Molecular dynamics (MD) simulation techniques are widely used for various natural science applications. Increasingly, machine learning (ML) force field (FF) models begin to replace ab-initio simulations by predicting forces directly from atomic structures. Despite significant progress in this area, such techniques are primarily benchmarked by their force/energy prediction errors, even though the practical use case would be to produce realistic MD trajectories. We aim to fill this gap by introducing a novel benchmark suite for learned MD simulation. We curate representative MD systems, including water, organic molecules, a peptide, and materials, and design evaluation metrics corresponding to the scientific objectives of respective systems. We benchmark a collection of state-of-the-art (SOTA) ML FF models and illustrate, in particular, how the commonly benchmarked force accuracy is not well aligned with relevant simulation metrics. We demonstrate when and how selected SOTA methods fail, along with offering directions for further improvement. Specifically, we identify stability as a key metric for ML models to improve. Our benchmark suite comes with a comprehensive open-source codebase for training and simulation with ML FFs to facilitate future work.
Creating a system that can have meaningful conversations with humans to help accomplish tasks is one of the ultimate goals of Artificial Intelligence (AI). It has defined the meaning of AI since the beginning. A lot has been accomplished in this area recently, with voice assistant products entering our daily lives and chat bot systems becoming commonplace in customer service. At first glance there seems to be no shortage of options for dialogue systems. However, the frequently deployed dialogue systems today seem to all struggle with a critical weakness - they are hard to build and harder to maintain. At the core of the struggle is the need to script every single turn of interactions between the bot and the human user. This makes the dialogue systems more difficult to maintain as the tasks become more complex and more tasks are added to the system. In this paper, we propose Converse, a flexible tree-based modular task-oriented dialogue system. Converse uses an and-or tree structure to represent tasks and offers powerful multi-task dialogue management. Converse supports task dependency and task switching, which are unique features compared to other open-source dialogue frameworks. At the same time, Converse aims to make the bot building process easy and simple, for both professional and non-professional software developers. The code is available at https://github.com/salesforce/Converse.
Open material databases storing hundreds of thousands of material structures and their corresponding properties have become the cornerstone of modern computational materials science. Yet, the raw outputs of the simulations, such as the trajectories from molecular dynamics simulations and charge densities from density functional theory calculations, are generally not shared due to their huge size. In this work, we describe a cloud-based platform to facilitate the sharing of raw data and enable the fast post-processing in the cloud to extract new properties defined by the user. As an initial demonstration, our database currently includes 6286 molecular dynamics trajectories for amorphous polymer electrolytes and 5.7 terabytes of data. We create a public analysis library at https://github.com/TRI-AMDD/htp_md to extract multiple properties from the raw data, using both expert designed functions and machine learning models. The analysis is run automatically with computation in the cloud, and results then populate a database that can be accessed publicly. Our platform encourages users to contribute both new trajectory data and analysis functions via public interfaces. Newly analyzed properties will be incorporated into the database. Finally, we create a front-end user interface at https://www.htpmd.matr.io for browsing and visualization of our data. We envision the platform to be a new way of sharing raw data and new insights for the computational materials science community.
Xiang Fu, Tian Xie, Andrew S. Rosen et al. · princeton
Metal-organic frameworks (MOFs) are of immense interest in applications such as gas storage and carbon capture due to their exceptional porosity and tunable chemistry. Their modular nature has enabled the use of template-based methods to generate hypothetical MOFs by combining molecular building blocks in accordance with known network topologies. However, the ability of these methods to identify top-performing MOFs is often hindered by the limited diversity of the resulting chemical space. In this work, we propose MOFDiff: a coarse-grained (CG) diffusion model that generates CG MOF structures through a denoising diffusion process over the coordinates and identities of the building blocks. The all-atom MOF structure is then determined through a novel assembly algorithm. Equivariant graph neural networks are used for the diffusion model to respect the permutational and roto-translational symmetries. We comprehensively evaluate our model's capability to generate valid and novel MOF structures and its effectiveness in designing outstanding MOF materials for carbon capture applications with molecular simulations.
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for many real-world applications due to slow inference for large systems and small time steps (femtosecond-level). We aim to address these challenges by learning a multi-scale graph neural network that directly simulates coarse-grained MD with a very large time step (nanosecond-level) and a novel refinement module based on diffusion models to mitigate simulation instability. The effectiveness of our method is demonstrated in two complex systems: single-chain coarse-grained polymers and multi-component Li-ion polymer electrolytes. For evaluation, we simulate trajectories much longer than the training trajectories for systems with different chemical compositions that the model is not trained on. Structural and dynamical properties can be accurately recovered at several orders of magnitude higher speed than classical force fields by getting out of the femtosecond regime.
