenon holds for a continuous target distribution concentrated on a small set. Second, we argue that it is often advantageous to run the Metropolis--Hastings algorithm with a tempered stationary distribution, $π(x)^β$, and correct for the bias by importance weighting. The dynamics of this "importance-tempered" sampling scheme can be described by a continuous-time Markov chain. We prove that for one-dimensional targets with polynomial tails, $π(x) \propto (1 + |x|)^{-γ}$, this chain is uniformly ergodic if and only if $1/γ< β< (γ- 2)/γ$. These results suggest that for target distributions with light or polynomial tails of order $γ> 3$, importance tempering can improve the precision of time-average estimators and essentially eliminate the need for burn-in.

Modeling the time evolution of discrete sets of items (e.g., genetic mutations) is a fundamental problem in many biomedical applications. We approach this problem through the lens of continuous-time Markov chains, and show that the resulting learning task is generally underspecified in the usual setting of cross-sectional data. We explore a perhaps surprising remedy: including a number of additional independent items can help determine time order, and hence resolve underspecification. This is in sharp contrast to the common practice of limiting the analysis to a small subset of relevant items, which is followed largely due to poor scaling of existing methods. To put our theoretical insight into practice, we develop an approximate likelihood maximization method for learning continuous-time Markov chains, which can scale to hundreds of items and is orders of magnitude faster than previous methods.

This paper establishes a new and comprehensive theoretical analysis for the application of reinforcement learning (RL) in high-frequency market making. We bridge the modern RL theory and the continuous-time statistical models in high-frequency financial economics. Different with most existing literature on methodological research about developing various RL methods for market making problem, our work is a pilot to provide the theoretical analysis. We target the effects of sampling frequency, and find an interesting tradeoff between error and complexity of RL algorithm when tweaking the values of the time increment $\Delta$ $-$ as $\Delta$ becomes smaller, the error will be smaller but the complexity will be larger. We also study the two-player case under the general-sum game framework and establish the convergence of Nash equilibrium to the continuous-time game equilibrium as $\Delta\rightarrow0$. The Nash Q-learning algorithm, which is an online multi-agent RL method, is applied to solve the equilibrium. Our theories are not only useful for practitioners to choose the sampling frequency, but also very general and applicable to other high-frequency financial decision making problems, e.g., optimal executions, as long as the time-discretization of a continuous-time markov decision process is adopted. Monte Carlo simulation evidence support all of our theories.

This study introduces a novel approach for learning mixtures of Markov chains, a critical process applicable to various fields, including healthcare and the analysis of web users. Existing research has identified a clear divide in methodologies for learning mixtures of discrete and continuous-time Markov chains, while the latter presents additional complexities for recovery accuracy and efficiency. We introduce a unifying strategy for learning mixtures of discrete and continuous-time Markov chains, focusing on hitting times, which are well defined for both types. Specifically, we design a reconstruction algorithm that outputs a mixture which accurately reflects the estimated hitting times and demonstrates resilience to noise. We introduce an efficient gradient-descent approach, specifically tailored to manage the computational complexity and non-symmetric characteristics inherent in the calculation of hitting time derivatives. Our approach is also of significant interest when applied to a single Markov chain, thus extending the methodologies previously established by Hoskins et al. and Wittmann et al. We complement our theoretical work with experiments conducted on synthetic and real-world datasets, providing a comprehensive evaluation of our methodology.

Continuous-time Markov chains are used to model systems in which transitions between states as well as the time the system spends in each state are random. Many computational problems related to such chains have been solved, including determining state distributions as a function of time, parameter estimation, and control. However, the problem of inferring most likely trajectories, where a trajectory is a sequence of states as well as the amount of time spent in each state, appears unsolved. We study three versions of this problem: (i) an initial value problem, in which an initial state is given and we seek the most likely trajectory until a given final time, (ii) a boundary value problem, in which initial and final states and times are given, and we seek the most likely trajectory connecting them, and (iii) trajectory inference under partial observability, analogous to finding maximum likelihood trajectories for hidden Markov models. We show that maximum likelihood trajectories are not always well-defined, and describe a polynomial time test for well-definedness.