arXiv subjects

Yizhou Sun

Publications and source records attributed to Yizhou Sun.

At least 109 records · Page 6Linked to original sources

arXiv2024

Cross-Modality Program Representation Learning for Electronic Design Automation with High-Level Synthesis

In recent years, domain-specific accelerators (DSAs) have gained popularity for applications such as deep learning and autonomous driving. To facilitate DSA designs, programmers use high-level synthesis (HLS) to compile a high-level description written in C/C++ into a design with low-level hardware description languages that eventually synthesize DSAs on circuits. However, creating a high-quality HLS design still demands significant domain knowledge, particularly in microarchitecture decisions expressed as \textit{pragmas}. Thus, it is desirable to automate such decisions with the help of machine learning for predicting the quality of HLS designs, requiring a deeper understanding of the program that consists of original code and pragmas. Naturally, these programs can be considered as sequence data. In addition, these programs can be compiled and converted into a control data flow graph (CDFG). But existing works either fail to leverage both modalities or combine the two in shallow or coarse ways. We propose ProgSG, a model that allows interaction between the source code sequence modality and the graph modality in a deep and fine-grained way. To alleviate the scarcity of labeled designs, a pre-training method is proposed based on a suite of compiler's data flow analysis tasks. Experimental results show that ProgSG reduces the RMSE of design performance predictions by up to $22\%$, and identifies designs with an average of $1.10\times$ and $1.26\times$ (up to $8.17\times$ and $13.31\times$) performance improvement in design space exploration (DSE) task compared to HARP and AutoDSE, respectively.

cs.LG↗

arXiv2024

SciBench: Evaluating College-Level Scientific Problem-Solving Abilities of Large Language Models

Most of the existing Large Language Model (LLM) benchmarks on scientific problem reasoning focus on problems grounded in high-school subjects and are confined to elementary algebraic operations. To systematically examine the reasoning capabilities required for solving complex scientific problems, we introduce an expansive benchmark suite SciBench for LLMs. SciBench contains a carefully curated dataset featuring a range of collegiate-level scientific problems from mathematics, chemistry, and physics domains. Based on the dataset, we conduct an in-depth benchmarking study of representative open-source and proprietary LLMs with various prompting strategies. The results reveal that the current LLMs fall short of delivering satisfactory performance, with the best overall score of merely 43.22%. Furthermore, through a detailed user study, we categorize the errors made by LLMs into ten problem-solving abilities. Our analysis indicates that no single prompting strategy significantly outperforms the others and some strategies that demonstrate improvements in certain problem-solving skills could result in declines in other skills. We envision that SciBench will catalyze further developments in the reasoning abilities of LLMs, thereby ultimately contributing to scientific research and discovery.

cs.CL↗

arXiv2024

PGODE: Towards High-quality System Dynamics Modeling

This paper studies the problem of modeling multi-agent dynamical systems, where agents could interact mutually to influence their behaviors. Recent research predominantly uses geometric graphs to depict these mutual interactions, which are then captured by powerful graph neural networks (GNNs). However, predicting interacting dynamics in challenging scenarios such as out-of-distribution shift and complicated underlying rules remains unsolved. In this paper, we propose a new approach named Prototypical Graph ODE (PGODE) to address the problem. The core of PGODE is to incorporate prototype decomposition from contextual knowledge into a continuous graph ODE framework. Specifically, PGODE employs representation disentanglement and system parameters to extract both object-level and system-level contexts from historical trajectories, which allows us to explicitly model their independent influence and thus enhances the generalization capability under system changes. Then, we integrate these disentangled latent representations into a graph ODE model, which determines a combination of various interacting prototypes for enhanced model expressivity. The entire model is optimized using an end-to-end variational inference framework to maximize the likelihood. Extensive experiments in both in-distribution and out-of-distribution settings validate the superiority of PGODE compared to various baselines.

