F$^3$low: Frame-to-Frame Coarse-grained Molecular Dynamics with SE Guided Flow Matching

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.

1Cademy @ Causal News Corpus 2022: Leveraging Self-Training in Causality Classification of Socio-Political Event Data

This paper details our participation in the Challenges and Applications of Automated Extraction of Socio-political Events from Text (CASE) workshop @ EMNLP 2022, where we take part in Subtask 1 of Shared Task 3. We approach the given task of event causality detection by proposing a self-training pipeline that follows a teacher-student classifier method. More specifically, we initially train a teacher model on the true, original task data, and use that teacher model to self-label data to be used in the training of a separate student model for the final task prediction. We test how restricting the number of positive or negative self-labeled examples in the self-training process affects classification performance. Our final results show that using self-training produces a comprehensive performance improvement across all models and self-labeled training sets tested within the task of event causality sequence classification. On top of that, we find that self-training performance did not diminish even when restricting either positive/negative examples used in training. Our code is be publicly available at https://github.com/Gzhang-umich/1CademyTeamOfCASE.

1Cademy @ Causal News Corpus 2022: Enhance Causal Span Detection via Beam-Search-based Position Selector

In this paper, we present our approach and empirical observations for Cause-Effect Signal Span Detection -- Subtask 2 of Shared task 3~\cite{tan-etal-2022-event} at CASE 2022. The shared task aims to extract the cause, effect, and signal spans from a given causal sentence. We model the task as a reading comprehension (RC) problem and apply a token-level RC-based span prediction paradigm to the task as the baseline. We explore different training objectives to fine-tune the model, as well as data augmentation (DA) tricks based on the language model (LM) for performance improvement. Additionally, we propose an efficient beam-search post-processing strategy to due with the drawbacks of span detection to obtain a further performance gain. Our approach achieves an average $F_1$ score of 54.15 and ranks \textbf{$1^{st}$} in the CASE competition. Our code is available at \url{https://github.com/Gzhang-umich/1CademyTeamOfCASE}.