arXiv subjects

Jia Li

Publications and source records attributed to Jia Li.

At least 397 records · Page 22Linked to original sources

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↗

arXiv2023

GADBench: Revisiting and Benchmarking Supervised Graph Anomaly Detection

With a long history of traditional Graph Anomaly Detection (GAD) algorithms and recently popular Graph Neural Networks (GNNs), it is still not clear (1) how they perform under a standard comprehensive setting, (2) whether GNNs can outperform traditional algorithms such as tree ensembles, and (3) how about their efficiency on large-scale graphs. In response, we introduce GADBench -- a benchmark tool dedicated to supervised anomalous node detection in static graphs. GADBench facilitates a detailed comparison across 29 distinct models on ten real-world GAD datasets, encompassing thousands to millions ($\sim$6M) nodes. Our main finding is that tree ensembles with simple neighborhood aggregation can outperform the latest GNNs tailored for the GAD task. We shed light on the current progress of GAD, setting a robust groundwork for subsequent investigations in this domain. GADBench is open-sourced at https://github.com/squareRoot3/GADBench.

cs.LG↗

arXiv2023

Enabling CMF Estimation in Data-Constrained Scenarios: A Semantic-Encoding Knowledge Mining Model

Precise estimation of Crash Modification Factors (CMFs) is central to evaluating the effectiveness of various road safety treatments and prioritizing infrastructure investment accordingly. While customized study for each countermeasure scenario is desired, the conventional CMF estimation approaches rely heavily on the availability of crash data at given sites. This not only makes the estimation costly, but the results are also less transferable, since the intrinsic similarities between different safety countermeasure scenarios are not fully explored. Aiming to fill this gap, this study introduces a novel knowledge-mining framework for CMF prediction. This framework delves into the connections of existing countermeasures and reduces the reliance of CMF estimation on crash data availability and manual data collection. Specifically, it draws inspiration from human comprehension processes and introduces advanced Natural Language Processing (NLP) techniques to extract intricate variations and patterns from existing CMF knowledge. It effectively encodes unstructured countermeasure scenarios into machine-readable representations and models the complex relationships between scenarios and CMF values. This new data-driven framework provides a cost-effective and adaptable solution that complements the case-specific approaches for CMF estimation, which is particularly beneficial when availability of crash data or time imposes constraints. Experimental validation using real-world CMF Clearinghouse data demonstrates the effectiveness of this new approach, which shows significant accuracy improvements compared to baseline methods. This approach provides insights into new possibilities of harnessing accumulated transportation knowledge in various applications.

cs.LG↗

arXiv2023

ChatCoder: Chat-based Refine Requirement Improves LLMs' Code Generation

Large language models have shown good performances in generating code to meet human requirements. However, human requirements expressed in natural languages can be vague, incomplete, and ambiguous, leading large language models to misunderstand human requirements and make mistakes. Worse, it is difficult for a human user to refine the requirement. To help human users refine their requirements and improve large language models' code generation performances, we propose ChatCoder: a method to refine the requirements via chatting with large language models. We design a chat scheme in which the large language models will guide the human users to refine their expression of requirements to be more precise, unambiguous, and complete than before. Experiments show that ChatCoder has improved existing large language models' performance by a large margin. Besides, ChatCoder has the advantage over refine-based methods and LLMs fine-tuned via human response.

cs.SE↗

arXiv2023

Large Language Model-Aware In-Context Learning for Code Generation

Large language models (LLMs) have shown impressive in-context learning (ICL) ability in code generation. LLMs take a prompt consisting of requirement-code examples and a new requirement as input, and output new programs. Existing studies have found that ICL is highly dominated by the examples and thus arises research on example selection. However, existing approaches randomly select examples or only consider the textual similarity of requirements to retrieve, leading to sub-optimal performance. In this paper, we propose a novel learning-based selection approach named LAIL (LLM-Aware In-context Learning) for code generation. Given a candidate example, we exploit LLMs themselves to estimate it by considering the generation probabilities of ground-truth programs given a requirement and the example. We then label candidate examples as positive or negative through the probability feedback. Based on the labeled data, we import a contrastive learning objective to train an effective retriever that acquires the preference of LLMs in code generation. We apply LAIL to three LLMs and evaluate it on three representative datasets (e.g., MBJP, MBPP, and MBCPP). LATA outperforms the state-of-the-art baselines by 11.58%, 6.89%, and 5.07% on CodeGen, and 4.38%, 2.85%, and 2.74% on GPT-3.5 in terms of Pass@1, respectively.

