Jian Zhang

Shaoning Li, Yusong Wang, Mingyu Li et al.

Molecular dynamics (MD) is a crucial technique for simulating biological systems, enabling the exploration of their dynamic nature and fostering an understanding of their functions and properties. To address exploration inefficiency, emerging enhanced sampling approaches like coarse-graining (CG) and generative models have been employed. In this work, we propose a \underline{Frame-to-Frame} generative model with guided \underline{Flow}-matching (F$3$low) for enhanced sampling, which (a) extends the domain of CG modeling to the SE(3) Riemannian manifold; (b) retreating CGMD simulations as autoregressively sampling guided by the former frame via flow-matching models; (c) targets the protein backbone, offering improved insights into secondary structure formation and intricate folding pathways. Compared to previous methods, F$3$low allows for broader exploration of conformational space. The ability to rapidly generate diverse conformations via force-free generative paradigm on SE(3) paves the way toward efficient enhanced sampling methods.

Etash Guha, Tianxiao Jiang, Andrew Deng et al.

Mapping a dataflow-graph of an ML model onto a reconfigurable system is difficult, as different mappings have different throughputs and consume resource constraints differently. To solve this, a model to evaluate the throughput of mappings is necessary as measuring throughput completely is expensive. Many use a hand-designed analytical model, relying on proxy features or intuition, introducing error. We provide a Learned Approach that predicts throughput 31%-52% more accurately over a variety of graphs. In addition, our approach shows no accuracy degradation after removing performance annotations. We show that using this approach results in 5.6% faster compiled graphs.