arXiv subjects

Chong Wang

Publications and source records attributed to Chong Wang.

At least 181 records · Page 10Linked to original sources

arXiv2024

A Survey for Large Language Models in Biomedicine

Recent breakthroughs in large language models (LLMs) offer unprecedented natural language understanding and generation capabilities. However, existing surveys on LLMs in biomedicine often focus on specific applications or model architectures, lacking a comprehensive analysis that integrates the latest advancements across various biomedical domains. This review, based on an analysis of 484 publications sourced from databases including PubMed, Web of Science, and arXiv, provides an in-depth examination of the current landscape, applications, challenges, and prospects of LLMs in biomedicine, distinguishing itself by focusing on the practical implications of these models in real-world biomedical contexts. Firstly, we explore the capabilities of LLMs in zero-shot learning across a broad spectrum of biomedical tasks, including diagnostic assistance, drug discovery, and personalized medicine, among others, with insights drawn from 137 key studies. Then, we discuss adaptation strategies of LLMs, including fine-tuning methods for both uni-modal and multi-modal LLMs to enhance their performance in specialized biomedical contexts where zero-shot fails to achieve, such as medical question answering and efficient processing of biomedical literature. Finally, we discuss the challenges that LLMs face in the biomedicine domain including data privacy concerns, limited model interpretability, issues with dataset quality, and ethics due to the sensitive nature of biomedical data, the need for highly reliable model outputs, and the ethical implications of deploying AI in healthcare. To address these challenges, we also identify future research directions of LLM in biomedicine including federated learning methods to preserve data privacy and integrating explainable AI methodologies to enhance the transparency of LLMs.

cs.CL↗

arXiv2024

Differential Private Stochastic Optimization with Heavy-tailed Data: Towards Optimal Rates

We study convex optimization problems under differential privacy (DP). With heavy-tailed gradients, existing works achieve suboptimal rates. The main obstacle is that existing gradient estimators have suboptimal tail properties, resulting in a superfluous factor of $d$ in the union bound. In this paper, we explore algorithms achieving optimal rates of DP optimization with heavy-tailed gradients. Our first method is a simple clipping approach. Under bounded $p$-th order moments of gradients, with $n$ samples, it achieves $\tilde{O}(\sqrt{d/n}+\sqrt{d}(\sqrt{d}/nε)^{1-1/p})$ population risk with $ε\leq 1/\sqrt{d}$. We then propose an iterative updating method, which is more complex but achieves this rate for all $ε\leq 1$. The results significantly improve over existing methods. Such improvement relies on a careful treatment of the tail behavior of gradient estimators. Our results match the minimax lower bound in \cite{kamath2022improved}, indicating that the theoretical limit of stochastic convex optimization under DP is achievable.

cs.LG↗

arXiv2024

Unraveling Instance Associations: A Closer Look for Audio-Visual Segmentation

Audio-visual segmentation (AVS) is a challenging task that involves accurately segmenting sounding objects based on audio-visual cues. The effectiveness of audio-visual learning critically depends on achieving accurate cross-modal alignment between sound and visual objects. Successful audio-visual learning requires two essential components: 1) a challenging dataset with high-quality pixel-level multi-class annotated images associated with audio files, and 2) a model that can establish strong links between audio information and its corresponding visual object. However, these requirements are only partially addressed by current methods, with training sets containing biased audio-visual data, and models that generalise poorly beyond this biased training set. In this work, we propose a new cost-effective strategy to build challenging and relatively unbiased high-quality audio-visual segmentation benchmarks. We also propose a new informative sample mining method for audio-visual supervised contrastive learning to leverage discriminative contrastive samples to enforce cross-modal understanding. We show empirical results that demonstrate the effectiveness of our benchmark. Furthermore, experiments conducted on existing AVS datasets and on our new benchmark show that our method achieves state-of-the-art (SOTA) segmentation accuracy.

