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Chen Lin 0003

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4 papers

1 author row

ICML Conference 2025 Conference Paper

Scalable Equilibrium Sampling with Sequential Boltzmann Generators

Charlie B. Tan
Avishek Joey Bose
Chen Lin 0003
Leon Klein
Michael M. Bronstein
Alexander Tong 0001

Scalable sampling of molecular states in thermodynamic equilibrium is a long-standing challenge in statistical physics. Boltzmann generators tackle this problem by pairing normalizing flows with importance sampling to obtain uncorrelated samples under the target distribution. In this paper, we extend the Boltzmann generator framework with two key contributions, denoting our framework Sequential Boltzmann Generators (SBG). The first is a highly efficient Transformer-based normalizing flow operating directly on all-atom Cartesian coordinates. In contrast to the equivariant continuous flows of prior methods, we leverage exactly invertible non-equivariant architectures which are highly efficient during both sample generation and likelihood evaluation. This efficiency unlocks more sophisticated inference strategies beyond standard importance sampling. In particular, we perform inference-time scaling of flow samples using a continuous-time variant of sequential Monte Carlo, in which flow samples are transported towards the target distribution with annealed Langevin dynamics. SBG achieves state-of-the-art performance w. r. t. all metrics on peptide systems, demonstrating the first equilibrium sampling in Cartesian coordinates of tri-, tetra- and hexa-peptides that were thus far intractable for prior Boltzmann generators.

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ICLR Conference 2023 Conference Paper

Designing BERT for Convolutional Networks: Sparse and Hierarchical Masked Modeling

Keyu Tian
Yi Jiang
Qishuai Diao
Chen Lin 0003
Liwei Wang
Zehuan Yuan

We identify and overcome two key obstacles in extending the success of BERT-style pre-training, or masked image modeling, to convolutional networks (convnets): (i) convolution operation cannot handle irregular, randomly masked input images; (ii) the single-scale nature of BERT pre-training is inconsistent with convnet’s hierarchical structure. For (i), we treat unmasked pixels as sparse voxels of 3D point clouds and use sparse convolution to encode. This is the first use of sparse convolution for 2D masked modeling. For (ii), we develop a hierarchical decoder to reconstruct images from multi-scale encoded features. Our method, called Sparse masKed modeling (SparK), is general: it can be used directly on any convolutional model without backbone modifications. We validate it on both classical (ResNet) and modern (ConvNeXt) models: on three downstream tasks, it surpasses both state-of-the-art contrastive learning and transformer-based masked modeling by similarly large margins (around +1.0%). The improvements on object detection and instance segmentation are more significant (up to +3.5%), validating the strong transferability of features learned. We also find SparK’s favorable scaling behavior by observing more gains on larger networks. All of these findings support the promising future of generative pre-training on convnets. Both codes and pre-trained models have been released at https://github.com/keyu-tian/SparK.

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ICML Conference 2023 Conference Paper

Graph Inductive Biases in Transformers without Message Passing

Liheng Ma
Chen Lin 0003
Derek Lim
Adriana Romero-Soriano
Puneet Kumar Dokania
Mark Coates
Philip H. S. Torr
Ser-Nam Lim

Transformers for graph data are increasingly widely studied and successful in numerous learning tasks. Graph inductive biases are crucial for Graph Transformers, and previous works incorporate them using message-passing modules and/or positional encodings. However, Graph Transformers that use message-passing inherit known issues of message-passing, and differ significantly from Transformers used in other domains, thus making transfer of research advances more difficult. On the other hand, Graph Transformers without message-passing often perform poorly on smaller datasets, where inductive biases are more crucial. To bridge this gap, we propose the Graph Inductive bias Transformer (GRIT) — a new Graph Transformer that incorporates graph inductive biases without using message passing. GRIT is based on several architectural changes that are each theoretically and empirically justified, including: learned relative positional encodings initialized with random walk probabilities, a flexible attention mechanism that updates node and node-pair representations, and injection of degree information in each layer. We prove that GRIT is expressive — it can express shortest path distances and various graph propagation matrices. GRIT achieves state-of-the-art empirical performance across a variety of graph datasets, thus showing the power that Graph Transformers without message-passing can deliver.

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ICLR Conference 2020 Conference Paper

Computation Reallocation for Object Detection

Feng Liang
Chen Lin 0003
Ronghao Guo
Ming Sun 0008
Wei Wu 0021
Junjie Yan
Wanli Ouyang

The allocation of computation resources in the backbone is a crucial issue in object detection. However, classification allocation pattern is usually adopted directly to object detector, which is proved to be sub-optimal. In order to reallocate the engaged computation resources in a more efficient way, we present CR-NAS (Computation Reallocation Neural Architecture Search) that can learn computation reallocation strategies across different feature resolution and spatial position diectly on the target detection dataset. A two-level reallocation space is proposed for both stage and spatial reallocation. A novel hierarchical search procedure is adopted to cope with the complex search space. We apply CR-NAS to multiple backbones and achieve consistent improvements. Our CR-ResNet50 and CR-MobileNetV2 outperforms the baseline by 1.9% and 1.7% COCO AP respectively without any additional computation budget. The models discovered by CR-NAS can be equiped to other powerful detection neck/head and be easily transferred to other dataset, e.g. PASCAL VOC, and other vision tasks, e.g. instance segmentation. Our CR-NAS can be used as a plugin to improve the performance of various networks, which is demanding.

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