arXiv subjects

Yufei Huang

Publications and source records attributed to Yufei Huang.

At least 73 records · Page 4Linked to original sources

arXiv2023

Evaluating Large Language Models: A Comprehensive Survey

Large language models (LLMs) have demonstrated remarkable capabilities across a broad spectrum of tasks. They have attracted significant attention and been deployed in numerous downstream applications. Nevertheless, akin to a double-edged sword, LLMs also present potential risks. They could suffer from private data leaks or yield inappropriate, harmful, or misleading content. Additionally, the rapid progress of LLMs raises concerns about the potential emergence of superintelligent systems without adequate safeguards. To effectively capitalize on LLM capacities as well as ensure their safe and beneficial development, it is critical to conduct a rigorous and comprehensive evaluation of LLMs. This survey endeavors to offer a panoramic perspective on the evaluation of LLMs. We categorize the evaluation of LLMs into three major groups: knowledge and capability evaluation, alignment evaluation and safety evaluation. In addition to the comprehensive review on the evaluation methodologies and benchmarks on these three aspects, we collate a compendium of evaluations pertaining to LLMs' performance in specialized domains, and discuss the construction of comprehensive evaluation platforms that cover LLM evaluations on capabilities, alignment, safety, and applicability. We hope that this comprehensive overview will stimulate further research interests in the evaluation of LLMs, with the ultimate goal of making evaluation serve as a cornerstone in guiding the responsible development of LLMs. We envision that this will channel their evolution into a direction that maximizes societal benefit while minimizing potential risks. A curated list of related papers has been publicly available at https://github.com/tjunlp-lab/Awesome-LLMs-Evaluation-Papers.

cs.CL↗

arXiv2023

Leveraging Foundation Models to Improve Lightweight Clients in Federated Learning

Federated Learning (FL) is a distributed training paradigm that enables clients scattered across the world to cooperatively learn a global model without divulging confidential data. However, FL faces a significant challenge in the form of heterogeneous data distributions among clients, which leads to a reduction in performance and robustness. A recent approach to mitigating the impact of heterogeneous data distributions is through the use of foundation models, which offer better performance at the cost of larger computational overheads and slower inference speeds. We introduce foundation model distillation to assist in the federated training of lightweight client models and increase their performance under heterogeneous data settings while keeping inference costs low. Our results show improvement in the global model performance on a balanced testing set, which contains rarely observed samples, even under extreme non-IID client data distributions. We conduct a thorough evaluation of our framework with different foundation model backbones on CIFAR10, with varying degrees of heterogeneous data distributions ranging from class-specific data partitions across clients to dirichlet data sampling, parameterized by values between 0.01 and 1.0.

cs.LG↗

arXiv2023

Protein 3D Graph Structure Learning for Robust Structure-based Protein Property Prediction

Protein structure-based property prediction has emerged as a promising approach for various biological tasks, such as protein function prediction and sub-cellular location estimation. The existing methods highly rely on experimental protein structure data and fail in scenarios where these data are unavailable. Predicted protein structures from AI tools (e.g., AlphaFold2) were utilized as alternatives. However, we observed that current practices, which simply employ accurately predicted structures during inference, suffer from notable degradation in prediction accuracy. While similar phenomena have been extensively studied in general fields (e.g., Computer Vision) as model robustness, their impact on protein property prediction remains unexplored. In this paper, we first investigate the reason behind the performance decrease when utilizing predicted structures, attributing it to the structure embedding bias from the perspective of structure representation learning. To study this problem, we identify a Protein 3D Graph Structure Learning Problem for Robust Protein Property Prediction (PGSL-RP3), collect benchmark datasets, and present a protein Structure embedding Alignment Optimization framework (SAO) to mitigate the problem of structure embedding bias between the predicted and experimental protein structures. Extensive experiments have shown that our framework is model-agnostic and effective in improving the property prediction of both predicted structures and experimental structures. The benchmark datasets and codes will be released to benefit the community.