cs.CV↗

arXiv2024

TIGER: A Generating-Then-Ranking Framework for Practical Python Type Inference

Python's dynamic typing system offers flexibility and expressiveness but can lead to type-related errors, prompting the need for automated type inference to enhance type hinting. While existing learning-based approaches show promising inference accuracy, they struggle with practical challenges in comprehensively handling various types, including complex generic types and (unseen) user-defined types. In this paper, we introduce TIGER, a two-stage generating-then-ranking (GTR) framework, designed to effectively handle Python's diverse type categories. TIGER leverages fine-tuned pre-trained code models to train a generative model with a span masking objective and a similarity model with a contrastive training objective. This approach allows TIGER to generate a wide range of type candidates, including complex generics in the generating stage, and accurately rank them with user-defined types in the ranking stage. Our evaluation on the ManyTypes4Py dataset shows TIGER's advantage over existing methods in various type categories, notably improving accuracy in inferring user-defined and unseen types by 11.2% and 20.1% respectively in Top-5 Exact Match. Moreover, the experimental results not only demonstrate TIGER's superior performance and efficiency, but also underscore the significance of its generating and ranking stages in enhancing automated type inference.

cs.SE↗

arXiv2024

Fractional Chern insulators in moiré flat bands with high Chern numbers

Recent discoveries of zero-field fractional Chern insulators in moiré materials have attracted intensive research interests. However, most current theoretical and experimental attempts focus on systems with low Chern number bands, in analogy to the Landau levels. Here we propose candidate material systems for realizing fractional Chern insulators with higher Chern numbers. The material setup involves $Γ$-valley twisted homobilayer transition metal dichalcogenides in proximity to a skyrmion lattice. The skyrmion exchange potential induces a flat band with a high Chern number $C = -2$. Using the momentum-space projected exact diagonalization method, we perform a comprehensive study at various filling factors, confirming the generalized Jain series. Our research provides theoretical guidance on realizing unconventional fractional Chern insulators beyond the Landau level picture.

cond-mat.str-el↗

arXiv2024

Deep learning density functional theory Hamiltonian in real space

Deep learning electronic structures from ab initio calculations holds great potential to revolutionize computational materials studies. While existing methods proved success in deep-learning density functional theory (DFT) Hamiltonian matrices, they are limited to DFT programs using localized atomic-like bases and heavily depend on the form of the bases. Here, we propose the DeepH-r method for deep-learning DFT Hamiltonians in real space, facilitating the prediction of DFT Hamiltonian in a basis-independent manner. An equivariant neural network architecture for modeling the real-space DFT potential is developed, targeting a more fundamental quantity in DFT. The real-space potential exhibits simplified principles of equivariance and enhanced nearsightedness, further boosting the performance of deep learning. When applied to evaluate the Hamiltonian matrix, this method significantly improved in accuracy, as exemplified in multiple case studies. Given the abundance of data in the real-space potential, this work may pave a novel pathway for establishing a ``large materials model" with increased accuracy.

physics.comp-ph↗

arXiv2024

Teaching Code LLMs to Use Autocompletion Tools in Repository-Level Code Generation

Code large language models (LLMs) face limitations in repository-level code generation due to their lack of awareness of repository-level dependencies (e.g., user-defined attributes), resulting in dependency errors such as undefined-variable and no-member errors. In this work, we introduce ToolGen, an approach that integrates autocompletion tools into the code LLM generation process to address these dependencies. ToolGen comprises two main phases: Trigger Insertion and Model Fine-tuning (Offline), and Tool-integrated Code Generation (Online). During the offline phase, ToolGen augments functions within a given code corpus with a special mark token, indicating positions to trigger autocompletion tools. These augmented functions, along with their corresponding docstrings, are then used to fine-tune a selected code LLM. In the online phase, ToolGen iteratively generates functions by predicting tokens step-by-step using the fine-tuned LLM. Whenever a mark token is encountered, ToolGen invokes the autocompletion tool to suggest code completions and selects the most appropriate one. We conduct comprehensive experiments to evaluate ToolGen's effectiveness in repository-level code generation. To facilitate this evaluation, we create a benchmark comprising 671 real-world code repositories and introduce two new dependency-based metrics: Dependency Coverage and Static Validity Rate. The results demonstrate that ToolGen significantly improves Dependency Coverage by 31.4% to 39.1% and Static Validity Rate by 44.9% to 57.7% across the three LLMs, while maintaining competitive or improved performance in widely recognized similarity metrics such as BLEU-4, CodeBLEU, Edit Similarity, and Exact Match. On the CoderEval dataset, ToolGen achieves improvements of 40.0% and 25.0% in Pass@1 for CodeT5 and CodeLlama, respectively.

