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.
Multimodal in-context learning (ICL) equips Large Vision-language Models (LVLMs) with the ability to adapt to new tasks via multiple user-provided demonstrations, without requiring any model parameter updates. However, its effectiveness is constrained by the token-intensive nature of multimodal inputs and the complexity of cross-modal few-shot reasoning, which together hinder LVLMs from extracting useful patterns from demonstrations. To address these challenges, we propose \textbf{M$^2$IV}, a novel representation engineering approach that replaces explicit token-level demonstrations with a set of learnable Multimodal In-context Vectors directly injected into the residual streams of LVLMs. By analyzing the distinct roles of multi-head attention (MHA) and multi-layer perceptrons (MLP) in the ICL process, we design a training strategy that enables M$^2$IV to perform fine-grained semantic distillation and robust cross-modal representation learning. M$^2$IV not only improves performance across diverse tasks and LVLMs but also significantly reduces token overhead, enabling graceful scaling to many-shot scenarios. To further enhance usability, we introduce \textbf{VLibrary}, a repository that stores trained M$^2$IVs for flexible retrieval and injection. With VLibrary, users can steer pre-trained LVLMs in a customized manner that meets diverse requirements. Extensive experiments demonstrate that M$^2$IV consistently outperforms vanilla ICL and prior representation engineering baselines, achieving an average accuracy gain of 3.74\% with substantial improvements in overall efficiency.
Searching for novel molecular compounds with desired properties is an important problem in drug discovery. Many existing frameworks generate molecules one atom at a time. We instead propose a flexible editing paradigm that generates molecules using learned molecular fragments--meaningful substructures of molecules. To do so, we train a variational autoencoder (VAE) to encode molecular fragments in a coherent latent space, which we then utilize as a vocabulary for editing molecules to explore the complex chemical property space. Equipped with the learned fragment vocabulary, we propose Fragment-based Sequential Translation (FaST), which learns a reinforcement learning (RL) policy to iteratively translate model-discovered molecules into increasingly novel molecules while satisfying desired properties. Empirical evaluation shows that FaST significantly improves over state-of-the-art methods on benchmark single/multi-objective molecular optimization tasks.