Search Results for author: Jianzhu Ma

Found 25 papers, 16 papers with code

Selecting Large Language Model to Fine-tune via Rectified Scaling Law

no code implementations4 Feb 2024 Haowei Lin, Baizhou Huang, Haotian Ye, Qinyu Chen, ZiHao Wang, Sujian Li, Jianzhu Ma, Xiaojun Wan, James Zou, Yitao Liang

The ever-growing ecosystem of LLMs has posed a challenge in selecting the most appropriate pre-trained model to fine-tune amidst a sea of options.

Language Modelling Large Language Model

MCU: A Task-centric Framework for Open-ended Agent Evaluation in Minecraft

1 code implementation12 Oct 2023 Haowei Lin, ZiHao Wang, Jianzhu Ma, Yitao Liang

To pursue the goal of creating an open-ended agent in Minecraft, an open-ended game environment with unlimited possibilities, this paper introduces a task-centric framework named MCU for Minecraft agent evaluation.

Out-of-Distribution Generalization

InstaFlow: One Step is Enough for High-Quality Diffusion-Based Text-to-Image Generation

1 code implementation12 Sep 2023 Xingchao Liu, Xiwen Zhang, Jianzhu Ma, Jian Peng, Qiang Liu

Leveraging our new pipeline, we create, to the best of our knowledge, the first one-step diffusion-based text-to-image generator with SD-level image quality, achieving an FID (Frechet Inception Distance) of $23. 3$ on MS COCO 2017-5k, surpassing the previous state-of-the-art technique, progressive distillation, by a significant margin ($37. 2$ $\rightarrow$ $23. 3$ in FID).

Text-to-Image Generation

3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction

2 code implementations6 Mar 2023 Jiaqi Guan, Wesley Wei Qian, Xingang Peng, Yufeng Su, Jian Peng, Jianzhu Ma

Rich data and powerful machine learning models allow us to design drugs for a specific protein target \textit{in silico}.

Scientific Computing with Diffractive Optical Neural Networks

no code implementations12 Feb 2023 Ruiyang Chen, Yingheng Tang, Jianzhu Ma, Weilu Gao

Diffractive optical neural networks (DONNs) have been emerging as a high-throughput and energy-efficient hardware platform to perform all-optical machine learning (ML) in machine vision systems.

Feature Engineering Image Classification

Efficient Meta Reinforcement Learning for Preference-based Fast Adaptation

1 code implementation20 Nov 2022 Zhizhou Ren, Anji Liu, Yitao Liang, Jian Peng, Jianzhu Ma

To bridge this gap, we study the problem of few-shot adaptation in the context of human-in-the-loop reinforcement learning.

Meta Reinforcement Learning reinforcement-learning +1

Boosting the Cycle Counting Power of Graph Neural Networks with I$^2$-GNNs

2 code implementations22 Oct 2022 Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang

To the best of our knowledge, it is the first linear-time GNN model that can count 6-cycles with theoretical guarantees.

3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design

1 code implementation15 May 2022 Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang

The main computational challenges include: 1) the generation of linkers is conditional on the two given molecules, in contrast to generating full molecules from scratch in previous works; 2) linkers heavily depend on the anchor atoms of the two molecules to be connected, which are not known beforehand; 3) 3D structures and orientations of the molecules need to be considered to avoid atom clashes, for which equivariance to E(3) group are necessary.

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets

3 code implementations15 May 2022 Xingang Peng, Shitong Luo, Jiaqi Guan, Qi Xie, Jian Peng, Jianzhu Ma

Deep generative models have achieved tremendous success in designing novel drug molecules in recent years.


Equivariant Point Cloud Analysis via Learning Orientations for Message Passing

1 code implementation CVPR 2022 Shitong Luo, Jiahan Li, Jiaqi Guan, Yufeng Su, Chaoran Cheng, Jian Peng, Jianzhu Ma

In this work, we propose a novel and simple framework to achieve equivariance for point cloud analysis based on the message passing (graph neural network) scheme.

Provable Constrained Stochastic Convex Optimization with XOR-Projected Gradient Descent

no code implementations22 Mar 2022 Fan Ding, Yijie Wang, Jianzhu Ma, Yexiang Xue

Here we propose XOR-PGD, a novel algorithm based on Projected Gradient Descent (PGD) coupled with the XOR sampler, which is guaranteed to solve the constrained stochastic convex optimization problem still in linear convergence rate by choosing proper step size.


A 3D Generative Model for Structure-Based Drug Design

3 code implementations NeurIPS 2021 Shitong Luo, Jiaqi Guan, Jianzhu Ma, Jian Peng

In this paper, we propose a 3D generative model that generates molecules given a designated 3D protein binding site.


Contrastive Cycle Adversarial Autoencoders for Single-cell Multi-omics Alignment and Integration

1 code implementation5 Dec 2021 Xuesong Wang, Zhihang Hu, Tingyang Yu, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li

Our approach can efficiently map the above data with high sparsity and noise from different spaces to a low-dimensional manifold in a unified space, making the downstream alignment and integration straightforward.

Fast Projection onto the Capped Simplex with Applications to Sparse Regression in Bioinformatics

no code implementations NeurIPS 2021 Andersen Ang, Jianzhu Ma, Nianjun Liu, Kun Huang, Yijie Wang

We demonstrate that the proposed algorithm can produce a solution of the projection problem with high precision on large scale datasets, and the algorithm is able to significantly outperform the state-of-the-art methods in terms of runtime (about 6-8 times faster than a commercial software with respect to CPU time for input vector with 1 million variables or more).


Neural Energy Minimization for Molecular Conformation Optimization

no code implementations ICLR 2022 Jiaqi Guan, Wesley Wei Qian, Qiang Liu, Wei-Ying Ma, Jianzhu Ma, Jian Peng

Assuming different forms of the underlying potential energy function, we can not only reinterpret and unify many of the existing models but also derive new variants of SE(3)-equivariant neural networks in a principled manner.

Neural Predicting Higher-order Patterns in Temporal Networks

2 code implementations10 Jun 2021 Yunyu Liu, Jianzhu Ma, Pan Li

HIT extracts the structural representation of a node triplet of interest on the temporal hypergraph and uses it to tell what type of, when, and why the interaction expansion could happen in this triplet.

Quantifying Spatial Homogeneity of Urban Road Networks via Graph Neural Networks

1 code implementation1 Jan 2021 Jiawei Xue, Nan Jiang, Senwei Liang, Qiyuan Pang, Takahiro Yabe, Satish V. Ukkusuri, Jianzhu Ma

We apply the method to 11, 790 urban road networks across 30 cities worldwide to measure the spatial homogeneity of road networks within each city and across different cities.

Protein Structure Prediction by Protein Alignments

no code implementations19 Oct 2015 Jianzhu Ma

In this thesis I introduce a new machine learning based method to predict the protein structure.

Protein Structure Prediction

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

no code implementations12 Jan 2014 Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu

A sequence profile is usually represented as a position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model) and accordingly PSSM-PSSM or HMM-HMM comparison is used for homolog detection.

Multiple Sequence Alignment

Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning

no code implementations10 Dec 2013 Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu

To further improve the accuracy of the estimated precision matrices, we employ a supervised learning method to predict contact probability from a variety of evolutionary and non-evolutionary information and then incorporate the predicted probability as prior into our GGL framework.

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