cs.LG↗

arXiv2024

SparseCL: Sparse Contrastive Learning for Contradiction Retrieval

Contradiction retrieval refers to identifying and extracting documents that explicitly disagree with or refute the content of a query, which is important to many downstream applications like fact checking and data cleaning. To retrieve contradiction argument to the query from large document corpora, existing methods such as similarity search and crossencoder models exhibit significant limitations. The former struggles to capture the essence of contradiction due to its inherent nature of favoring similarity, while the latter suffers from computational inefficiency, especially when the size of corpora is large. To address these challenges, we introduce a novel approach: SparseCL that leverages specially trained sentence embeddings designed to preserve subtle, contradictory nuances between sentences. Our method utilizes a combined metric of cosine similarity and a sparsity function to efficiently identify and retrieve documents that contradict a given query. This approach dramatically enhances the speed of contradiction detection by reducing the need for exhaustive document comparisons to simple vector calculations. We validate our model using the Arguana dataset, a benchmark dataset specifically geared towards contradiction retrieval, as well as synthetic contradictions generated from the MSMARCO and HotpotQA datasets using GPT-4. Our experiments demonstrate the efficacy of our approach not only in contradiction retrieval with more than 30% accuracy improvements on MSMARCO and HotpotQA across different model architectures but also in applications such as cleaning corrupted corpora to restore high-quality QA retrieval. This paper outlines a promising direction for improving the accuracy and efficiency of contradiction retrieval in large-scale text corpora.

cs.CL↗

arXiv2024

Hierarchical Compression of Text-Rich Graphs via Large Language Models

Text-rich graphs, prevalent in data mining contexts like e-commerce and academic graphs, consist of nodes with textual features linked by various relations. Traditional graph machine learning models, such as Graph Neural Networks (GNNs), excel in encoding the graph structural information, but have limited capability in handling rich text on graph nodes. Large Language Models (LLMs), noted for their superior text understanding abilities, offer a solution for processing the text in graphs but face integration challenges due to their limitation for encoding graph structures and their computational complexities when dealing with extensive text in large neighborhoods of interconnected nodes. This paper introduces ``Hierarchical Compression'' (HiCom), a novel method to align the capabilities of LLMs with the structure of text-rich graphs. HiCom processes text in a node's neighborhood in a structured manner by organizing the extensive textual information into a more manageable hierarchy and compressing node text step by step. Therefore, HiCom not only preserves the contextual richness of the text but also addresses the computational challenges of LLMs, which presents an advancement in integrating the text processing power of LLMs with the structural complexities of text-rich graphs. Empirical results show that HiCom can outperform both GNNs and LLM backbones for node classification on e-commerce and citation graphs. HiCom is especially effective for nodes from a dense region in a graph, where it achieves a 3.48% average performance improvement on five datasets while being more efficient than LLM backbones.

cs.SI↗

arXiv2024

Networked Inequality: Preferential Attachment Bias in Graph Neural Network Link Prediction

Graph neural network (GNN) link prediction is increasingly deployed in citation, collaboration, and online social networks to recommend academic literature, collaborators, and friends. While prior research has investigated the dyadic fairness of GNN link prediction, the within-group (e.g., queer women) fairness and "rich get richer" dynamics of link prediction remain underexplored. However, these aspects have significant consequences for degree and power imbalances in networks. In this paper, we shed light on how degree bias in networks affects Graph Convolutional Network (GCN) link prediction. In particular, we theoretically uncover that GCNs with a symmetric normalized graph filter have a within-group preferential attachment bias. We validate our theoretical analysis on real-world citation, collaboration, and online social networks. We further bridge GCN's preferential attachment bias with unfairness in link prediction and propose a new within-group fairness metric. This metric quantifies disparities in link prediction scores within social groups, towards combating the amplification of degree and power disparities. Finally, we propose a simple training-time strategy to alleviate within-group unfairness, and we show that it is effective on citation, social, and credit networks.

cs.LG↗

arXiv2024

Fast Inference of Removal-Based Node Influence

Graph neural networks (GNNs) are widely utilized to capture the information spreading patterns in graphs. While remarkable performance has been achieved, there is a new trending topic of evaluating node influence. We propose a new method of evaluating node influence, which measures the prediction change of a trained GNN model caused by removing a node. A real-world application is, "In the task of predicting Twitter accounts' polarity, had a particular account been removed, how would others' polarity change?". We use the GNN as a surrogate model whose prediction could simulate the change of nodes or edges caused by node removal. Our target is to obtain the influence score for every node, and a straightforward way is to alternately remove every node and apply the trained GNN on the modified graph to generate new predictions. It is reliable but time-consuming, so we need an efficient method. The related lines of work, such as graph adversarial attack and counterfactual explanation, cannot directly satisfy our needs, since their problem settings are different. We propose an efficient, intuitive, and effective method, NOde-Removal-based fAst GNN inference (NORA), which uses the gradient information to approximate the node-removal influence. It only costs one forward propagation and one backpropagation to approximate the influence score for all nodes. Extensive experiments on six datasets and six GNN models verify the effectiveness of NORA. Our code is available at https://github.com/weikai-li/NORA.git.