cs.SE↗

arXiv2023

Orca: A Few-shot Benchmark for Chinese Conversational Machine Reading Comprehension

The conversational machine reading comprehension (CMRC) task aims to answer questions in conversations, which has been a hot research topic in recent years because of its wide applications. However, existing CMRC benchmarks in which each conversation is assigned a static passage are inconsistent with real scenarios. Thus, model's comprehension ability towards real scenarios are hard to evaluate reasonably. To this end, we propose the first Chinese CMRC benchmark Orca and further provide zero-shot/few-shot settings to evaluate model's generalization ability towards diverse domains. We collect 831 hot-topic driven conversations with 4,742 turns in total. Each turn of a conversation is assigned with a response-related passage, aiming to evaluate model's comprehension ability more reasonably. The topics of conversations are collected from social media platform and cover 33 domains, trying to be consistent with real scenarios. Importantly, answers in Orca are all well-annotated natural responses rather than the specific spans or short phrase in previous datasets. Besides, we implement three strong baselines to tackle the challenge in Orca. The results indicate the great challenge of our CMRC benchmark. Our datatset and checkpoints are available at https://github.com/nuochenpku/Orca.

cs.CL↗

arXiv2023

Exploring Sparse Spatial Relation in Graph Inference for Text-Based VQA

Text-based visual question answering (TextVQA) faces the significant challenge of avoiding redundant relational inference. To be specific, a large number of detected objects and optical character recognition (OCR) tokens result in rich visual relationships. Existing works take all visual relationships into account for answer prediction. However, there are three observations: (1) a single subject in the images can be easily detected as multiple objects with distinct bounding boxes (considered repetitive objects). The associations between these repetitive objects are superfluous for answer reasoning; (2) two spatially distant OCR tokens detected in the image frequently have weak semantic dependencies for answer reasoning; and (3) the co-existence of nearby objects and tokens may be indicative of important visual cues for predicting answers. Rather than utilizing all of them for answer prediction, we make an effort to identify the most important connections or eliminate redundant ones. We propose a sparse spatial graph network (SSGN) that introduces a spatially aware relation pruning technique to this task. As spatial factors for relation measurement, we employ spatial distance, geometric dimension, overlap area, and DIoU for spatially aware pruning. We consider three visual relationships for graph learning: object-object, OCR-OCR tokens, and object-OCR token relationships. SSGN is a progressive graph learning architecture that verifies the pivotal relations in the correlated object-token sparse graph, and then in the respective object-based sparse graph and token-based sparse graph. Experiment results on TextVQA and ST-VQA datasets demonstrate that SSGN achieves promising performances. And some visualization results further demonstrate the interpretability of our method.

cs.MM↗

arXiv2023

A Machine Learning Paradigm for Studying Pictorial Realism: Are Constable's Clouds More Real than His Contemporaries?

The British landscape painter John Constable is considered foundational for the Realist movement in 19th-century European painting. Constable's painted skies, in particular, were seen as remarkably accurate by his contemporaries, an impression shared by many viewers today. Yet, assessing the accuracy of realist paintings like Constable's is subjective or intuitive, even for professional art historians, making it difficult to say with certainty what set Constable's skies apart from those of his contemporaries. Our goal is to contribute to a more objective understanding of Constable's realism. We propose a new machine-learning-based paradigm for studying pictorial realism in an explainable way. Our framework assesses realism by measuring the similarity between clouds painted by artists noted for their skies, like Constable, and photographs of clouds. The experimental results of cloud classification show that Constable approximates more consistently than his contemporaries the formal features of actual clouds in his paintings. The study, as a novel interdisciplinary approach that combines computer vision and machine learning, meteorology, and art history, is a springboard for broader and deeper analyses of pictorial realism.

cs.CV↗