An enhanced label propagation (LP) method called GraphHop was proposed recently. It outperforms graph convolutional networks (GCNs) in the semi-supervised node classification task on various networks. Although the performance of GraphHop was explained intuitively with joint node attribute and label signal smoothening, its rigorous mathematical treatment is lacking. In this paper, we propose a label efficient regularization and propagation (LERP) framework for graph node classification, and present an alternate optimization procedure for its solution. Furthermore, we show that GraphHop only offers an approximate solution to this framework and has two drawbacks. First, it includes all nodes in the classifier training without taking the reliability of pseudo-labeled nodes into account in the label update step. Second, it provides a rough approximation to the optimum of a subproblem in the label aggregation step. Based on the LERP framework, we propose a new method, named the LERP method, to solve these two shortcomings. LERP determines reliable pseudo-labels adaptively during the alternate optimization and provides a better approximation to the optimum with computational efficiency. Theoretical convergence of LERP is guaranteed. Extensive experiments are conducted to demonstrate the effectiveness and efficiency of LERP. That is, LERP outperforms all benchmarking methods, including GraphHop, consistently on five test datasets and an object recognition task at extremely low label rates (i.e., 1, 2, 4, 8, 16, and 20 labeled samples per class).
A scalable semi-supervised node classification method on graph-structured data, called GraphHop, is proposed in this work. The graph contains attributes of all nodes but labels of a few nodes. The classical label propagation (LP) method and the emerging graph convolutional network (GCN) are two popular semi-supervised solutions to this problem. The LP method is not effective in modeling node attributes and labels jointly or facing a slow convergence rate on large-scale graphs. GraphHop is proposed to its shortcoming. With proper initial label vector embeddings, each iteration of GraphHop contains two steps: 1) label aggregation and 2) label update. In Step 1, each node aggregates its neighbors' label vectors obtained in the previous iteration. In Step 2, a new label vector is predicted for each node based on the label of the node itself and the aggregated label information obtained in Step 1. This iterative procedure exploits the neighborhood information and enables GraphHop to perform well in an extremely small label rate setting and scale well for very large graphs. Experimental results show that GraphHop outperforms state-of-the-art graph learning methods on a wide range of tasks (e.g., multi-label and multi-class classification on citation networks, social graphs, and commodity consumption graphs) in graphs of various sizes. Our codes are publicly available on GitHub (https://github.com/TianXieUSC/GraphHop).
Generating temporally-consistent high-fidelity videos can be computationally expensive, especially over longer temporal spans. More-recent Diffusion Transformers (DiTs) -- despite making significant headway in this context -- have only heightened such challenges as they rely on larger models and heavier attention mechanisms, resulting in slower inference speeds. In this paper, we introduce a training-free method to accelerate video DiTs, termed Adaptive Caching (AdaCache), which is motivated by the fact that "not all videos are created equal": meaning, some videos require fewer denoising steps to attain a reasonable quality than others. Building on this, we not only cache computations through the diffusion process, but also devise a caching schedule tailored to each video generation, maximizing the quality-latency trade-off. We further introduce a Motion Regularization (MoReg) scheme to utilize video information within AdaCache, essentially controlling the compute allocation based on motion content. Altogether, our plug-and-play contributions grant significant inference speedups (e.g. up to 4.7x on Open-Sora 720p - 2s video generation) without sacrificing the generation quality, across multiple video DiT baselines.
This paper studies algorithmic decision-making under human's strategic behavior, where a decision maker uses an algorithm to make decisions about human agents, and the latter with information about the algorithm may exert effort strategically and improve to receive favorable decisions. Unlike prior works that assume agents benefit from their efforts immediately, we consider realistic scenarios where the impacts of these efforts are persistent and agents benefit from efforts by making improvements gradually. We first develop a dynamic model to characterize persistent improvements and based on this construct a Stackelberg game to model the interplay between agents and the decision-maker. We analytically characterize the equilibrium strategies and identify conditions under which agents have incentives to improve. With the dynamics, we then study how the decision-maker can design an optimal policy to incentivize the largest improvements inside the agent population. We also extend the model to settings where 1) agents may be dishonest and game the algorithm into making favorable but erroneous decisions; 2) honest efforts are forgettable and not sufficient to guarantee persistent improvements. With the extended models, we further examine conditions under which agents prefer honest efforts over dishonest behavior and the impacts of forgettable efforts.
Tian Xie, Zhiqun Zuo, Mohammad Mahdi Khalili et al.