cs.LG↗

arXiv2024

Mixture of In-Context Prompters for Tabular PFNs

Recent benchmarks found In-Context Learning (ICL) outperforms both deep learning and tree-based algorithms on small tabular datasets. However, on larger datasets, ICL for tabular learning cannot run without severely compromising performance, due to its quadratic space and time complexity w.r.t. dataset size. We propose MIXTUREPFN, which both extends nearest-neighbor sampling to the state-of-the-art ICL for tabular learning model and uses bootstrapping to finetune said model on the inference-time dataset. MIXTUREPFN is the Condorcet winner across 36 diverse tabular datasets against 19 strong deep learning and tree-based baselines, achieving the highest mean rank among Top-10 aforementioned algorithms with statistical significance.

cs.LG↗

arXiv2024

Resprompt: Residual Connection Prompting Advances Multi-Step Reasoning in Large Language Models

Chain-of-thought (CoT) prompting, which offers step-by-step problem-solving rationales, has impressively unlocked the reasoning potential of large language models (LLMs). Yet, the standard CoT is less effective in problems demanding multiple reasoning steps. This limitation arises from the complex reasoning process in multi-step problems: later stages often depend on the results of several steps earlier, not just the results of the immediately preceding step. Such complexities suggest the reasoning process is naturally represented as a graph. The almost linear and straightforward structure of CoT prompting, however, struggles to capture this complex reasoning graph. To address this challenge, we propose Residual Connection Prompting (RESPROMPT), a new prompting strategy that advances multi-step reasoning in LLMs. Our key idea is to reconstruct the reasoning graph within prompts. We achieve this by integrating necessary connections-links present in the reasoning graph but missing in the linear CoT flow-into the prompts. Termed "residual connections", these links are pivotal in morphing the linear CoT structure into a graph representation, effectively capturing the complex reasoning graphs inherent in multi-step problems. We evaluate RESPROMPT on six benchmarks across three diverse domains: math, sequential, and commonsense reasoning. For the open-sourced LLaMA family of models, RESPROMPT yields a significant average reasoning accuracy improvement of 12.5% on LLaMA-65B and 6.8% on LLaMA2-70B. Breakdown analysis further highlights RESPROMPT particularly excels in complex multi-step reasoning: for questions demanding at least five reasoning steps, RESPROMPT outperforms the best CoT based benchmarks by a remarkable average improvement of 21.1% on LLaMA-65B and 14.3% on LLaMA2-70B. Through extensive ablation studies and analyses, we pinpoint how to most effectively build residual connections.

cs.CL↗

arXiv2024

BrainODE: Dynamic Brain Signal Analysis via Graph-Aided Neural Ordinary Differential Equations

Brain network analysis is vital for understanding the neural interactions regarding brain structures and functions, and identifying potential biomarkers for clinical phenotypes. However, widely used brain signals such as Blood Oxygen Level Dependent (BOLD) time series generated from functional Magnetic Resonance Imaging (fMRI) often manifest three challenges: (1) missing values, (2) irregular samples, and (3) sampling misalignment, due to instrumental limitations, impacting downstream brain network analysis and clinical outcome predictions. In this work, we propose a novel model called BrainODE to achieve continuous modeling of dynamic brain signals using Ordinary Differential Equations (ODE). By learning latent initial values and neural ODE functions from irregular time series, BrainODE effectively reconstructs brain signals at any time point, mitigating the aforementioned three data challenges of brain signals altogether. Comprehensive experimental results on real-world neuroimaging datasets demonstrate the superior performance of BrainODE and its capability of addressing the three data challenges.

cs.LG↗

arXiv2024

Parameter-Efficient Tuning Large Language Models for Graph Representation Learning

