Search Results for author: Ziqi Chen

Found 15 papers, 8 papers with code

LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset

1 code implementation14 Feb 2024 Botao Yu, Frazier N. Baker, Ziqi Chen, Xia Ning, Huan Sun

Using SMolInstruct, we fine-tune a set of open-source LLMs, among which, we find that Mistral serves as the best base model for chemistry tasks.

Drug Discovery

Modeling Sequences as Star Graphs to Address Over-smoothing in Self-attentive Sequential Recommendation

no code implementations13 Nov 2023 Bo Peng, Ziqi Chen, Srinivasan Parthasarathy, Xia Ning

As widely demonstrated in the literature, this issue could lead to a loss of information in individual items, and significantly degrade models' scalability and performance.

Sequential Recommendation

Towards Efficient and Effective Adaptation of Large Language Models for Sequential Recommendation

no code implementations2 Oct 2023 Bo Peng, Ben Burns, Ziqi Chen, Srinivasan Parthasarathy, Xia Ning

In addition, SSNA adapts the top-a layers of LLMs jointly, and integrates adapters sequentially for enhanced effectiveness (i. e., recommendation performance).

Sequential Recommendation

RLSynC: Offline-Online Reinforcement Learning for Synthon Completion

1 code implementation6 Sep 2023 Frazier N. Baker, Ziqi Chen, Daniel Adu-Ampratwum, Xia Ning

Retrosynthesis is the process of determining the set of reactant molecules that can react to form a desired product.

reinforcement-learning Retrosynthesis

Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Models

no code implementations23 Aug 2023 Ziqi Chen, Bo Peng, Srinivasan Parthasarathy, Xia Ning

Ligand-based drug design aims to identify novel drug candidates of similar shapes with known active molecules.

3D Molecule Generation

Nearest-Neighbor Sampling Based Conditional Independence Testing

1 code implementation9 Apr 2023 Shuai Li, Ziqi Chen, Hongtu Zhu, Christina Dan Wang, Wang Wen

The CRT assumes that the conditional distribution of X given Z is known under the null hypothesis and then it is compared to the distribution of the observed samples of the original data.

$\mathsf{G^2Retro}$ as a Two-Step Graph Generative Models for Retrosynthesis Prediction

1 code implementation10 Jun 2022 Ziqi Chen, Oluwatosin R. Ayinde, James R. Fuchs, Huan Sun, Xia Ning

It first predicts the reaction centers in the target molecules (products), identifies the synthons needed to assemble the products, and transforms these synthons into reactants.

Retrosynthesis Vocal Bursts Valence Prediction

A comparative study of non-deep learning, deep learning, and ensemble learning methods for sunspot number prediction

1 code implementation11 Mar 2022 Yuchen Dang, Ziqi Chen, Heng Li, Hai Shu

An open-source Python package of our XGBoost-DL for the sunspot number prediction is available at https://github. com/yd1008/ts_ensemble_sunspot.

Ensemble Learning

A Deep Generative Model for Molecule Optimization via One Fragment Modification

2 code implementations8 Dec 2020 Ziqi Chen, Martin Renqiang Min, Srinivasan Parthasarathy, Xia Ning

A pipeline of multiple, identical Modof models is implemented into Modof-pipe to modify an input molecule at multiple disconnection sites.

Drug Discovery

Ranking-based Convolutional Neural Network Models for Peptide-MHC Binding Prediction

1 code implementation4 Dec 2020 Ziqi Chen, Martin Renqiang Min, Xia Ning

T-cell receptors can recognize foreign peptides bound to major histocompatibility complex (MHC) class-I proteins, and thus trigger the adaptive immune response.

MHC presentation prediction

Network reinforcement driven drug repurposing for COVID-19 by exploiting disease-gene-drug associations

no code implementations12 Aug 2020 Yonghyun Nam, Jae-Seung Yun, Seung Mi Lee, Ji Won Park, Ziqi Chen, Brian Lee, Anurag Verma, Xia Ning, Li Shen, Dokyoon Kim

To reduce trial and error in finding treatments for COVID-19, we propose building a network-based drug repurposing framework to prioritize repurposable drugs.

mFI-PSO: A Flexible and Effective Method in Adversarial Image Generation for Deep Neural Networks

1 code implementation5 Jun 2020 Hai Shu, Ronghua Shi, Qiran Jia, Hongtu Zhu, Ziqi Chen

Deep neural networks (DNNs) have achieved great success in image classification, but can be very vulnerable to adversarial attacks with small perturbations to images.

Adversarial Defense Image Classification +1

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