arXiv subjects

Pratyush Tiwary

Publications and source records attributed to Pratyush Tiwary.

At least 19 recordsLinked to original sources

arXiv2026

SPIBER: Reconstructing Free Energy Landscapes from Short, Unconverged Trajectories with Generative Flow Networks

Molecular systems have many degrees of freedom, but their metastable behavior can often be described by a few collective variables. Identifying these variables and estimating free energies along them from limited simulation data remains a challenging, important problem. Separate short trajectories may sample different metastable states without capturing transitions or establishing their relative equilibrium populations. For unbiased trajectories generated with the same Hamiltonian at a single temperature, alternate methods based on histogram reweighting cannot correct this imbalance. Here we present SPIBER, which combines the State Predictive Information Bottleneck (SPIB) with Generative Flow Networks (GFlowNets). SPIB uses deep learning to approximate slow degrees of freedom through a past-future information bottleneck, retaining information needed to predict future metastable states. We show that this compression limits conditional entropy variations in populated regions, allowing conditional mean potential energies, which are much easier to calculate, to be used to approximate free energy differences. Given sufficient local sampling to estimate these energies, they define the target distribution for GFlowNets, energy-based generative samplers that sample according to estimated thermodynamic stability rather than observed populations. For a particle in a radial double-well potential, for alanine dipeptide, and for the nine-residue peptide AIB9, SPIBER recovers free energy differences between sampled metastable states to within one thermal energy unit of reference values. The method combines collective-variable learning and free energy estimation in up to four latent dimensions, without requiring converged state populations or additional molecular dynamics simulations.

physics.chem-ph↗

arXiv2026

Expanding Protein Structure Prediction into Conformational State Space

Recent AI advances have enabled protein structure prediction at near-experimental accuracy, largely solving the problem of identifying a dominant conformation from sequence. Many proteins, however, function as dynamic systems populating multiple conformational states with activity emerging from shifts in relative occupancy--an incomplete picture when reduced to one structure. Here, we argue that structure prediction should be reformulated as a state-space inference problem: recovering not one conformation's coordinates but accessible states, their energetic and kinetic relationships, context dependence, and responses to perturbations. We review emerging strategies--deep learning ensemble generators, physics-based simulations, and experimental constraints--and outline a roadmap toward state-space prediction.

q-bio.BM↗

arXiv2026

The Future of Artificial Intelligence and the Mathematical and Physical Sciences (AI+MPS)

This community paper developed out of the NSF Workshop on the Future of Artificial Intelligence (AI) and the Mathematical and Physics Sciences (MPS), which was held in March 2025 with the goal of understanding how the MPS domains (Astronomy, Chemistry, Materials Research, Mathematical Sciences, and Physics) can best capitalize on, and contribute to, the future of AI. We present here a summary and snapshot of the MPS community's perspective, as of Spring/Summer 2025, in a rapidly developing field. The link between AI and MPS is becoming increasingly inextricable; now is a crucial moment to strengthen the link between AI and Science by pursuing a strategy that proactively and thoughtfully leverages the potential of AI for scientific discovery and optimizes opportunities to impact the development of AI by applying concepts from fundamental science. To achieve this, we propose activities and strategic priorities that: (1) enable AI+MPS research in both directions; (2) build up an interdisciplinary community of AI+MPS researchers; and (3) foster education and workforce development in AI for MPS researchers and students. We conclude with a summary of suggested priorities for funding agencies, educational institutions, and individual researchers to help position the MPS community to be a leader in, and take full advantage of, the transformative potential of AI+MPS.

cs.AI↗

arXiv2025

Combined Representation and Generation with Diffusive State Predictive Information Bottleneck

