arXiv subjects

Chang Ma

Publications and source records attributed to Chang Ma.

27 records · Page 2Linked to original sources

arXiv2024

PFWNN: A deep learning method for solving forward and inverse problems of phase-field models

Phase-field models have been widely used to investigate the phase transformation phenomena. However, it is difficult to solve the problems numerically due to their strong nonlinearities and higher-order terms. This work is devoted to solving forward and inverse problems of the phase-field models by a novel deep learning framework named Phase-Field Weak-form Neural Networks (PFWNN), which is based on the weak forms of the phase-field equations. In this framework, the weak solutions are parameterized as deep neural networks with a periodic layer, while the test function space is constructed by functions compactly supported in small regions. The PFWNN can efficiently solve the phase-field equations characterizing the sharp transitions and identify the important parameters by employing the weak forms. It also allows local training in small regions, which significantly reduce the computational cost. Moreover, it can guarantee the residual descending along the time marching direction, enhancing the convergence of the method. Numerical examples are presented for several benchmark problems. The results validate the efficiency and accuracy of the PFWNN. This work also sheds light on solving the forward and inverse problems of general high-order time-dependent partial differential equations.

math.NA↗

arXiv2024

KS-Lottery: Finding Certified Lottery Tickets for Multilingual Language Models

The lottery ticket hypothesis posits the existence of ``winning tickets'' within a randomly initialized neural network. Do winning tickets exist for LLMs in fine-tuning scenarios? How can we find such winning tickets? In this paper, we propose KS-Lottery, a method to identify a small subset of LLM parameters highly effective in multilingual fine-tuning. Our key idea is to use Kolmogorov-Smirnov Test to analyze the distribution shift of parameters before and after fine-tuning. We further theoretically prove that KS-Lottery can find the certified winning tickets in the embedding layer, fine-tuning on the found parameters is guaranteed to perform as well as full fine-tuning. Comparing KS-Lottery with other parameter-efficient tuning algorithms on translation tasks, the experimental results show that KS-Lottery finds a much smaller set of parameters for fine-tuning while achieving the comparable performance as full fine-tuning LLM. Surprisingly, we find that fine-tuning 18 tokens' embedding of LLaMA suffices to reach the fine-tuning translation performance~\footnote{https://github.com/CONE-MT/KS-Lottery.}.

cs.CL↗

arXiv2023

GIMLET: A Unified Graph-Text Model for Instruction-Based Molecule Zero-Shot Learning

Molecule property prediction has gained significant attention in recent years. The main bottleneck is the label insufficiency caused by expensive lab experiments. In order to alleviate this issue and to better leverage textual knowledge for tasks, this study investigates the feasibility of employing natural language instructions to accomplish molecule-related tasks in a zero-shot setting. We discover that existing molecule-text models perform poorly in this setting due to inadequate treatment of instructions and limited capacity for graphs. To overcome these issues, we propose GIMLET, which unifies language models for both graph and text data. By adopting generalized position embedding, our model is extended to encode both graph structures and instruction text without additional graph encoding modules. GIMLET also decouples encoding of the graph from tasks instructions in the attention mechanism, enhancing the generalization of graph features across novel tasks. We construct a dataset consisting of more than two thousand molecule tasks with corresponding instructions derived from task descriptions. We pretrain GIMLET on the molecule tasks along with instructions, enabling the model to transfer effectively to a broad range of tasks. Experimental results demonstrate that GIMLET significantly outperforms molecule-text baselines in instruction-based zero-shot learning, even achieving closed results to supervised GNN models on tasks such as toxcast and muv.

cs.LG↗

arXiv2023

A Challenging Benchmark for Low-Resource Learning

With promising yet saturated results in high-resource settings, low-resource datasets have gradually become popular benchmarks for evaluating the learning ability of advanced neural networks (e.g., BigBench, superGLUE). Some models even surpass humans according to benchmark test results. However, we find that there exists a set of hard examples in low-resource settings that challenge neural networks but are not well evaluated, which causes over-estimated performance. We first give a theoretical analysis on which factors bring the difficulty of low-resource learning. It then motivate us to propose a challenging benchmark hardBench to better evaluate the learning ability, which covers 11 datasets, including 3 computer vision (CV) datasets and 8 natural language process (NLP) datasets. Experiments on a wide range of models show that neural networks, even pre-trained language models, have sharp performance drops on our benchmark, demonstrating the effectiveness on evaluating the weaknesses of neural networks. On NLP tasks, we surprisingly find that despite better results on traditional low-resource benchmarks, pre-trained networks, does not show performance improvements on our benchmarks. These results demonstrate that there are still a large robustness gap between existing models and human-level performance.

