This review explores the use of machine learning in discovering collective variables for biomolecular dynamics.
arXiv research
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Understanding biological network dynamics is a fundamental issue in various scientific and engineering fields. Network theory is capable of revealing the relationship between elements and their propagation; however, for complex collective motions, the network properties often transiently and complexly change. A fundame…
We derive a class of macroscopic differential equations that describe collective adaptation, starting from a discrete-time stochastic microscopic model. The behavior of each agent is a dynamic balance between adaptation that locally achieves the best action and memory loss that leads to randomized behavior. We show tha…
A universal collection of 4 invariants improves neural network accuracy for molecular dynamics.
We present a simple model of firm rating evolution. We consider two sources of defaults: individual dynamics of economic development and Potts-like interactions between firms. We show that such a defined model leads to phase transition, which results in collective defaults. The existence of the collective phase depends…
ISOKANN learns collective variables and effective dynamics for metastable transitions.
The paper analyzes cryptocurrency and equity markets using advanced statistical methods.
The study initiates a theoretical analysis of dynamic benchmarking models.
Study reveals subdominant correlations in motorway network dynamics.
Investigates cryptocurrency maturity through collective dynamics and diversification.
We describe parallel Markov chain Monte Carlo methods that propagate a collective ensemble of paths, with local covariance information calculated from neighboring replicas. The use of collective dynamics eliminates multiplicative noise and stabilizes the dynamics thus providing a practical approach to difficult anisotr…
Study on cryptocurrency market dynamics and correlations over time.
Extracts intrinsic spatial coordinates for complex agent systems to learn PDEs.
Estimates RL data for dynamic treatment effects using GMM.
We present an adversarial active exploration for inverse dynamics model learning, a simple yet effective learning scheme that incentivizes exploration in an environment without any human intervention. Our framework consists of a deep reinforcement learning (DRL) agent and an inverse dynamics model contesting with each …
A tutorial on dynamic Laplacian for time-evolving data clusters.
We characterize the collective phenomena of a liquid market. By interpreting the behavior of a no-arbitrage N asset market in terms of a particle system scenario, (thermo)dynamical-like properties can be extracted from the asset kinetics. In this scheme the mechanisms of the particle interaction can be widely investiga…
Study shows similarities and differences in crypto and equity dynamics during pandemic.
Paper proposes active learning for mining conflict dynamics from textual data.
NFTs with diverse rare attributes sell at higher prices.
New algorithm for collective Gaussian hidden Markov models inference.
In this paper, we develop the continuous time dynamic topic model (cDTM). The cDTM is a dynamic topic model that uses Brownian motion to model the latent topics through a sequential collection of documents, where a "topic" is a pattern of word use that we expect to evolve over the course of the collection. We derive an…
Study shows gain-loss asymmetry in stock indices using a q-spin Potts model.
Particle- and agent-based systems are a ubiquitous modeling tool in many disciplines. We consider the fundamental problem of inferring interaction kernels from observations of agent-based dynamical systems given observations of trajectories, in particular for collective dynamical systems exhibiting emergent behaviors w…
Topic models are probabilistic models for discovering topical themes in collections of documents. In real world applications, these models provide us with the means of organizing what would otherwise be unstructured collections. They can help us cluster a huge collection into different topics or find a subset of the co…
Model learns collective and individual dynamics in time series data.
Financial market is an example of complex system, which is characterized by a highly intricate organization and the emergence of collective behavior. In this paper, we quantify this emergent dynamics in the financial market by using concepts of network synchronization. We consider networks constructed by the correlatio…
In this article we discuss some of the consequences of the mixed membership perspective on time series analysis. In its most abstract form, a mixed membership model aims to associate an individual entity with some set of attributes based on a collection of observed data. Although much of the literature on mixed members…
Measures collectivity in financial covariances and correlations to reveal trends and precursors.
Study examines NFT market dynamics using correlation and noise analysis.
New CVs preserve transition rates in molecular dynamics.
A microscopic model is established for financial Brownian motion from the direct observation of the dynamics of high-frequency traders (HFTs) in a foreign exchange market. Furthermore, a theoretical framework parallel to molecular kinetic theory is developed for the systematic description of the financial market from m…
Detailed study of the financial empirical correlation matrix of the 30 companies comprised by DAX within the period of the last 11 years, using the time-window of 30 trading days, is presented. This allows to clearly identify a nontrivial time-dependence of the resulting correlations. In addition, as a rule, the draw d…
CUDC collects diverse data for offline RL by predicting future states.
Flocking refers to collective behavior of a large number of interacting entities, where the interactions between discrete individuals produce collective motion on the large scale. We employ an agent-based model to describe the microscopic dynamics of each individual in a flock, and use a fractional PDE to model the evo…
Topic modeling analyzes documents to learn meaningful patterns of words. For documents collected in sequence, dynamic topic models capture how these patterns vary over time. We develop the dynamic embedded topic model (D-ETM), a generative model of documents that combines dynamic latent Dirichlet allocation (D-LDA) and…
This paper proposes a geometry-aware active learning framework for spatiotemporal dynamic systems.
Financial markets modeled like brain networks using dMNC.
Macromolecular and biomolecular folding landscapes typically contain high free energy barriers that impede efficient sampling of configurational space by standard molecular dynamics simulation. Biased sampling can artificially drive the simulation along pre-specified collective variables (CVs), but success depends crit…
Financial economic models often assume that investors know (or agree on) the fundamental value of the shares of the firm, easing the passage from the individual to the collective dimension of the financial system generated by the Share Exchange over time. Our model relaxes that heroic assumption of one unique "true val…
Study financial crises using mathematical techniques to compare equity performance.
Many systems of interest in science and engineering are made up of interacting subsystems. These subsystems, in turn, could be made up of collections of smaller interacting subsystems and so on. In a series of papers David Spivak with collaborators formalized these kinds of structures (systems of systems) as algebras o…
Study financial markets using synchronization measures and clustering algorithms.
We propose a probabilistic modeling framework for learning the dynamic patterns in the collective behaviors of social agents and developing profiles for different behavioral groups, using data collected from multiple information sources. The proposed model is based on a hierarchical Bayesian process, in which each obse…
This work learns visual representations for deformable objects using contrastive estimation.
We document a mechanism operating in complex adaptive systems leading to dynamical pockets of predictability (``prediction days''), in which agents collectively take predetermined courses of action, transiently decoupled from past history. We demonstrate and test it out-of-sample on synthetic minority and majority game…
We show that the emergence of systemic risk in complex systems can be understood from the evolution of functional networks representing interactions inferred from fluctuation correlations between macroscopic observables. Specifically, we analyze the long-term collective dynamics of the New York Stock Exchange between 1…
New method uses normalizing flows to improve force fields for coarse-grained molecular dynamics.