Generative modeling becomes increasingly data-intensive in high-dimensional spaces. In molecular science, where data collection is expensive and important events are rare, compression to lower-dimensional manifolds is especially important for various downstream tasks, including generation. We combine a time-lagged information bottleneck designed to characterize molecular important representations and a diffusion model in one joint training objective. The resulting protocol, which we term Diffusive State Predictive Information Bottleneck (D-SPIB), enables the balancing of representation learning and generation aims in one flexible architecture. Additionally, the model is capable of combining temperature information from different molecular simulation trajectories to learn a coherent and useful internal representation of thermodynamics. We benchmark D-SPIB on multiple molecular tasks and showcase its potential for exploring physical conditions outside the training set.

cs.LG↗

arXiv2025

Latent Thermodynamic Flows: Unified Representation Learning and Generative Modeling of Temperature-Dependent Behaviors from Limited Data

Accurate characterization of the equilibrium distributions of complex molecular systems and their dependence on environmental factors such as temperature is essential for understanding thermodynamic properties and transition mechanisms. Projecting these distributions onto meaningful low-dimensional representations enables interpretability and downstream analysis. Recent advances in generative AI, particularly flow models such as Normalizing Flows (NFs), have shown promise in modeling such distributions, but their scope is limited without tailored representation learning. In this work, we introduce Latent Thermodynamic Flows (LaTF), an end-to-end framework that tightly integrates representation learning and generative modeling. LaTF unifies the State Predictive Information Bottleneck (SPIB) with NFs to simultaneously learn low-dimensional latent representations, referred to as Collective Variables (CVs), classify metastable states, and generate equilibrium distributions across temperatures beyond the training data. The two components of representation learning and generative modeling are optimized jointly, ensuring that the learned latent features capture the system's slow, important degrees of freedom while the generative model accurately reproduces the system's equilibrium behavior. We demonstrate LaTF's effectiveness across diverse systems, including a model potential, the Chignolin protein, and cluster of Lennard Jones particles, with thorough evaluations and benchmarking using multiple metrics and extensive simulations. Finally, we apply LaTF to a RNA tetraloop system, where despite using simulation data from only two temperatures, LaTF reconstructs the temperature-dependent structural ensemble and melting behavior, consistent with experimental and prior extensive computational results.

cs.LG↗

arXiv2025

Exponentially Tilted Thermodynamic Maps (expTM): Predicting Phase Transitions Across Temperature, Pressure, and Chemical Potential

Predicting and characterizing phase transitions is crucial for understanding generic physical phenomena such as crystallization, protein folding and others. However, directly observing phase transitions is not always easy, and often one has limited observations far from the phase boundary and measured under some specific thermodynamic conditions. In this study, we propose a statistical physics and Generative AI driven framework that can take such limited information to generate samples of different phases under arbitrary thermodynamic conditions, which we name Exponentially Tilted Thermodynamic Maps (expTM). The central idea is to map collected data into a tractable simple prior expressed as an exponentially tilted Gaussian. We demonstrate how the variance and mean of the prior can be correlated with pairs of thermodynamic control variables, including temperature, pressure, and chemical potential. This gives us the ability to generate thermodynamically correct samples under any values of the control variables. To demonstrate the practical applicability of this approach, we use expTM to sample the lattice gas models with the Grand Canonical ensemble, capturing phase transitions under varying chemical potentials and temperatures. We further demonstrate how expTM can model the isothermal-isobaric ensemble, with which we predict different phases of CO2 under varying pressure conditions. Both examples are trained on very limited data far from the phase boundary. These results establish expTM as a robust tool for understanding phase transitions across diverse thermodynamic conditions requiring only a small number of observations.

cond-mat.stat-mech↗

arXiv2024

PLUMED Tutorials: a collaborative, community-driven learning ecosystem

In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several challenges. Common methods like direct knowledge transfer and in-person workshops are limited in reach and comprehensiveness. Furthermore, while the COVID-19 pandemic highlighted the benefits of online training, traditional online tutorials can quickly become outdated and may not cover all the software's functionalities. To address these issues, here we introduce ``PLUMED Tutorials'', a collaborative model for developing, sharing, and updating online tutorials. This initiative utilizes repository management and continuous integration to ensure compatibility with software updates. Moreover, the tutorials are interconnected to form a structured learning path and are enriched with automatic annotations to provide broader context. This paper illustrates the development, features, and advantages of PLUMED Tutorials, aiming to foster an open community for creating and sharing educational resources.