cs.LG↗

arXiv2023

Large Language Model Alignment: A Survey

Recent years have witnessed remarkable progress made in large language models (LLMs). Such advancements, while garnering significant attention, have concurrently elicited various concerns. The potential of these models is undeniably vast; however, they may yield texts that are imprecise, misleading, or even detrimental. Consequently, it becomes paramount to employ alignment techniques to ensure these models to exhibit behaviors consistent with human values. This survey endeavors to furnish an extensive exploration of alignment methodologies designed for LLMs, in conjunction with the extant capability research in this domain. Adopting the lens of AI alignment, we categorize the prevailing methods and emergent proposals for the alignment of LLMs into outer and inner alignment. We also probe into salient issues including the models' interpretability, and potential vulnerabilities to adversarial attacks. To assess LLM alignment, we present a wide variety of benchmarks and evaluation methodologies. After discussing the state of alignment research for LLMs, we finally cast a vision toward the future, contemplating the promising avenues of research that lie ahead. Our aspiration for this survey extends beyond merely spurring research interests in this realm. We also envision bridging the gap between the AI alignment research community and the researchers engrossed in the capability exploration of LLMs for both capable and safe LLMs.

cs.CL↗

arXiv2023

CBBQ: A Chinese Bias Benchmark Dataset Curated with Human-AI Collaboration for Large Language Models

Holistically measuring societal biases of large language models is crucial for detecting and reducing ethical risks in highly capable AI models. In this work, we present a Chinese Bias Benchmark dataset that consists of over 100K questions jointly constructed by human experts and generative language models, covering stereotypes and societal biases in 14 social dimensions related to Chinese culture and values. The curation process contains 4 essential steps: bias identification via extensive literature review, ambiguous context generation, AI-assisted disambiguous context generation, snd manual review \& recomposition. The testing instances in the dataset are automatically derived from 3K+ high-quality templates manually authored with stringent quality control. The dataset exhibits wide coverage and high diversity. Extensive experiments demonstrate the effectiveness of the dataset in detecting model bias, with all 10 publicly available Chinese large language models exhibiting strong bias in certain categories. Additionally, we observe from our experiments that fine-tuned models could, to a certain extent, heed instructions and avoid generating outputs that are morally harmful in some types, in the way of "moral self-correction". Our dataset and results are publicly available at \href{https://github.com/YFHuangxxxx/CBBQ}{https://github.com/YFHuangxxxx/CBBQ}, offering debiasing research opportunities to a widened community.

cs.CL↗

arXiv2023

Quantifying the Knowledge in GNNs for Reliable Distillation into MLPs

To bridge the gaps between topology-aware Graph Neural Networks (GNNs) and inference-efficient Multi-Layer Perceptron (MLPs), GLNN proposes to distill knowledge from a well-trained teacher GNN into a student MLP. Despite their great progress, comparatively little work has been done to explore the reliability of different knowledge points (nodes) in GNNs, especially their roles played during distillation. In this paper, we first quantify the knowledge reliability in GNN by measuring the invariance of their information entropy to noise perturbations, from which we observe that different knowledge points (1) show different distillation speeds (temporally); (2) are differentially distributed in the graph (spatially). To achieve reliable distillation, we propose an effective approach, namely Knowledge-inspired Reliable Distillation (KRD), that models the probability of each node being an informative and reliable knowledge point, based on which we sample a set of additional reliable knowledge points as supervision for training student MLPs. Extensive experiments show that KRD improves over the vanilla MLPs by 12.62% and outperforms its corresponding teacher GNNs by 2.16% averaged over 7 datasets and 3 GNN architectures.

cs.LG↗

arXiv2023

Fair Patient Model: Mitigating Bias in the Patient Representation Learned from the Electronic Health Records

Objective: To pre-train fair and unbiased patient representations from Electronic Health Records (EHRs) using a novel weighted loss function that reduces bias and improves fairness in deep representation learning models. Methods: We defined a new loss function, called weighted loss function, in the deep representation learning model to balance the importance of different groups of patients and features. We applied the proposed model, called Fair Patient Model (FPM), to a sample of 34,739 patients from the MIMIC-III dataset and learned patient representations for four clinical outcome prediction tasks. Results: FPM outperformed the baseline models in terms of three fairness metrics: demographic parity, equality of opportunity difference, and equalized odds ratio. FPM also achieved comparable predictive performance with the baselines, with an average accuracy of 0.7912. Feature analysis revealed that FPM captured more information from clinical features than the baselines. Conclusion: FPM is a novel method to pre-train fair and unbiased patient representations from EHR data using a weighted loss function. The learned representations can be used for various downstream tasks in healthcare and can be extended to other domains where bias and fairness are important.

