arXiv subjects

Jia Li

Publications and source records attributed to Jia Li.

At least 379 records · Page 21Linked to original sources

arXiv2024

All in One: Multi-Task Prompting for Graph Neural Networks (Extended Abstract)

This paper is an extended abstract of our original work published in KDD23, where we won the best research paper award (Xiangguo Sun, Hong Cheng, Jia Li, Bo Liu, and Jihong Guan. All in one: Multi-task prompting for graph neural networks. KDD 23) The paper introduces a novel approach to bridging the gap between pre-trained graph models and the diverse tasks they're applied to, inspired by the success of prompt learning in NLP. Recognizing the challenge of aligning pre-trained models with varied graph tasks (node level, edge level, and graph level), which can lead to negative transfer and poor performance, we propose a multi-task prompting method for graphs. This method involves unifying graph and language prompt formats, enabling NLP's prompting strategies to be adapted for graph tasks. By analyzing the task space of graph applications, we reformulate problems to fit graph-level tasks and apply meta-learning to improve prompt initialization for multiple tasks. Experiments show our method's effectiveness in enhancing model performance across different graph tasks. Beyond the original work, in this extended abstract, we further discuss the graph prompt from a bigger picture and provide some of the latest work toward this area.

cs.LG↗

arXiv2024

Fair Text-to-Image Diffusion via Fair Mapping

In this paper, we address the limitations of existing text-to-image diffusion models in generating demographically fair results when given human-related descriptions. These models often struggle to disentangle the target language context from sociocultural biases, resulting in biased image generation. To overcome this challenge, we propose Fair Mapping, a flexible, model-agnostic, and lightweight approach that modifies a pre-trained text-to-image diffusion model by controlling the prompt to achieve fair image generation. One key advantage of our approach is its high efficiency. It only requires updating an additional linear network with few parameters at a low computational cost. By developing a linear network that maps conditioning embeddings into a debiased space, we enable the generation of relatively balanced demographic results based on the specified text condition. With comprehensive experiments on face image generation, we show that our method significantly improves image generation fairness with almost the same image quality compared to conventional diffusion models when prompted with descriptions related to humans. By effectively addressing the issue of implicit language bias, our method produces more fair and diverse image outputs.

cs.CV↗

arXiv2024

DevEval: Evaluating Code Generation in Practical Software Projects

How to evaluate Large Language Models (LLMs) in code generation is an open question. Many benchmarks have been proposed but are inconsistent with practical software projects, e.g., unreal program distributions, insufficient dependencies, and small-scale project contexts. Thus, the capabilities of LLMs in practical projects are still unclear. In this paper, we propose a new benchmark named DevEval, aligned with Developers' experiences in practical projects. DevEval is collected through a rigorous pipeline, containing 2,690 samples from 119 practical projects and covering 10 domains. Compared to previous benchmarks, DevEval aligns to practical projects in multiple dimensions, e.g., real program distributions, sufficient dependencies, and enough-scale project contexts. We assess five popular LLMs on DevEval (e.g., gpt-4, gpt-3.5-turbo, CodeLLaMa, and StarCoder) and reveal their actual abilities in code generation. For instance, the highest Pass@1 of gpt-3.5-turbo only is 42 in our experiments. We also discuss the challenges and future directions of code generation in practical projects. We open-source DevEval and hope it can facilitate the development of code generation in practical projects.

cs.SE↗

arXiv2024

Relation-First Modeling Paradigm for Causal Representation Learning toward the Development of AGI

The traditional i.i.d.-based learning paradigm faces inherent challenges in addressing causal relationships, which has become increasingly evident with the rise of applications in causal representation learning. Our understanding of causality naturally requires a perspective as the creator rather than observer, as the ``what...if'' questions only hold within the possible world we conceive. The traditional perspective limits capturing dynamic causal outcomes and leads to compensatory efforts such as the reliance on hidden confounders. This paper lays the groundwork for the new perspective, which enables the \emph{relation-first} modeling paradigm for causality. Also, it introduces the Relation-Indexed Representation Learning (RIRL) as a practical implementation, supported by experiments that validate its efficacy.