physics.ed-ph↗

arXiv2024

Augmenting Human Expertise in Weighted Ensemble Simulations through Deep Learning based Information Bottleneck

The weighted ensemble (WE) method stands out as a widely used segment-based sampling technique renowned for its rigorous treatment of kinetics. The WE framework typically involves initially mapping the configuration space onto a low-dimensional collective variable (CV) space and then partitioning it into bins. The efficacy of WE simulations heavily depends on the selection of CVs and binning schemes. The recently proposed State Predictive Information Bottleneck (SPIB) method has emerged as a promising tool for automatically constructing CVs from data and guiding enhanced sampling through an iterative manner. In this work, we advance this data-driven pipeline by incorporating prior expert knowledge. Our hybrid approach combines SPIB-learned CVs to enhance sampling in explored regions with expert-based CVs to guide exploration in regions of interest, synergizing the strengths of both methods. Through benchmarking on alanine dipeptide and chignoin systems, we demonstrate that our hybrid approach effectively guides WE simulations to sample states of interest, and reduces run-to-run variances. Moreover, our integration of the SPIB model also enhances the analysis and interpretation of WE simulation data by effectively identifying metastable states and pathways, and offering direct visualization of dynamics.

physics.comp-ph↗

arXiv2024

A survey of probabilistic generative frameworks for molecular simulations

Generative artificial intelligence is now a widely used tool in molecular science. Despite the popularity of probabilistic generative models, numerical experiments benchmarking their performance on molecular data are lacking. In this work, we introduce and explain several classes of generative models, broadly sorted into two categories: flow-based models and diffusion models. We select three representative models: Neural Spline Flows, Conditional Flow Matching, and Denoising Diffusion Probabilistic Models, and examine their accuracy, computational cost, and generation speed across datasets with tunable dimensionality, complexity, and modal asymmetry. Our findings are varied, with no one framework being the best for all purposes. In a nutshell, (i) Neural Spline Flows do best at capturing mode asymmetry present in low-dimensional data, (ii) Conditional Flow Matching outperforms other models for high-dimensional data with low complexity, and (iii) Denoising Diffusion Probabilistic Models appears the best for low-dimensional data with high complexity. Our datasets include a Gaussian mixture model and the dihedral torsion angle distribution of the Aib\textsubscript{9} peptide, generated via a molecular dynamics simulation. We hope our taxonomy of probabilistic generative frameworks and numerical results may guide model selection for a wide range of molecular tasks.

cs.LG↗

arXiv2024

Inferring the Isotropic-nematic Phase Transition with Generative Machine Learning

Contemporary work implies generative machine learning models are capable of learning the phase behavior in condensed matter systems such as the Ising model. In this Letter, we utilize a score-based modeling procedure called Thermodynamic Maps to describe the isotropic-nematic phase transition in a melt of $N=343$ calamitic Gay-Berne ellipsoids. When trained on samples generated by molecular dynamics simulation from a single temperature on either side of the phase transition, we demonstrate this generative machine learning approach infers information regarding the critical behavior and estimates effectively the nematic order parameter at sampled temperatures between the two training temperatures. These results demonstrate score-based models' ability to learn the physics of a non-trivial liquid crystalline phase transition driven by anisotropic interactions both entropic and energetic in nature.