Text-rich graphs, which exhibit rich textual information on nodes and edges, are prevalent across a wide range of real-world business applications. Large Language Models (LLMs) have demonstrated remarkable abilities in understanding text, which also introduced the potential for more expressive modeling in text-rich graphs. Despite these capabilities, efficiently applying LLMs to representation learning on graphs presents significant challenges. Recently, parameter-efficient fine-tuning methods for LLMs have enabled efficient new task generalization with minimal time and memory consumption. Inspired by this, we introduce Graph-aware Parameter-Efficient Fine-Tuning - GPEFT, a novel approach for efficient graph representation learning with LLMs on text-rich graphs. Specifically, we utilize a graph neural network (GNN) to encode structural information from neighboring nodes into a graph prompt. This prompt is then inserted at the beginning of the text sequence. To improve the quality of graph prompts, we pre-trained the GNN to assist the frozen LLM in predicting the next token in the node text. Compared with existing joint GNN and LMs, our method directly generate the node embeddings from large language models with an affordable fine-tuning cost. We validate our approach through comprehensive experiments conducted on 8 different text-rich graphs, observing an average improvement of 2% in hit@1 and Mean Reciprocal Rank (MRR) in link prediction evaluations. Our results demonstrate the efficacy and efficiency of our model, showing that it can be smoothly integrated with various large language models, including OPT, LLaMA and Falcon.

cs.CL↗

arXiv2024

Hierarchical Attention Models for Multi-Relational Graphs

We present Bi-Level Attention-Based Relational Graph Convolutional Networks (BR-GCN), unique neural network architectures that utilize masked self-attentional layers with relational graph convolutions, to effectively operate on highly multi-relational data. BR-GCN models use bi-level attention to learn node embeddings through (1) node-level attention, and (2) relation-level attention. The node-level self-attentional layers use intra-relational graph interactions to learn relation-specific node embeddings using a weighted aggregation of neighborhood features in a sparse subgraph region. The relation-level self-attentional layers use inter-relational graph interactions to learn the final node embeddings using a weighted aggregation of relation-specific node embeddings. The BR-GCN bi-level attention mechanism extends Transformer-based multiplicative attention from the natural language processing (NLP) domain, and Graph Attention Networks (GAT)-based attention, to large-scale heterogeneous graphs (HGs). On node classification, BR-GCN outperforms baselines from 0.29% to 14.95% as a stand-alone model, and on link prediction, BR-GCN outperforms baselines from 0.02% to 7.40% as an auto-encoder model. We also conduct ablation studies to evaluate the quality of BR-GCN's relation-level attention and discuss how its learning of graph structure may be transferred to enrich other graph neural networks (GNNs). Through various experiments, we show that BR-GCN's attention mechanism is both scalable and more effective in learning compared to state-of-the-art GNNs.

cs.LG↗

arXiv2024

Weisfeiler and Leman Go Measurement Modeling: Probing the Validity of the WL Test

The expressive power of graph neural networks is usually measured by comparing how many pairs of graphs or nodes an architecture can possibly distinguish as non-isomorphic to those distinguishable by the $k$-dimensional Weisfeiler-Leman ($k$-WL) test. In this paper, we uncover misalignments between graph machine learning practitioners' conceptualizations of expressive power and $k$-WL through a systematic analysis of the reliability and validity of $k$-WL. We conduct a survey ($n = 18$) of practitioners to surface their conceptualizations of expressive power and their assumptions about $k$-WL. In contrast to practitioners' beliefs, our analysis (which draws from graph theory and benchmark auditing) reveals that $k$-WL does not guarantee isometry, can be irrelevant to real-world graph tasks, and may not promote generalization or trustworthiness. We argue for extensional definitions and measurement of expressive power based on benchmarks. We further contribute guiding questions for constructing such benchmarks, which is critical for graph machine learning practitioners to develop and transparently communicate our understandings of expressive power.

cs.LG↗

arXiv2024

Causal Graph ODE: Continuous Treatment Effect Modeling in Multi-agent Dynamical Systems

Real-world multi-agent systems are often dynamic and continuous, where the agents co-evolve and undergo changes in their trajectories and interactions over time. For example, the COVID-19 transmission in the U.S. can be viewed as a multi-agent system, where states act as agents and daily population movements between them are interactions. Estimating the counterfactual outcomes in such systems enables accurate future predictions and effective decision-making, such as formulating COVID-19 policies. However, existing methods fail to model the continuous dynamic effects of treatments on the outcome, especially when multiple treatments (e.g., "stay-at-home" and "get-vaccine" policies) are applied simultaneously. To tackle this challenge, we propose Causal Graph Ordinary Differential Equations (CAG-ODE), a novel model that captures the continuous interaction among agents using a Graph Neural Network (GNN) as the ODE function. The key innovation of our model is to learn time-dependent representations of treatments and incorporate them into the ODE function, enabling precise predictions of potential outcomes. To mitigate confounding bias, we further propose two domain adversarial learning-based objectives, which enable our model to learn balanced continuous representations that are not affected by treatments or interference. Experiments on two datasets (i.e., COVID-19 and tumor growth) demonstrate the superior performance of our proposed model.