cs.AI↗

arXiv2024

Protein Multimer Structure Prediction via Prompt Learning

Understanding the 3D structures of protein multimers is crucial, as they play a vital role in regulating various cellular processes. It has been empirically confirmed that the multimer structure prediction~(MSP) can be well handled in a step-wise assembly fashion using provided dimer structures and predicted protein-protein interactions~(PPIs). However, due to the biological gap in the formation of dimers and larger multimers, directly applying PPI prediction techniques can often cause a \textit{poor generalization} to the MSP task. To address this challenge, we aim to extend the PPI knowledge to multimers of different scales~(i.e., chain numbers). Specifically, we propose \textbf{\textsc{PromptMSP}}, a pre-training and \textbf{Prompt} tuning framework for \textbf{M}ultimer \textbf{S}tructure \textbf{P}rediction. First, we tailor the source and target tasks for effective PPI knowledge learning and efficient inference, respectively. We design PPI-inspired prompt learning to narrow the gaps of two task formats and generalize the PPI knowledge to multimers of different scales. We provide a meta-learning strategy to learn a reliable initialization of the prompt model, enabling our prompting framework to effectively adapt to limited data for large-scale multimers. Empirically, we achieve both significant accuracy (RMSD and TM-Score) and efficiency improvements compared to advanced MSP models. The code, data and checkpoints are released at \url{https://github.com/zqgao22/PromptMSP}.

cs.CE↗

arXiv2024

StarCoder 2 and The Stack v2: The Next Generation

The BigCode project, an open-scientific collaboration focused on the responsible development of Large Language Models for Code (Code LLMs), introduces StarCoder2. In partnership with Software Heritage (SWH), we build The Stack v2 on top of the digital commons of their source code archive. Alongside the SWH repositories spanning 619 programming languages, we carefully select other high-quality data sources, such as GitHub pull requests, Kaggle notebooks, and code documentation. This results in a training set that is 4x larger than the first StarCoder dataset. We train StarCoder2 models with 3B, 7B, and 15B parameters on 3.3 to 4.3 trillion tokens and thoroughly evaluate them on a comprehensive set of Code LLM benchmarks. We find that our small model, StarCoder2-3B, outperforms other Code LLMs of similar size on most benchmarks, and also outperforms StarCoderBase-15B. Our large model, StarCoder2- 15B, significantly outperforms other models of comparable size. In addition, it matches or outperforms CodeLlama-34B, a model more than twice its size. Although DeepSeekCoder- 33B is the best-performing model at code completion for high-resource languages, we find that StarCoder2-15B outperforms it on math and code reasoning benchmarks, as well as several low-resource languages. We make the model weights available under an OpenRAIL license and ensure full transparency regarding the training data by releasing the SoftWare Heritage persistent IDentifiers (SWHIDs) of the source code data.

cs.SE↗

arXiv2024

Regularized double shuffle relations of $μ$-multiple Hurwitz zeta values

In this paper we consider a family of multiple Hurwitz zeta values with bi-indices parameterized by $μ$ with $\Ree(μ)>0$. These values are equipped with both the $μ$-stuffle product from their series definition and the shuffle product from their integral expressions. We will give a detailed analysis of the two different products and discuss their regularization when the bi-indices are non-admissible. Our main goal is to prove the comparison theorem relating the two ways of regularization, which is an analog of Ihara, Kaneko, and Zagier's celebrated result concerning the regularization of multiple zeta values. We will see that the comparison formula is $μ$-invariant, that is, it is independent of the parameter $μ$. As applications, we will first provide a few interesting closed formulas for some multi-fold infinite sums that are closely related to the multiple zeta values of level $N$ studied by Yuan and the second author. We will also derive two sum formulas for $μ$-double Hurwitz zeta values which generalize the sum formulas for double zeta values and double zeta star values, respectively, and a weighted sum formula which generalizes the weighted sum formulas for both double zeta values and double $T$-values simultaneously. At the end of the paper, we will propose a problem extending that for multiple zeta values first conjectured by Ihara et al.

math.NT↗

arXiv2024

Cross-scale Multi-instance Learning for Pathological Image Diagnosis

Analyzing high resolution whole slide images (WSIs) with regard to information across multiple scales poses a significant challenge in digital pathology. Multi-instance learning (MIL) is a common solution for working with high resolution images by classifying bags of objects (i.e. sets of smaller image patches). However, such processing is typically performed at a single scale (e.g., 20x magnification) of WSIs, disregarding the vital inter-scale information that is key to diagnoses by human pathologists. In this study, we propose a novel cross-scale MIL algorithm to explicitly aggregate inter-scale relationships into a single MIL network for pathological image diagnosis. The contribution of this paper is three-fold: (1) A novel cross-scale MIL (CS-MIL) algorithm that integrates the multi-scale information and the inter-scale relationships is proposed; (2) A toy dataset with scale-specific morphological features is created and released to examine and visualize differential cross-scale attention; (3) Superior performance on both in-house and public datasets is demonstrated by our simple cross-scale MIL strategy. The official implementation is publicly available at https://github.com/hrlblab/CS-MIL.