Machine learning systems have been widely used to make decisions about individuals who may behave strategically to receive favorable outcomes, e.g., they may genuinely improve the true labels or manipulate observable features directly to game the system without changing labels. Although both behaviors have been studied (often as two separate problems) in the literature, most works assume individuals can (i) perfectly foresee the outcomes of their behaviors when they best respond; (ii) change their features arbitrarily as long as it is affordable, and the costs they need to pay are deterministic functions of feature changes. In this paper, we consider a different setting and focus on imitative strategic behaviors with unforeseeable outcomes, i.e., individuals manipulate/improve by imitating the features of those with positive labels, but the induced feature changes are unforeseeable. We first propose a Stackelberg game to model the interplay between individuals and the decision-maker, under which we examine how the decision-maker's ability to anticipate individual behavior affects its objective function and the individual's best response. We show that the objective difference between the two can be decomposed into three interpretable terms, with each representing the decision-maker's preference for a certain behavior. By exploring the roles of each term, we theoretically illustrate how a decision-maker with adjusted preferences may simultaneously disincentivize manipulation, incentivize improvement, and promote fairness. Such theoretical results provide a guideline for decision-makers to inform better and socially responsible decisions in practice.
As machine learning (ML) models are increasingly used in social domains to make consequential decisions about humans, they often have the power to reshape data distributions. Humans, as strategic agents, continuously adapt their behaviors in response to the learning system. As populations change dynamically, ML systems may need frequent updates to ensure high performance. However, acquiring high-quality human-annotated samples can be highly challenging and even infeasible in social domains. A common practice to address this issue is using the model itself to annotate unlabeled data samples. This paper investigates the long-term impacts when ML models are retrained with model-annotated samples when they incorporate human strategic responses. We first formalize the interactions between strategic agents and the model and then analyze how they evolve under such dynamic interactions. We find that agents are increasingly likely to receive positive decisions as the model gets retrained, whereas the proportion of agents with positive labels may decrease over time. We thus propose a refined retraining process to stabilize the dynamics. Last, we examine how algorithmic fairness can be affected by these retraining processes and find that enforcing common fairness constraints at every round may not benefit the disadvantaged group in the long run. Experiments on (semi-)synthetic and real data validate the theoretical findings.
Land surface temperature (LST) retrieval from remote sensing data is pivotal for analyzing climate processes and surface energy budgets. However, LST retrieval is an ill-posed inverse problem, which becomes particularly severe when only a single band is available. In this paper, we propose a deeply coupled framework integrating mechanistic modeling and machine learning to enhance the accuracy and generalizability of single-channel LST retrieval. Training samples are generated using a physically-based radiative transfer model and a global collection of 5810 atmospheric profiles. A physics-informed machine learning framework is proposed to systematically incorporate the first principles from classical physical inversion models into the learning workflow, with optimization constrained by radiative transfer equations. Global validation demonstrated a 30% reduction in root-mean-square error versus standalone methods. Under extreme humidity, the mean absolute error decreased from 4.87 K to 2.29 K (53% improvement). Continental-scale tests across five continents confirmed the superior generalizability of this model.
Tian Xie, Tongxin Yin, Vaishakh Keshava et al. · cmu
While large language models (LLMs) already play significant roles in society, research has shown that LLMs still generate content including social bias against certain sensitive groups. While existing benchmarks have effectively identified social biases in LLMs, a critical gap remains in our understanding of the underlying reasoning that leads to these biased outputs. This paper goes one step further to evaluate the causal reasoning process of LLMs when they answer questions eliciting social biases. We first propose a novel conceptual framework to classify the causal reasoning produced by LLMs. Next, we use LLMs to synthesize $1788$ questions covering $8$ sensitive attributes and manually validate them. The questions can test different kinds of causal reasoning by letting LLMs disclose their reasoning process with causal graphs. We then test 4 state-of-the-art LLMs. All models answer the majority of questions with biased causal reasoning, resulting in a total of $4135$ biased causal graphs. Meanwhile, we discover $3$ strategies for LLMs to avoid biased causal reasoning by analyzing the "bias-free" cases. Finally, we reveal that LLMs are also prone to "mistaken-biased" causal reasoning, where they first confuse correlation with causality to infer specific sensitive group names and then incorporate biased causal reasoning.
As machine learning (ML) algorithms are used in applications that involve humans, concerns have arisen that these algorithms may be biased against certain social groups. \textit{Counterfactual fairness} (CF) is a fairness notion proposed in Kusner et al. (2017) that measures the unfairness of ML predictions; it requires that the prediction perceived by an individual in the real world has the same marginal distribution as it would be in a counterfactual world, in which the individual belongs to a different group. Although CF ensures fair ML predictions, it fails to consider the downstream effects of ML predictions on individuals. Since humans are strategic and often adapt their behaviors in response to the ML system, predictions that satisfy CF may not lead to a fair future outcome for the individuals. In this paper, we introduce \textit{lookahead counterfactual fairness} (LCF), a fairness notion accounting for the downstream effects of ML models which requires the individual \textit{future status} to be counterfactually fair. We theoretically identify conditions under which LCF can be satisfied and propose an algorithm based on the theorems. We also extend the concept to path-dependent fairness. Experiments on both synthetic and real data validate the proposed method.