cs.LG↗

arXiv2023

Extracting Low-/High- Frequency Knowledge from Graph Neural Networks and Injecting it into MLPs: An Effective GNN-to-MLP Distillation Framework

Recent years have witnessed the great success of Graph Neural Networks (GNNs) in handling graph-related tasks. However, MLPs remain the primary workhorse for practical industrial applications due to their desirable inference efficiency and scalability. To reduce their gaps, one can directly distill knowledge from a well-designed teacher GNN to a student MLP, which is termed as GNN-to-MLP distillation. However, the process of distillation usually entails a loss of information, and ``which knowledge patterns of GNNs are more likely to be left and distilled into MLPs?" becomes an important question. In this paper, we first factorize the knowledge learned by GNNs into low- and high-frequency components in the spectral domain and then derive their correspondence in the spatial domain. Furthermore, we identified a potential information drowning problem for existing GNN-to-MLP distillation, i.e., the high-frequency knowledge of the pre-trained GNNs may be overwhelmed by the low-frequency knowledge during distillation; we have described in detail what it represents, how it arises, what impact it has, and how to deal with it. In this paper, we propose an efficient Full-Frequency GNN-to-MLP (FF-G2M) distillation framework, which extracts both low-frequency and high-frequency knowledge from GNNs and injects it into MLPs. Extensive experiments show that FF-G2M improves over the vanilla MLPs by 12.6% and outperforms its corresponding teacher GNNs by 2.6% averaged over six graph datasets and three common GNN architectures.

cs.LG↗

arXiv2023

Note on VDB Topological Indices of k-Cyclic Graphs

Let $G$ be a connected graph with $n$ vertices and $m$ edges. The vertex-degree-based topological index (VDB) (or graphical function-index) $TI(G)$ of $G$ with edge-weight function $I(x,y)$ is defined as $$TI(G)=\sum\limits_{uv\in E(G)}I(d_{u},d_{v}),$$ where $I(x,y)>0$ is a symmetric real function with $x\geq 1$ and $y\geq 1$, $d_{u}$ is the degree of vertex $u$ in $G$. In this note, we deduce a number of previously established results, and state a few new. For a VDB topological index $TI$ with the property $P^{*}$, we can obtain the minimum $k$-cyclic (chemical) graphs for $k\geq3$, $n\geq 5(k-1)$. These VDB topological indices include the Sombor index, the general Sombor index, the $p$-Sombor index, the general sum-connectivity index and so on. Thus this note extends the results of Liu et al. [H. Liu, L. You, Y. Huang, Sombor index of c-cyclic chemical graphs, MATCH Commun. Math. Comput. Chem. 90 (2023) 495-504] and Ali et al. [A. Ali, D. Dimitrov, Z. Du, F. Ishfaq, On the extremal graphs for general sum-connectivity index $(χ_α)$ with given cyclomatic number when $α>1$, Discrete Appl. Math. 257 (2019) 19-30].

math.GM↗

arXiv2023

Using Context-to-Vector with Graph Retrofitting to Improve Word Embeddings

Although contextualized embeddings generated from large-scale pre-trained models perform well in many tasks, traditional static embeddings (e.g., Skip-gram, Word2Vec) still play an important role in low-resource and lightweight settings due to their low computational cost, ease of deployment, and stability. In this paper, we aim to improve word embeddings by 1) incorporating more contextual information from existing pre-trained models into the Skip-gram framework, which we call Context-to-Vec; 2) proposing a post-processing retrofitting method for static embeddings independent of training by employing priori synonym knowledge and weighted vector distribution. Through extrinsic and intrinsic tasks, our methods are well proven to outperform the baselines by a large margin.

