arXiv subjects

Zilong Wang

Publications and source records attributed to Zilong Wang.

At least 73 records · Page 4Linked to original sources

arXiv2025

ImageFlowNet: Forecasting Multiscale Image-Level Trajectories of Disease Progression with Irregularly-Sampled Longitudinal Medical Images

Advances in medical imaging technologies have enabled the collection of longitudinal images, which involve repeated scanning of the same patients over time, to monitor disease progression. However, predictive modeling of such data remains challenging due to high dimensionality, irregular sampling, and data sparsity. To address these issues, we propose ImageFlowNet, a novel model designed to forecast disease trajectories from initial images while preserving spatial details. ImageFlowNet first learns multiscale joint representation spaces across patients and time points, then optimizes deterministic or stochastic flow fields within these spaces using a position-parameterized neural ODE/SDE framework. The model leverages a UNet architecture to create robust multiscale representations and mitigates data scarcity by combining knowledge from all patients. We provide theoretical insights that support our formulation of ODEs, and motivate our regularizations involving high-level visual features, latent space organization, and trajectory smoothness. We validate ImageFlowNet on three longitudinal medical image datasets depicting progression in geographic atrophy, multiple sclerosis, and glioblastoma, demonstrating its ability to effectively forecast disease progression and outperform existing methods. Our contributions include the development of ImageFlowNet, its theoretical underpinnings, and empirical validation on real-world datasets. The official implementation is available at https://github.com/KrishnaswamyLab/ImageFlowNet.

eess.IV↗

arXiv2025

Speculative RAG: Enhancing Retrieval Augmented Generation through Drafting

Retrieval augmented generation (RAG) combines the generative abilities of large language models (LLMs) with external knowledge sources to provide more accurate and up-to-date responses. Recent RAG advancements focus on improving retrieval outcomes through iterative LLM refinement or self-critique capabilities acquired through additional instruction tuning of LLMs. In this work, we introduce Speculative RAG - a framework that leverages a larger generalist LM to efficiently verify multiple RAG drafts produced in parallel by a smaller, distilled specialist LM. Each draft is generated from a distinct subset of retrieved documents, offering diverse perspectives on the evidence while reducing input token counts per draft. This approach enhances comprehension of each subset and mitigates potential position bias over long context. Our method accelerates RAG by delegating drafting to the smaller specialist LM, with the larger generalist LM performing a single verification pass over the drafts. Extensive experiments demonstrate that Speculative RAG achieves state-of-the-art performance with reduced latency on TriviaQA, MuSiQue, PopQA, PubHealth, and ARC-Challenge benchmarks. It notably enhances accuracy by up to 12.97% while reducing latency by 50.83% compared to conventional RAG systems on PubHealth.

cs.CL↗

arXiv2025

Cuckoo: An IE Free Rider Hatched by Massive Nutrition in LLM's Nest

Massive high-quality data, both pre-training raw texts and post-training annotations, have been carefully prepared to incubate advanced large language models (LLMs). In contrast, for information extraction (IE), pre-training data, such as BIO-tagged sequences, are hard to scale up. We show that IE models can act as free riders on LLM resources by reframing next-token \emph{prediction} into \emph{extraction} for tokens already present in the context. Specifically, our proposed next tokens extraction (NTE) paradigm learns a versatile IE model, \emph{Cuckoo}, with 102.6M extractive data converted from LLM's pre-training and post-training data. Under the few-shot setting, Cuckoo adapts effectively to traditional and complex instruction-following IE with better performance than existing pre-trained IE models. As a free rider, Cuckoo can naturally evolve with the ongoing advancements in LLM data preparation, benefiting from improvements in LLM training pipelines without additional manual effort.

cs.CL↗

arXiv2025

A Note on "Constructing Bent Functions Outside the Maiorana-McFarland Class Using a General Form of Rothaus"

In 2017, Zhang et al. proposed a question (not open problem) and two open problems in [IEEE TIT 63 (8): 5336--5349, 2017] about constructing bent functions by using Rothaus' construction. In this note, we prove that the sufficient conditions of Rothaus' construction are also necessary, which answers their question. Besides, we demonstrate that the second open problem, which considers the iterative method of constructing bent functions by using Rothaus' construction, has only a trivial solution. It indicates that all bent functions obtained by using Rothaus' construction iteratively can be generated from the direct sum of an initial bent function and a quadratic bent function. This directly means that Zhang et al.'s construction idea makes no contribution to the construction of bent functions. To compensate the weakness of their work, we propose an iterative construction of bent functions by using a secondary construction in [DCC 88: 2007--2035, 2020].