eess.IV↗

arXiv2024

Weakly Supervised Anomaly Detection via Knowledge-Data Alignment

Anomaly detection (AD) plays a pivotal role in numerous web-based applications, including malware detection, anti-money laundering, device failure detection, and network fault analysis. Most methods, which rely on unsupervised learning, are hard to reach satisfactory detection accuracy due to the lack of labels. Weakly Supervised Anomaly Detection (WSAD) has been introduced with a limited number of labeled anomaly samples to enhance model performance. Nevertheless, it is still challenging for models, trained on an inadequate amount of labeled data, to generalize to unseen anomalies. In this paper, we introduce a novel framework Knowledge-Data Alignment (KDAlign) to integrate rule knowledge, typically summarized by human experts, to supplement the limited labeled data. Specifically, we transpose these rules into the knowledge space and subsequently recast the incorporation of knowledge as the alignment of knowledge and data. To facilitate this alignment, we employ the Optimal Transport (OT) technique. We then incorporate the OT distance as an additional loss term to the original objective function of WSAD methodologies. Comprehensive experimental results on five real-world datasets demonstrate that our proposed KDAlign framework markedly surpasses its state-of-the-art counterparts, achieving superior performance across various anomaly types.

cs.LG↗

arXiv2024

Nucleus subtype classification using inter-modality learning

Understanding the way cells communicate, co-locate, and interrelate is essential to understanding human physiology. Hematoxylin and eosin (H&E) staining is ubiquitously available both for clinical studies and research. The Colon Nucleus Identification and Classification (CoNIC) Challenge has recently innovated on robust artificial intelligence labeling of six cell types on H&E stains of the colon. However, this is a very small fraction of the number of potential cell classification types. Specifically, the CoNIC Challenge is unable to classify epithelial subtypes (progenitor, endocrine, goblet), lymphocyte subtypes (B, helper T, cytotoxic T), or connective subtypes (fibroblasts, stromal). In this paper, we propose to use inter-modality learning to label previously un-labelable cell types on virtual H&E. We leveraged multiplexed immunofluorescence (MxIF) histology imaging to identify 14 subclasses of cell types. We performed style transfer to synthesize virtual H&E from MxIF and transferred the higher density labels from MxIF to these virtual H&E images. We then evaluated the efficacy of learning in this approach. We identified helper T and progenitor nuclei with positive predictive values of $0.34 \pm 0.15$ (prevalence $0.03 \pm 0.01$) and $0.47 \pm 0.1$ (prevalence $0.07 \pm 0.02$) respectively on virtual H&E. This approach represents a promising step towards automating annotation in digital pathology.

cs.CV↗

arXiv2024

Is Bigger and Deeper Always Better? Probing LLaMA Across Scales and Layers

This paper presents an in-depth analysis of Large Language Models (LLMs), focusing on LLaMA, a prominent open-source foundational model in natural language processing. Instead of assessing LLaMA through its generative output, we design multiple-choice tasks to probe its intrinsic understanding in high-order tasks such as reasoning and computation. We examine the model horizontally, comparing different sizes, and vertically, assessing different layers. We unveil several key and uncommon findings based on the designed probing tasks: (1) Horizontally, enlarging model sizes almost could not automatically impart additional knowledge or computational prowess. Instead, it can enhance reasoning abilities, especially in math problem solving, and helps reduce hallucinations, but only beyond certain size thresholds; (2) In vertical analysis, the lower layers of LLaMA lack substantial arithmetic and factual knowledge, showcasing logical thinking, multilingual and recognitive abilities, with top layers housing most computational power and real-world knowledge.

cs.CL↗

arXiv2024

Rectangular carbon nitrides C4N monolayers with a zigzag buckled structure: Quasi-one-dimensional Dirac nodal lines and topological flat edge states