cs.CL↗

arXiv2023

Non-equispaced Fourier Neural Solvers for PDEs

Solving partial differential equations is difficult. Recently proposed neural resolution-invariant models, despite their effectiveness and efficiency, usually require equispaced spatial points of data. However, sampling in spatial domain is sometimes inevitably non-equispaced in real-world systems, limiting their applicability. In this paper, we propose a Non-equispaced Fourier PDE Solver (\textsc{NFS}) with adaptive interpolation on resampled equispaced points and a variant of Fourier Neural Operators as its components. Experimental results on complex PDEs demonstrate its advantages in accuracy and efficiency. Compared with the spatially-equispaced benchmark methods, it achieves superior performance with $42.85\%$ improvements on MAE, and is able to handle non-equispaced data with a tiny loss of accuracy. Besides, to our best knowledge, \textsc{NFS} is the first ML-based method with mesh invariant inference ability to successfully model turbulent flows in non-equispaced scenarios, with a minor deviation of the error on unseen spatial points.

cs.LG↗

arXiv2023

Data-Efficient Protein 3D Geometric Pretraining via Refinement of Diffused Protein Structure Decoy

Learning meaningful protein representation is important for a variety of biological downstream tasks such as structure-based drug design. Having witnessed the success of protein sequence pretraining, pretraining for structural data which is more informative has become a promising research topic. However, there are three major challenges facing protein structure pretraining: insufficient sample diversity, physically unrealistic modeling, and the lack of protein-specific pretext tasks. To try to address these challenges, we present the 3D Geometric Pretraining. In this paper, we propose a unified framework for protein pretraining and a 3D geometric-based, data-efficient, and protein-specific pretext task: RefineDiff (Refine the Diffused Protein Structure Decoy). After pretraining our geometric-aware model with this task on limited data(less than 1% of SOTA models), we obtained informative protein representations that can achieve comparable performance for various downstream tasks.

cs.LG↗

arXiv2023

Risk-aware Vehicle Motion Planning Using Bayesian LSTM-Based Model Predictive Control

Understanding the probabilistic traffic environment is a vital challenge for the motion planning of autonomous vehicles. To make feasible control decisions, forecasting future trajectories of adjacent cars is essential for intelligent vehicles to assess potential conflicts and react to reduce the risk. This paper first introduces a Bayesian Long Short-term Memory (BLSTM) model to learn human drivers' behaviors and habits from their historical trajectory data. The model predicts the probability distribution of surrounding vehicles' positions, which are used to estimate dynamic conflict risks. Next, a hybrid automaton is built to model the basic motions of a car, and the conflict risks are assessed for real-time state-space transitions based on environmental information. Finally, a BLSTM-based Model Predictive Control (MPC) is built to navigate vehicles through safe paths with the least predicted conflict risk. By merging BLSTM with MPC, the designed neural-based MPC overcomes the defect that traditional MPC is hard to model uncertain conflict risks. The simulation results show that our proposed BLSTM-based MPC performs better than human drivers because it can foresee potential conflicts and take action to avoid them.

cs.RO↗

arXiv2022

A Survey on Protein Representation Learning: Retrospect and Prospect

Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physicochemical world, forming a special kind of sequence-structure data. With the development of Artificial Intelligence (AI) techniques, Protein Representation Learning (PRL) has recently emerged as a promising research topic for extracting informative knowledge from massive protein sequences or structures. To pave the way for AI researchers with little bioinformatics background, we present a timely and comprehensive review of PRL formulations and existing PRL methods from the perspective of model architectures, pretext tasks, and downstream applications. We first briefly introduce the motivations for protein representation learning and formulate it in a general and unified framework. Next, we divide existing PRL methods into three main categories: sequence-based, structure-based, and sequence-structure co-modeling. Finally, we discuss some technical challenges and potential directions for improving protein representation learning. The latest advances in PRL methods are summarized in a GitHub repository https://github.com/LirongWu/awesome-protein-representation-learning.