cs.SE↗

arXiv2024

Cephalometric Landmark Detection across Ages with Prototypical Network

Automated cephalometric landmark detection is crucial in real-world orthodontic diagnosis. Current studies mainly focus on only adult subjects, neglecting the clinically crucial scenario presented by adolescents whose landmarks often exhibit significantly different appearances compared to adults. Hence, an open question arises about how to develop a unified and effective detection algorithm across various age groups, including adolescents and adults. In this paper, we propose CeLDA, the first work for Cephalometric Landmark Detection across Ages. Our method leverages a prototypical network for landmark detection by comparing image features with landmark prototypes. To tackle the appearance discrepancy of landmarks between age groups, we design new strategies for CeLDA to improve prototype alignment and obtain a holistic estimation of landmark prototypes from a large set of training images. Moreover, a novel prototype relation mining paradigm is introduced to exploit the anatomical relations between the landmark prototypes. Extensive experiments validate the superiority of CeLDA in detecting cephalometric landmarks on both adult and adolescent subjects. To our knowledge, this is the first effort toward developing a unified solution and dataset for cephalometric landmark detection across age groups. Our code and dataset will be made public on https://github.com/ShanghaiTech-IMPACT/Cephalometric-Landmark-Detection-across-Ages-with-Prototypical-Network

cs.CV↗

arXiv2024

Universal materials model of deep-learning density functional theory Hamiltonian

Realizing large materials models has emerged as a critical endeavor for materials research in the new era of artificial intelligence, but how to achieve this fantastic and challenging objective remains elusive. Here, we propose a feasible pathway to address this paramount pursuit by developing universal materials models of deep-learning density functional theory Hamiltonian (DeepH), enabling computational modeling of the complicated structure-property relationship of materials in general. By constructing a large materials database and substantially improving the DeepH method, we obtain a universal materials model of DeepH capable of handling diverse elemental compositions and material structures, achieving remarkable accuracy in predicting material properties. We further showcase a promising application of fine-tuning universal materials models for enhancing specific materials models. This work not only demonstrates the concept of DeepH's universal materials model but also lays the groundwork for developing large materials models, opening up significant opportunities for advancing artificial intelligence-driven materials discovery.

physics.comp-ph↗

arXiv2024

How LLMs Aid in UML Modeling: An Exploratory Study with Novice Analysts

Since the emergence of GPT-3, Large Language Models (LLMs) have caught the eyes of researchers, practitioners, and educators in the field of software engineering. However, there has been relatively little investigation regarding the performance of LLMs in assisting with requirements analysis and UML modeling. This paper explores how LLMs can assist novice analysts in creating three types of typical UML models: use case models, class diagrams, and sequence diagrams. For this purpose, we designed the modeling tasks of these three UML models for 45 undergraduate students who participated in a requirements modeling course, with the help of LLMs. By analyzing their project reports, we found that LLMs can assist undergraduate students as novice analysts in UML modeling tasks, but LLMs also have shortcomings and limitations that should be considered when using them.

