Lin Yan

Shihan Dou, Ming Zhang, Chenhao Huang et al.

We introduce EvaLearn, a pioneering benchmark designed to evaluate large language models (LLMs) on their learning capability and efficiency in challenging tasks, a critical, yet underexplored aspect of model potential. EvaLearn contains 648 challenging problems across six task types, grouped into 182 sequences, each sequence dedicated to one task type. Diverging from most existing benchmarks that evaluate models in parallel, EvaLearn requires models to solve problems sequentially, allowing them to leverage the experience gained from previous solutions. EvaLearn provides five comprehensive automated metrics to evaluate models and quantify their learning capability and efficiency. We extensively benchmark nine frontier models and observe varied performance profiles: some models, such as Claude-3.7-sonnet, start with moderate initial performance but exhibit strong learning ability, while some models struggle to benefit from experience and may even show negative transfer. Moreover, we investigate model performance under two learning settings and find that instance-level rubrics and teacher-model feedback further facilitate model learning. Importantly, we observe that current LLMs with stronger static abilities do not show a clear advantage in learning capability across all tasks, highlighting that EvaLearn evaluates a new dimension of model performance. We hope EvaLearn provides a novel evaluation perspective for assessing LLM potential and understanding the gap between models and human capabilities, promoting the development of deeper and more dynamic evaluation approaches. All datasets, the automatic evaluation framework, and the results studied in this paper are available at the GitHub repository.

Qingsong Zhong, Haomin Yu, Yan Lin et al.

Structure-Based drug design (SBDD) has emerged as a popular approach in drug discovery, leveraging three-dimensional protein structures to generate drug ligands. However, existing generative models encounter several key challenges: (1) incorporating boundary condition constraints, (2) integrating hierarchical structural conditions, and (3) ensuring spatial modeling fidelity. To address these limitations, we propose SculptDrug, a spatial condition-aware generative model based on Bayesian flow networks (BFNs). First, SculptDrug follows a BFN-based framework and employs a progressive denoising strategy to ensure spatial modeling fidelity, iteratively refining atom positions while enhancing local interactions for precise spatial alignment. Second, we introduce a Boundary Awareness Block that incorporates protein surface constraints into the generative process to ensure that generated ligands are geometrically compatible with the target protein. Third, we design a Hierarchical Encoder that captures global structural context while preserving fine-grained molecular interactions, ensuring overall consistency and accurate ligand-protein conformations. We evaluate SculptDrug on the CrossDocked dataset, and experimental results demonstrate that SculptDrug outperforms state-of-the-art baselines, highlighting the effectiveness of spatial condition-aware modeling.

Lin Yan, Talha Bin Masood, Raghavendra Sridharamurthy et al.

In topological data analysis and visualization, topological descriptors such as persistence diagrams, merge trees, contour trees, Reeb graphs, and Morse-Smale complexes play an essential role in capturing the shape of scalar field data. We present a state-of-the-art report on scalar field comparison using topological descriptors. We provide a taxonomy of existing approaches based on visualization tasks associated with three categories of data: single fields, time-varying fields, and ensembles. These tasks include symmetry detection, periodicity detection, key event/feature detection, feature tracking, clustering, and structure statistics. Our main contributions include the formulation of a set of desirable mathematical and computational properties of comparative measures, and the classification of visualization tasks and applications that are enabled by these measures.

Mingzhe Li, Sourabh Palande, Lin Yan et al.

Merge trees are a type of topological descriptors that record the connectivity among the sublevel sets of scalar fields. They are among the most widely used topological tools in visualization. In this paper, we are interested in sketching a set of merge trees. That is, given a large set T of merge trees, we would like to find a much smaller basis set S such that each tree in T can be approximately reconstructed from a linear combination of merge trees in S. A set of high-dimensional vectors can be sketched via matrix sketching techniques such as principal component analysis and column subset selection. However, up until now, topological descriptors such as merge trees have not been known to be sketchable. We develop a framework for sketching a set of merge trees that combines the Gromov-Wasserstein probabilistic matching with techniques from matrix sketching. We demonstrate the applications of our framework in sketching merge trees that arise from time-varying scientific simulations. Specifically, our framework obtains a much smaller representation of a large set of merge trees for downstream analysis and visualization. It is shown to be useful in identifying good representatives and outliers with respect to a chosen basis. Finally, our work shows a promising direction of utilizing randomized linear algebra within scientific visualization.

Lin Yan, Yusu Wang, Elizabeth Munch et al.

Physical phenomena in science and engineering are frequently modeled using scalar fields. In scalar field topology, graph-based topological descriptors such as merge trees, contour trees, and Reeb graphs are commonly used to characterize topological changes in the (sub)level sets of scalar fields. One of the biggest challenges and opportunities to advance topology-based visualization is to understand and incorporate uncertainty into such topological descriptors to effectively reason about their underlying data. In this paper, we study a structural average of a set of labeled merge trees and use it to encode uncertainty in data. Specifically, we compute a 1-center tree that minimizes its maximum distance to any other tree in the set under a well-defined metric called the interleaving distance. We provide heuristic strategies that compute structural averages of merge trees whose labels do not fully agree. We further provide an interactive visualization system that resembles a numerical calculator that takes as input a set of merge trees and outputs a tree as their structural average. We also highlight structural similarities between the input and the average and incorporate uncertainty information for visual exploration. We develop a novel measure of uncertainty, referred to as consistency, via a metric-space view of the input trees. Finally, we demonstrate an application of our framework through merge trees that arise from ensembles of scalar fields. Our work is the first to employ interleaving distances and consistency to study a global, mathematically rigorous, structural average of merge trees in the context of uncertainty visualization.