cs.LG↗

arXiv2022

Protein Language Models and Structure Prediction: Connection and Progression

The prediction of protein structures from sequences is an important task for function prediction, drug design, and related biological processes understanding. Recent advances have proved the power of language models (LMs) in processing the protein sequence databases, which inherit the advantages of attention networks and capture useful information in learning representations for proteins. The past two years have witnessed remarkable success in tertiary protein structure prediction (PSP), including evolution-based and single-sequence-based PSP. It seems that instead of using energy-based models and sampling procedures, protein language model (pLM)-based pipelines have emerged as mainstream paradigms in PSP. Despite the fruitful progress, the PSP community needs a systematic and up-to-date survey to help bridge the gap between LMs in the natural language processing (NLP) and PSP domains and introduce their methodologies, advancements and practical applications. To this end, in this paper, we first introduce the similarities between protein and human languages that allow LMs extended to pLMs, and applied to protein databases. Then, we systematically review recent advances in LMs and pLMs from the perspectives of network architectures, pre-training strategies, applications, and commonly-used protein databases. Next, different types of methods for PSP are discussed, particularly how the pLM-based architectures function in the process of protein folding. Finally, we identify challenges faced by the PSP community and foresee promising research directions along with the advances of pLMs. This survey aims to be a hands-on guide for researchers to understand PSP methods, develop pLMs and tackle challenging problems in this field for practical purposes.

q-bio.QM↗

arXiv2022

FPT: Improving Prompt Tuning Efficiency via Progressive Training

Recently, prompt tuning (PT) has gained increasing attention as a parameter-efficient way of tuning pre-trained language models (PLMs). Despite extensively reducing the number of tunable parameters and achieving satisfying performance, PT is training-inefficient due to its slow convergence. To improve PT's training efficiency, we first make some novel observations about the prompt transferability of "partial PLMs", which are defined by compressing a PLM in depth or width. We observe that the soft prompts learned by different partial PLMs of various sizes are similar in the parameter space, implying that these soft prompts could potentially be transferred among partial PLMs. Inspired by these observations, we propose Fast Prompt Tuning (FPT), which starts by conducting PT using a small-scale partial PLM, and then progressively expands its depth and width until the full-model size. After each expansion, we recycle the previously learned soft prompts as initialization for the enlarged partial PLM and then proceed PT. We demonstrate the feasibility of FPT on 5 tasks and show that FPT could save over 30% training computations while achieving comparable performance.

cs.CL↗

arXiv2022

Regular graphs with a complete bipartite graph as a star complement

Let $G$ be a graph of order $n$ and $μ$ be an adjacency eigenvalue of $G$ with multiplicity $k\geq 1$. A star complement $H$ for $μ$ in $G$ is an induced subgraph of $G$ of order $n-k$ with no eigenvalue $μ$, and the vertex subset $X=V(G-H)$ is called a star set for $μ$ in $G$. The study of star complements and star sets provides a strong link between graph structure and linear algebra. In this paper, we study the regular graphs with $K_{t,s}\ (s\geq t\geq 2)$ as a star complement for an eigenvalue $μ$, especially, characterize the case of $t=3$ completely, obtain some properties when $t=s$, and propose some problems for further study.

math.CO↗

arXiv2022

Automated Graph Self-supervised Learning via Multi-teacher Knowledge Distillation

Self-supervised learning on graphs has recently achieved remarkable success in graph representation learning. With hundreds of self-supervised pretext tasks proposed over the past few years, the research community has greatly developed, and the key is no longer to design more powerful but complex pretext tasks, but to make more effective use of those already on hand. This paper studies the problem of how to automatically, adaptively, and dynamically learn instance-level self-supervised learning strategies for each node from a given pool of pretext tasks. In this paper, we propose a novel multi-teacher knowledge distillation framework for Automated Graph Self-Supervised Learning (AGSSL), which consists of two main branches: (i) Knowledge Extraction: training multiple teachers with different pretext tasks, so as to extract different levels of knowledge with different inductive biases; (ii) Knowledge Integration: integrating different levels of knowledge and distilling them into the student model. Without simply treating different teachers as equally important, we provide a provable theoretical guideline for how to integrate the knowledge of different teachers, i.e., the integrated teacher probability should be close to the true Bayesian class-probability. To approach the theoretical optimum in practice, two adaptive knowledge integration strategies are proposed to construct a relatively "good" integrated teacher. Extensive experiments on eight datasets show that AGSSL can benefit from multiple pretext tasks, outperforming the corresponding individual tasks; by combining a few simple but classical pretext tasks, the resulting performance is comparable to other leading counterparts.

cs.LG↗