cs.SE↗

arXiv2024

Encryption in ghost imaging with Kronecker products of random matrices

By forming measurement matrices with the Kronecker product of two random matrices, image encryption in computational ghost imaging is investigated. The two-dimensional images are conveniently reconstructed with the pseudo-inverse matrices of the two random matrices. To suppress the noise, the method of truncated singular value decomposition can be applied to either or both of the two pseudo-inverse matrices. Further, our proposal facilitates for image encryption since more matrices can be involved in forming the measurement matrix. Two permutation matrices are inserted into the matrix sequence. The image information can only be reconstructed with the correct permutation matrices and the matrix sequence in image decryption. The experimental results show the facilitations our proposal. The technique paves the way for the practicality and flexibility of computational ghost imaging.

eess.IV↗

arXiv2024

Distinguish Any Fake Videos: Unleashing the Power of Large-scale Data and Motion Features

The development of AI-Generated Content (AIGC) has empowered the creation of remarkably realistic AI-generated videos, such as those involving Sora. However, the widespread adoption of these models raises concerns regarding potential misuse, including face video scams and copyright disputes. Addressing these concerns requires the development of robust tools capable of accurately determining video authenticity. The main challenges lie in the dataset and neural classifier for training. Current datasets lack a varied and comprehensive repository of real and generated content for effective discrimination. In this paper, we first introduce an extensive video dataset designed specifically for AI-Generated Video Detection (GenVidDet). It includes over 2.66 M instances of both real and generated videos, varying in categories, frames per second, resolutions, and lengths. The comprehensiveness of GenVidDet enables the training of a generalizable video detector. We also present the Dual-Branch 3D Transformer (DuB3D), an innovative and effective method for distinguishing between real and generated videos, enhanced by incorporating motion information alongside visual appearance. DuB3D utilizes a dual-branch architecture that adaptively leverages and fuses raw spatio-temporal data and optical flow. We systematically explore the critical factors affecting detection performance, achieving the optimal configuration for DuB3D. Trained on GenVidDet, DuB3D can distinguish between real and generated video content with 96.77% accuracy, and strong generalization capability even for unseen types.

cs.CV↗

arXiv2024

Higher-form Symmetries under Weak Measurement

We aim to address the following question: if we start with a quantum state with a spontaneously broken higher-form symmetry, what is the fate of the system under weak local quantum measurements? We demonstrate that under certain conditions, a phase transition can be driven by weak measurements, which suppresses the spontaneous breaking of the 1-form symmetry and weakens the 1-form symmetry charge fluctuation. We analyze the nature of the transitions employing the tool of duality, and we demonstrate that some of the transitions driven by weak measurement enjoy a line of fixed points with self-duality.

cond-mat.str-el↗

arXiv2024

Computational ghost imaging with hybrid transforms by integrating Hadamard, discrete cosine, and Haar matrices

A scenario of ghost imaging with hybrid transform approach is proposed by integrating Hadamard, discrete cosine, and Haar matrices. The measurement matrix is formed by the Kronecker product of the two different transform matrices. The image information can be conveniently reconstructed by the corresponding inverse matrices. In experiment, six hybridization sets are performed in computational ghost imaging. For an object of staggered stripes, only one bucket signal survives in the Hadamard-cosine, Haar-Hadamard, and Haar-cosine hybridization sets, demonstrating flexible image compression. For a handmade windmill object, the quality factors of the reconstructed images vary with the hybridization sets. Sub-Nyquist sampling can be applied to either or both of the different transform matrices in each hybridization set in experiment. The hybridization method can be extended to apply more transforms at once. Ghost imaging with hybrid transforms may find flexible applications in image processing, such as image compression and image encryption.

