Author name cluster

Zeming Lin

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

5 papers

2 author rows

ICML Conference 2022 Conference Paper

Learning inverse folding from millions of predicted structures

Chloe Hsu
Robert Verkuil
Jason Liu
Zeming Lin
Brian Hie
Tom Sercu
Adam Lerer
Alexander Rives

We consider the problem of predicting a protein sequence from its backbone atom coordinates. Machine learning approaches to this problem to date have been limited by the number of available experimentally determined protein structures. We augment training data by nearly three orders of magnitude by predicting structures for 12M protein sequences using AlphaFold2. Trained with this additional data, a sequence-to-sequence transformer with invariant geometric input processing layers achieves 51% native sequence recovery on structurally held-out backbones with 72% recovery for buried residues, an overall improvement of almost 10 percentage points over existing methods. The model generalizes to a variety of more complex tasks including design of protein complexes, partially masked structures, binding interfaces, and multiple states.

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ICML Conference 2020 Conference Paper

Growing Action Spaces

Gregory Farquhar
Laura Gustafson
Zeming Lin
Shimon Whiteson
Nicolas Usunier
Gabriel Synnaeve

In complex tasks, such as those with large combinatorial action spaces, random exploration may be too inefficient to achieve meaningful learning progress. In this work, we use a curriculum of progressively growing action spaces to accelerate learning. We assume the environment is out of our control, but that the agent may set an internal curriculum by initially restricting its action space. Our approach uses off-policy reinforcement learning to estimate optimal value functions for multiple action spaces simultaneously and efficiently transfers data, value estimates, and state representations from restricted action spaces to the full task. We show the efficacy of our approach in proof-of-concept control tasks and on challenging large-scale StarCraft micromanagement tasks with large, multi-agent action spaces.

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NeurIPS Conference 2019 Conference Paper

PyTorch: An Imperative Style, High-Performance Deep Learning Library

Adam Paszke
Sam Gross
Francisco Massa
Adam Lerer
James Bradbury
Gregory Chanan
Trevor Killeen
Zeming Lin

Deep learning frameworks have often focused on either usability or speed, but not both. PyTorch is a machine learning library that shows that these two goals are in fact compatible: it was designed from first principles to support an imperative and Pythonic programming style that supports code as a model, makes debugging easy and is consistent with other popular scientific computing libraries, while remaining efficient and supporting hardware accelerators such as GPUs. In this paper, we detail the principles that drove the implementation of PyTorch and how they are reflected in its architecture. We emphasize that every aspect of PyTorch is a regular Python program under the full control of its user. We also explain how the careful and pragmatic implementation of the key components of its runtime enables them to work together to achieve compelling performance. We demonstrate the efficiency of individual subsystems, as well as the overall speed of PyTorch on several commonly used benchmarks.

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NeurIPS Conference 2018 Conference Paper

Forward Modeling for Partial Observation Strategy Games - A StarCraft Defogger

Gabriel Synnaeve
Zeming Lin
Jonas Gehring
Dan Gant
Vegard Mella
Vasil Khalidov
Nicolas Carion
Nicolas Usunier

We formulate the problem of defogging as state estimation and future state prediction from previous, partial observations in the context of real-time strategy games. We propose to employ encoder-decoder neural networks for this task, and introduce proxy tasks and baselines for evaluation to assess their ability of capturing basic game rules and high-level dynamics. By combining convolutional neural networks and recurrent networks, we exploit spatial and sequential correlations and train well-performing models on a large dataset of human games of StarCraft: Brood War. Finally, we demonstrate the relevance of our models to downstream tasks by applying them for enemy unit prediction in a state-of-the-art, rule-based StarCraft bot. We observe improvements in win rates against several strong community bots.

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AAAI Conference 2016 Conference Paper

MUST-CNN: A Multilayer Shift-and-Stitch Deep Convolutional Architecture for Sequence-Based Protein Structure Prediction

Zeming Lin
Jack Lanchantin
Yanjun Qi

Predicting protein properties such as solvent accessibility and secondary structure from its primary amino acid sequence is an important task in bioinformatics. Recently, a few deep learning models have surpassed the traditional window based multilayer perceptron. Taking inspiration from the image classification domain we propose a deep convolutional neural network architecture, MUST-CNN, to predict protein properties. This architecture uses a novel multilayer shift-and-stitch (MUST) technique to generate fully dense per-position predictions on protein sequences. Our model is significantly simpler than the state-of-the-art, yet achieves better results. By combining MUST and the efficient convolution operation, we can consider far more parameters while retaining very fast prediction speeds. We beat the state-of-the-art performance on two large protein property prediction datasets.

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