cond-mat.stat-mech↗

arXiv2024

Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics

Molecular dynamics simulations offer detailed insights into atomic motions but face timescale limitations. Enhanced sampling methods have addressed these challenges but even with machine learning, they often rely on pre-selected expert-based features. In this work, we present the Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) framework, which combines graph neural networks and the State Predictive Information Bottleneck to automatically learn low-dimensional representations directly from atomic coordinates. Tested on three benchmark systems, our approach predicts essential structural, thermodynamic and kinetic information for slow processes, demonstrating robustness across diverse systems. The method shows promise for complex systems, enabling effective enhanced sampling without requiring pre-defined reaction coordinates or input features.

cs.LG↗

arXiv2024

Generative artificial intelligence for computational chemistry: a roadmap to predicting emergent phenomena

The recent surge in Generative Artificial Intelligence (AI) has introduced exciting possibilities for computational chemistry. Generative AI methods have made significant progress in sampling molecular structures across chemical species, developing force fields, and speeding up simulations. This Perspective offers a structured overview, beginning with the fundamental theoretical concepts in both Generative AI and computational chemistry. It then covers widely used Generative AI methods, including autoencoders, generative adversarial networks, reinforcement learning, flow models and language models, and highlights their selected applications in diverse areas including force field development, and protein/RNA structure prediction. A key focus is on the challenges these methods face before they become truly predictive, particularly in predicting emergent chemical phenomena. We believe that the ultimate goal of a simulation method or theory is to predict phenomena not seen before, and that Generative AI should be subject to these same standards before it is deemed useful for chemistry. We suggest that to overcome these challenges, future AI models need to integrate core chemical principles, especially from statistical mechanics.

cond-mat.stat-mech↗

arXiv2024

Atomic scale insights into NaCl nucleation in nanoconfined environments

In this work we examine the nucleation from NaCl aqueous solutions within nano-confined environments, employing enhanced sampling molecular dynamics simulations integrated with machine learning-derived reaction coordinates. Through our simulations, we successfully induce phase transitions between solid, liquid, and a hydrated phase, typically observed at lower temperatures in bulk environments. Interestingly, nano-confinement serves to stabilize the solid phase and elevate melting points. Our simulations explain these findings by underscoring the significant role of water, alongside ion aggregation and subtle, anistropic dielectric behavior, in driving nucleation within nano-constrained environments. This letter thus provides a framework for sampling, analyzing and understanding nucleation processes under nano-confinement.

physics.chem-ph↗

arXiv2024

Empowering AlphaFold2 for protein conformation selective drug discovery with AlphaFold2-RAVE

Small molecule drug design hinges on obtaining co-crystallized ligand-protein structures. Despite AlphaFold2's strides in protein native structure prediction, its focus on apo structures overlooks ligands and associated holo structures. Moreover, designing selective drugs often benefits from the targeting of diverse metastable conformations. Therefore, direct application of AlphaFold2 models in virtual screening and drug discovery remains tentative. Here, we demonstrate an AlphaFold2 based framework combined with all-atom enhanced sampling molecular dynamics and induced fit docking, named AF2RAVE-Glide, to conduct computational model based small molecule binding of metastable protein kinase conformations, initiated from protein sequences. We demonstrate the AF2RAVE-Glide workflow on three different protein kinases and their type I and II inhibitors, with special emphasis on binding of known type II kinase inhibitors which target the metastable classical DFG-out state. These states are not easy to sample from AlphaFold2. Here we demonstrate how with AF2RAVE these metastable conformations can be sampled for different kinases with high enough accuracy to enable subsequent docking of known type II kinase inhibitors with more than 50% success rates across docking calculations. We believe the protocol should be deployable for other kinases and more proteins generally.