Due to the flexibility of C and N atoms in forming different types of bonds, the prediction of new two-dimensional (2D) carbon nitrides is a hot topic in the field of carbon-based materials. Using first-principles calculations, we propose two C4N monolayers with a zigzag buckled (ZB) structure. The ZB C4N monolayers contain raised-C (raised-N) atoms with sp3 hybridization, different from the traditional 2D graphene-like carbon nitride materials with sp2 hybridization. Interestingly, the band structures of the ZB C4N monolayers exhibit quasi-one-dimensional (quasi-1D) Dirac nodal line that results from the corresponding quasi-1D structure of the zigzag carbon chains, which is essentially different from the more common ring-shaped nodal line. The quasi-1D Dirac nodal line exhibits the following features: (i) gapless Dirac points, (ii) varying Fermi velocity, and (iii) slightly curved band along the high-symmetry path. All these features are successfully explained by our proposed tight-binding model that includes interactions up to the third nearest-neighbor. The Fermi velocity of the 2D system can reach 105 m/s, which is promising for applications in high-speed electronic devices. The topological flat band structure determined by the Zak phase and band inversion of the corresponding 1D system is edge-dependent, which is corresponding to the Su-Schrieffer-Heeger model, providing to rich physical phenomena.

cond-mat.mtrl-sci↗

arXiv2023

Hot or Cold? Adaptive Temperature Sampling for Code Generation with Large Language Models

Recently, Large Language Models (LLMs) have shown impressive abilities in code generation. However, existing LLMs' decoding strategies are designed for Natural Language (NL) generation, overlooking the differences between NL and programming languages (PL). Due to this oversight, a better decoding strategy for code generation remains an open question. In this paper, we conduct the first systematic study to explore a decoding strategy specialized in code generation. With an analysis of loss distributions of code tokens, we find that code tokens can be divided into two categories: challenging tokens that are difficult to predict and confident tokens that can be easily inferred. Among them, the challenging tokens mainly appear at the beginning of a code block. Inspired by the above findings, we propose a simple yet effective method: Adaptive Temperature (AdapT) sampling, which dynamically adjusts the temperature coefficient when decoding different tokens. We apply a larger temperature when sampling for challenging tokens, allowing LLMs to explore diverse choices. We employ a smaller temperature for confident tokens avoiding the influence of tail randomness noises. We apply AdapT sampling to LLMs with different sizes and conduct evaluations on two popular datasets. Results show that AdapT sampling significantly outperforms state-of-the-art decoding strategy.

cs.SE↗

arXiv2023

From Good to Great: Improving Math Reasoning with Tool-Augmented Interleaf Prompting

This paper investigates the performance of Large Language Models (LLMs) and Tool-augmented LLMs in tackling complex mathematical reasoning tasks. We introduce IMP-TIP: Improving Math Reasoning with Tool-augmented Interleaf Prompting, a framework that combines the strengths of both LLMs and Tool-augmented LLMs. IMP-TIP follows the ``From Good to Great" concept, collecting multiple potential solutions from both LLMs and their Tool-Augmented counterparts for the same math problem, and then selecting or re-generating the most accurate answer after cross-checking these solutions via tool-augmented interleaf prompting. The framework incorporates two key aspects: self-prompt and tool-augmented interleaf prompting (TIP). The former allows LLMs to autonomously refine and improve an initial prompt related to tool usage, while the latter enables LLMs to derive the final answer by dynamically analyzing the problem, cross-checking potential solutions, and revising previous reasoning hints in an interleaved manner. Experimental analysis shows that IMP-TIP achieves enhanced mathematical capabilities and outperforms traditional LLMs and tool-augmented LLMs in accuracy and reasoning diversity on math reasoning tasks. For instance, IMP-TIP can improve Tool-augmented ChatGPT on GSM8K-Hard from 56.0% to 65.2%.

math.HO↗

arXiv2023

All in One: Multi-task Prompting for Graph Neural Networks

Recently, ''pre-training and fine-tuning'' has been adopted as a standard workflow for many graph tasks since it can take general graph knowledge to relieve the lack of graph annotations from each application. However, graph tasks with node level, edge level, and graph level are far diversified, making the pre-training pretext often incompatible with these multiple tasks. This gap may even cause a ''negative transfer'' to the specific application, leading to poor results. Inspired by the prompt learning in natural language processing (NLP), which has presented significant effectiveness in leveraging prior knowledge for various NLP tasks, we study the prompting topic for graphs with the motivation of filling the gap between pre-trained models and various graph tasks. In this paper, we propose a novel multi-task prompting method for graph models. Specifically, we first unify the format of graph prompts and language prompts with the prompt token, token structure, and inserting pattern. In this way, the prompting idea from NLP can be seamlessly introduced to the graph area. Then, to further narrow the gap between various graph tasks and state-of-the-art pre-training strategies, we further study the task space of various graph applications and reformulate downstream problems to the graph-level task. Afterward, we introduce meta-learning to efficiently learn a better initialization for the multi-task prompt of graphs so that our prompting framework can be more reliable and general for different tasks. We conduct extensive experiments, results from which demonstrate the superiority of our method.

cs.SI↗

arXiv2023

StarCoder: may the source be with you!