eess.IV↗

arXiv2024

MM1: Methods, Analysis & Insights from Multimodal LLM Pre-training

In this work, we discuss building performant Multimodal Large Language Models (MLLMs). In particular, we study the importance of various architecture components and data choices. Through careful and comprehensive ablations of the image encoder, the vision language connector, and various pre-training data choices, we identified several crucial design lessons. For example, we demonstrate that for large-scale multimodal pre-training using a careful mix of image-caption, interleaved image-text, and text-only data is crucial for achieving state-of-the-art (SOTA) few-shot results across multiple benchmarks, compared to other published pre-training results. Further, we show that the image encoder together with image resolution and the image token count has substantial impact, while the vision-language connector design is of comparatively negligible importance. By scaling up the presented recipe, we build MM1, a family of multimodal models up to 30B parameters, including both dense models and mixture-of-experts (MoE) variants, that are SOTA in pre-training metrics and achieve competitive performance after supervised fine-tuning on a range of established multimodal benchmarks. Thanks to large-scale pre-training, MM1 enjoys appealing properties such as enhanced in-context learning, and multi-image reasoning, enabling few-shot chain-of-thought prompting.

cs.CV↗

arXiv2024

Demystifying Code Snippets in Code Reviews: A Study of the OpenStack and Qt Communities and A Practitioner Survey

Code review is widely known as one of the best practices for software quality assurance in software development. In a typical code review process, reviewers check the code committed by developers to ensure the quality of the code, during which reviewers and developers would communicate with each other in review comments to exchange necessary information. As a result, understanding the information in review comments is a prerequisite for reviewers and developers to conduct an effective code review. Code snippet, as a special form of code, can be used to convey necessary information in code reviews. For example, reviewers can use code snippets to make suggestions or elaborate their ideas to meet developers' information needs in code reviews. However, little research has focused on the practices of providing code snippets in code reviews. To bridge this gap, we conduct a mixed-methods study to mine information and knowledge related to code snippets in code reviews, which can help practitioners and researchers get a better understanding about using code snippets in code review. Specifically, our study includes two phases: mining code review data and conducting practitioners' survey. The study results highlight that reviewers can provide code snippets in appropriate scenarios to meet developers' specific information needs in code reviews, which will facilitate and accelerate the code review process.

cs.SE↗

arXiv2024

BRAIxDet: Learning to Detect Malignant Breast Lesion with Incomplete Annotations

Methods to detect malignant lesions from screening mammograms are usually trained with fully annotated datasets, where images are labelled with the localisation and classification of cancerous lesions. However, real-world screening mammogram datasets commonly have a subset that is fully annotated and another subset that is weakly annotated with just the global classification (i.e., without lesion localisation). Given the large size of such datasets, researchers usually face a dilemma with the weakly annotated subset: to not use it or to fully annotate it. The first option will reduce detection accuracy because it does not use the whole dataset, and the second option is too expensive given that the annotation needs to be done by expert radiologists. In this paper, we propose a middle-ground solution for the dilemma, which is to formulate the training as a weakly- and semi-supervised learning problem that we refer to as malignant breast lesion detection with incomplete annotations. To address this problem, our new method comprises two stages, namely: 1) pre-training a multi-view mammogram classifier with weak supervision from the whole dataset, and 2) extending the trained classifier to become a multi-view detector that is trained with semi-supervised student-teacher learning, where the training set contains fully and weakly-annotated mammograms. We provide extensive detection results on two real-world screening mammogram datasets containing incomplete annotations, and show that our proposed approach achieves state-of-the-art results in the detection of malignant breast lesions with incomplete annotations.

cs.CV↗

arXiv2024

Polarization-driven band topology evolution in twisted MoTe$_2$ and WSe$_2$

Motivated by recent experimental observations of opposite Chern numbers in $R$-type twisted MoTe$_2$ and WSe$_2$ homobilayers, we perform large-scale density-functional-theory (DFT) calculations with machine learning force fields to investigate moiré band topology from large to small twist angles in both materials. We find that the Chern numbers of the moiré frontier bands change sign as a function of twist angle, and this change is driven by the competition between moiré ferroelectricity and piezoelectricity. Our large-scale calculations, enabled by machine learning methods, reveal crucial insights into interactions across different scales in twisted bilayer systems. The interplay between atomic-level relaxation effects and moiré-scale electrostatic potential variation opens new avenues for the design of intertwined topological and correlated states, including the possibility of mimicking higher Landau-level physics in the absence of a magnetic field.

cond-mat.mtrl-sci↗