physics.bio-ph↗

arXiv2024

An Information Bottleneck Approach for Markov Model Construction

Markov state models (MSMs) are valuable for studying dynamics of protein conformational changes via statistical analysis of molecular dynamics (MD) simulations. In MSMs, the complex configuration space is coarse-grained into conformational states, with the dynamics modeled by a series of Markovian transitions among these states at discrete lag times. Constructing the Markovian model at a specific lag time requires state defined without significant internal energy barriers, enabling internal dynamics relaxation within the lag time. This process coarse grains time and space, integrating out rapid motions within metastable states. This work introduces a continuous embedding approach for molecular conformations using the state predictive information bottleneck (SPIB), which unifies dimensionality reduction and state space partitioning via a continuous, machine learned basis set. Without explicit optimization of VAMP-based scores, SPIB demonstrates state-of-the-art performance in identifying slow dynamical processes and constructing predictive multi-resolution Markovian models. When applied to mini-proteins trajectories, SPIB showcases unique advantages compared to competing methods. It automatically adjusts the number of metastable states based on a specified minimal time resolution, eliminating the need for manual tuning. While maintaining efficacy in dynamical properties, SPIB excels in accurately distinguishing metastable states and capturing numerous well-populated macrostates. Furthermore, SPIB's ability to learn a low-dimensional continuous embedding of the underlying MSMs enhances the interpretation of dynamic pathways. Accordingly, we propose SPIB as an easy-to-implement methodology for end-to-end MSM construction.

physics.bio-ph↗

arXiv2024

Simulating Crystallization in a Colloidal System Using State Predictive Information Bottleneck based Enhanced Sampling

We investigate crystal nucleation in supersaturated colloid suspensions using enhanced molecular dynamics simulations augmented with machine learning techniques. The simulations reveal that crystallization in the model colloidal system studied here, with particles interacting through a repulsive screened Coulomb Yukawa potential, proceeds from vapor to dense liquid droplet to crystalline phases across multiple high barriers. Employing a one-dimensional reaction coordinate derived from the State Predictive Information Bottleneck framework, our simulations capture backand-forth phase transitions across multiple barriers effectively in biased metadynamics simulations. We obtain relative free energy differences between different phases and also quantify the roles of different molecular level features in driving the phase changes.

cond-mat.soft↗

arXiv2024

From latent dynamics to meaningful representations

While representation learning has been central to the rise of machine learning and artificial intelligence, a key problem remains in making the learned representations meaningful. For this, the typical approach is to regularize the learned representation through prior probability distributions. However, such priors are usually unavailable or are ad hoc. To deal with this, recent efforts have shifted towards leveraging the insights from physical principles to guide the learning process. In this spirit, we propose a purely dynamics-constrained representation learning framework. Instead of relying on predefined probabilities, we restrict the latent representation to follow overdamped Langevin dynamics with a learnable transition density - a prior driven by statistical mechanics. We show this is a more natural constraint for representation learning in stochastic dynamical systems, with the crucial ability to uniquely identify the ground truth representation. We validate our framework for different systems including a real-world fluorescent DNA movie dataset. We show that our algorithm can uniquely identify orthogonal, isometric and meaningful latent representations.

cs.LG↗

arXiv2024

Thermodynamics-inspired Explanations of Artificial Intelligence

In recent years, predictive machine learning methods have gained prominence in various scientific domains. However, due to their black-box nature, it is essential to establish trust in these models before accepting them as accurate. One promising strategy for assigning trust involves employing explanation techniques that elucidate the rationale behind a black-box model's predictions in a manner that humans can understand. However, assessing the degree of human interpretability of the rationale generated by such methods is a nontrivial challenge. In this work, we introduce interpretation entropy as a universal solution for assessing the degree of human interpretability associated with any linear model. Using this concept and drawing inspiration from classical thermodynamics, we present Thermodynamics-inspired Explainable Representations of AI and other black-box Paradigms (TERP), a method for generating accurate, and human-interpretable explanations for black-box predictions in a model-agnostic manner. To demonstrate the wide-ranging applicability of TERP, we successfully employ it to explain various black-box model architectures, including deep learning Autoencoders, Recurrent Neural Networks, and Convolutional Neural Networks, across diverse domains such as molecular simulations, text, and image classification.

cond-mat.stat-mech↗