The BigCode community, an open-scientific collaboration working on the responsible development of Large Language Models for Code (Code LLMs), introduces StarCoder and StarCoderBase: 15.5B parameter models with 8K context length, infilling capabilities and fast large-batch inference enabled by multi-query attention. StarCoderBase is trained on 1 trillion tokens sourced from The Stack, a large collection of permissively licensed GitHub repositories with inspection tools and an opt-out process. We fine-tuned StarCoderBase on 35B Python tokens, resulting in the creation of StarCoder. We perform the most comprehensive evaluation of Code LLMs to date and show that StarCoderBase outperforms every open Code LLM that supports multiple programming languages and matches or outperforms the OpenAI code-cushman-001 model. Furthermore, StarCoder outperforms every model that is fine-tuned on Python, can be prompted to achieve 40\% pass@1 on HumanEval, and still retains its performance on other programming languages. We take several important steps towards a safe open-access model release, including an improved PII redaction pipeline and a novel attribution tracing tool, and make the StarCoder models publicly available under a more commercially viable version of the Open Responsible AI Model license.

cs.CL↗

arXiv2023

Graph Prompt Learning: A Comprehensive Survey and Beyond

Artificial General Intelligence (AGI) has revolutionized numerous fields, yet its integration with graph data, a cornerstone in our interconnected world, remains nascent. This paper presents a pioneering survey on the emerging domain of graph prompts in AGI, addressing key challenges and opportunities in harnessing graph data for AGI applications. Despite substantial advancements in AGI across natural language processing and computer vision, the application to graph data is relatively underexplored. This survey critically evaluates the current landscape of AGI in handling graph data, highlighting the distinct challenges in cross-modality, cross-domain, and cross-task applications specific to graphs. Our work is the first to propose a unified framework for understanding graph prompt learning, offering clarity on prompt tokens, token structures, and insertion patterns in the graph domain. We delve into the intrinsic properties of graph prompts, exploring their flexibility, expressiveness, and interplay with existing graph models. A comprehensive taxonomy categorizes over 100 works in this field, aligning them with pre-training tasks across node-level, edge-level, and graph-level objectives. Additionally, we present, ProG, a Python library, and an accompanying website, to support and advance research in graph prompting. The survey culminates in a discussion of current challenges and future directions, offering a roadmap for research in graph prompting within AGI. Through this comprehensive analysis, we aim to catalyze further exploration and practical applications of AGI in graph data, underlining its potential to reshape AGI fields and beyond. ProG and the website can be accessed by \url{https://github.com/WxxShirley/Awesome-Graph-Prompt}, and \url{https://github.com/sheldonresearch/ProG}, respectively.

cs.AI↗

arXiv2023

SSIN: Self-Supervised Learning for Rainfall Spatial Interpolation

The acquisition of accurate rainfall distribution in space is an important task in hydrological analysis and natural disaster pre-warning. However, it is impossible to install rain gauges on every corner. Spatial interpolation is a common way to infer rainfall distribution based on available raingauge data. However, the existing works rely on some unrealistic pre-settings to capture spatial correlations, which limits their performance in real scenarios. To tackle this issue, we propose the SSIN, which is a novel data-driven self-supervised learning framework for rainfall spatial interpolation by mining latent spatial patterns from historical observation data. Inspired by the Cloze task and BERT, we fully consider the characteristics of spatial interpolation and design the SpaFormer model based on the Transformer architecture as the core of SSIN. Our main idea is: by constructing rich self-supervision signals via random masking, SpaFormer can learn informative embeddings for raw data and then adaptively model spatial correlations based on rainfall spatial context. Extensive experiments on two real-world raingauge datasets show that our method outperforms the state-of-the-art solutions. In addition, we take traffic spatial interpolation as another use case to further explore the performance of our method, and SpaFormer achieves the best performance on one large real-world traffic dataset, which further confirms the effectiveness and generality of our method.

cs.LG↗