cs.LG↗

arXiv2024

An Evaluation of Large Language Models in Bioinformatics Research

Large language models (LLMs) such as ChatGPT have gained considerable interest across diverse research communities. Their notable ability for text completion and generation has inaugurated a novel paradigm for language-interfaced problem solving. However, the potential and efficacy of these models in bioinformatics remain incompletely explored. In this work, we study the performance LLMs on a wide spectrum of crucial bioinformatics tasks. These tasks include the identification of potential coding regions, extraction of named entities for genes and proteins, detection of antimicrobial and anti-cancer peptides, molecular optimization, and resolution of educational bioinformatics problems. Our findings indicate that, given appropriate prompts, LLMs like GPT variants can successfully handle most of these tasks. In addition, we provide a thorough analysis of their limitations in the context of complicated bioinformatics tasks. In conclusion, we believe that this work can provide new perspectives and motivate future research in the field of LLMs applications, AI for Science and bioinformatics.

q-bio.QM↗

arXiv2024

Structure Guided Prompt: Instructing Large Language Model in Multi-Step Reasoning by Exploring Graph Structure of the Text

Although Large Language Models (LLMs) excel at addressing straightforward reasoning tasks, they frequently struggle with difficulties when confronted by more complex multi-step reasoning due to a range of factors. Firstly, natural language often encompasses complex relationships among entities, making it challenging to maintain a clear reasoning chain over longer spans. Secondly, the abundance of linguistic diversity means that the same entities and relationships can be expressed using different terminologies and structures, complicating the task of identifying and establishing connections between multiple pieces of information. Graphs provide an effective solution to represent data rich in relational information and capture long-term dependencies among entities. To harness the potential of graphs, our paper introduces Structure Guided Prompt, an innovative three-stage task-agnostic prompting framework designed to improve the multi-step reasoning capabilities of LLMs in a zero-shot setting. This framework explicitly converts unstructured text into a graph via LLMs and instructs them to navigate this graph using task-specific strategies to formulate responses. By effectively organizing information and guiding navigation, it enables LLMs to provide more accurate and context-aware responses. Our experiments show that this framework significantly enhances the reasoning capabilities of LLMs, enabling them to excel in a broader spectrum of natural language scenarios.

cs.CL↗

arXiv2023

A Primer on Deep Learning for Causal Inference

This review systematizes the emerging literature for causal inference using deep neural networks under the potential outcomes framework. It provides an intuitive introduction on how deep learning can be used to estimate/predict heterogeneous treatment effects and extend causal inference to settings where confounding is non-linear, time varying, or encoded in text, networks, and images. To maximize accessibility, we also introduce prerequisite concepts from causal inference and deep learning. The survey differs from other treatments of deep learning and causal inference in its sharp focus on observational causal estimation, its extended exposition of key algorithms, and its detailed tutorials for implementing, training, and selecting among deep estimators in Tensorflow 2 available at github.com/kochbj/Deep-Learning-for-Causal-Inference.

cs.LG↗

arXiv2023

AVIS: Autonomous Visual Information Seeking with Large Language Model Agent

In this paper, we propose an autonomous information seeking visual question answering framework, AVIS. Our method leverages a Large Language Model (LLM) to dynamically strategize the utilization of external tools and to investigate their outputs, thereby acquiring the indispensable knowledge needed to provide answers to the posed questions. Responding to visual questions that necessitate external knowledge, such as "What event is commemorated by the building depicted in this image?", is a complex task. This task presents a combinatorial search space that demands a sequence of actions, including invoking APIs, analyzing their responses, and making informed decisions. We conduct a user study to collect a variety of instances of human decision-making when faced with this task. This data is then used to design a system comprised of three components: an LLM-powered planner that dynamically determines which tool to use next, an LLM-powered reasoner that analyzes and extracts key information from the tool outputs, and a working memory component that retains the acquired information throughout the process. The collected user behavior serves as a guide for our system in two key ways. First, we create a transition graph by analyzing the sequence of decisions made by users. This graph delineates distinct states and confines the set of actions available at each state. Second, we use examples of user decision-making to provide our LLM-powered planner and reasoner with relevant contextual instances, enhancing their capacity to make informed decisions. We show that AVIS achieves state-of-the-art results on knowledge-intensive visual question answering benchmarks such as Infoseek and OK-VQA.

cs.CV↗