cs.CL↗

arXiv2023

Retrieved Sequence Augmentation for Protein Representation Learning

Protein language models have excelled in a variety of tasks, ranging from structure prediction to protein engineering. However, proteins are highly diverse in functions and structures, and current state-of-the-art models including the latest version of AlphaFold rely on Multiple Sequence Alignments (MSA) to feed in the evolutionary knowledge. Despite their success, heavy computational overheads, as well as the de novo and orphan proteins remain great challenges in protein representation learning. In this work, we show that MSAaugmented models inherently belong to retrievalaugmented methods. Motivated by this finding, we introduce Retrieved Sequence Augmentation(RSA) for protein representation learning without additional alignment or pre-processing. RSA links query protein sequences to a set of sequences with similar structures or properties in the database and combines these sequences for downstream prediction. We show that protein language models benefit from the retrieval enhancement on both structure prediction and property prediction tasks, with a 5% improvement on MSA Transformer on average while being 373 times faster. In addition, we show that our model can transfer to new protein domains better and outperforms MSA Transformer on de novo protein prediction. Our study fills a much-encountered gap in protein prediction and brings us a step closer to demystifying the domain knowledge needed to understand protein sequences. Code is available on https://github.com/HKUNLP/RSA.

q-bio.BM↗

arXiv2022

Domain Adaptation via Maximizing Surrogate Mutual Information

Unsupervised domain adaptation (UDA) aims to predict unlabeled data from target domain with access to labeled data from the source domain. In this work, we propose a novel framework called SIDA (Surrogate Mutual Information Maximization Domain Adaptation) with strong theoretical guarantees. To be specific, SIDA implements adaptation by maximizing mutual information (MI) between features. In the framework, a surrogate joint distribution models the underlying joint distribution of the unlabeled target domain. Our theoretical analysis validates SIDA by bounding the expected risk on target domain with MI and surrogate distribution bias. Experiments show that our approach is comparable with state-of-the-art unsupervised adaptation methods on standard UDA tasks.

cs.LG↗

arXiv2022

Certified Robustness Against Natural Language Attacks by Causal Intervention

Deep learning models have achieved great success in many fields, yet they are vulnerable to adversarial examples. This paper follows a causal perspective to look into the adversarial vulnerability and proposes Causal Intervention by Semantic Smoothing (CISS), a novel framework towards robustness against natural language attacks. Instead of merely fitting observational data, CISS learns causal effects p(y|do(x)) by smoothing in the latent semantic space to make robust predictions, which scales to deep architectures and avoids tedious construction of noise customized for specific attacks. CISS is provably robust against word substitution attacks, as well as empirically robust even when perturbations are strengthened by unknown attack algorithms. For example, on YELP, CISS surpasses the runner-up by 6.7% in terms of certified robustness against word substitutions, and achieves 79.4% empirical robustness when syntactic attacks are integrated.

cs.LG↗

arXiv2022

PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding

We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the progress of deep learning in this field. In this paper, we propose such a benchmark called PEER, a comprehensive and multi-task benchmark for Protein sEquence undERstanding. PEER provides a set of diverse protein understanding tasks including protein function prediction, protein localization prediction, protein structure prediction, protein-protein interaction prediction, and protein-ligand interaction prediction. We evaluate different types of sequence-based methods for each task including traditional feature engineering approaches, different sequence encoding methods as well as large-scale pre-trained protein language models. In addition, we also investigate the performance of these methods under the multi-task learning setting. Experimental results show that large-scale pre-trained protein language models achieve the best performance for most individual tasks, and jointly training multiple tasks further boosts the performance. The datasets and source codes of this benchmark are all available at https://github.com/DeepGraphLearning/PEER_Benchmark

cs.LG↗

arXiv2022

TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery

Machine learning has huge potential to revolutionize the field of drug discovery and is attracting increasing attention in recent years. However, lacking domain knowledge (e.g., which tasks to work on), standard benchmarks and data preprocessing pipelines are the main obstacles for machine learning researchers to work in this domain. To facilitate the progress of machine learning for drug discovery, we develop TorchDrug, a powerful and flexible machine learning platform for drug discovery built on top of PyTorch. TorchDrug benchmarks a variety of important tasks in drug discovery, including molecular property prediction, pretrained molecular representations, de novo molecular design and optimization, retrosynthsis prediction, and biomedical knowledge graph reasoning. State-of-the-art techniques based on geometric deep learning (or graph machine learning), deep generative models, reinforcement learning and knowledge graph reasoning are implemented for these tasks. TorchDrug features a hierarchical interface that facilitates customization from both novices and experts in this domain. Tutorials, benchmark results and documentation are available at https://torchdrug.ai. Code is released under Apache License 2.0.

cs.LG↗