cs.IT↗

arXiv2025

RMAvatar: Photorealistic Human Avatar Reconstruction from Monocular Video Based on Rectified Mesh-embedded Gaussians

We introduce RMAvatar, a novel human avatar representation with Gaussian splatting embedded on mesh to learn clothed avatar from a monocular video. We utilize the explicit mesh geometry to represent motion and shape of a virtual human and implicit appearance rendering with Gaussian Splatting. Our method consists of two main modules: Gaussian initialization module and Gaussian rectification module. We embed Gaussians into triangular faces and control their motion through the mesh, which ensures low-frequency motion and surface deformation of the avatar. Due to the limitations of LBS formula, the human skeleton is hard to control complex non-rigid transformations. We then design a pose-related Gaussian rectification module to learn fine-detailed non-rigid deformations, further improving the realism and expressiveness of the avatar. We conduct extensive experiments on public datasets, RMAvatar shows state-of-the-art performance on both rendering quality and quantitative evaluations. Please see our project page at https://rm-avatar.github.io.

cs.CV↗

arXiv2024

TableRAG: Million-Token Table Understanding with Language Models

Recent advancements in language models (LMs) have notably enhanced their ability to reason with tabular data, primarily through program-aided mechanisms that manipulate and analyze tables. However, these methods often require the entire table as input, leading to scalability challenges due to the positional bias or context length constraints. In response to these challenges, we introduce TableRAG, a Retrieval-Augmented Generation (RAG) framework specifically designed for LM-based table understanding. TableRAG leverages query expansion combined with schema and cell retrieval to pinpoint crucial information before providing it to the LMs. This enables more efficient data encoding and precise retrieval, significantly reducing prompt lengths and mitigating information loss. We have developed two new million-token benchmarks from the Arcade and BIRD-SQL datasets to thoroughly evaluate TableRAG's effectiveness at scale. Our results demonstrate that TableRAG's retrieval design achieves the highest retrieval quality, leading to the new state-of-the-art performance on large-scale table understanding.

cs.CL↗

arXiv2024

Position Engineering: Boosting Large Language Models through Positional Information Manipulation

The performance of large language models (LLMs) is significantly influenced by the quality of the prompts provided. In response, researchers have developed enormous prompt engineering strategies aimed at modifying the prompt text to enhance task performance. In this paper, we introduce a novel technique termed position engineering, which offers a more efficient way to guide large language models. Unlike prompt engineering, which requires substantial effort to modify the text provided to LLMs, position engineering merely involves altering the positional information in the prompt without modifying the text itself. We have evaluated position engineering in two widely-used LLM scenarios: retrieval-augmented generation (RAG) and in-context learning (ICL). Our findings show that position engineering substantially improves upon the baseline in both cases. Position engineering thus represents a promising new strategy for exploiting the capabilities of large language models.

cs.CL↗

arXiv2024

Machine Unlearning in Forgettability Sequence

Machine unlearning (MU) is becoming a promising paradigm to achieve the "right to be forgotten", where the training trace of any chosen data points could be eliminated, while maintaining the model utility on general testing samples after unlearning. With the advancement of forgetting research, many fundamental open questions remain unanswered: do different samples exhibit varying levels of difficulty in being forgotten? Further, does the sequence in which samples are forgotten, determined by their respective difficulty levels, influence the performance of forgetting algorithms? In this paper, we identify key factor affecting unlearning difficulty and the performance of unlearning algorithms. We find that samples with higher privacy risks are more likely to be unlearning, indicating that the unlearning difficulty varies among different samples which motives a more precise unlearning mode. Built upon this insight, we propose a general unlearning framework, dubbed RSU, which consists of Ranking module and SeqUnlearn module.

cs.LG↗

arXiv2024

MixEHR-Nest: Identifying Subphenotypes within Electronic Health Records through Hierarchical Guided-Topic Modeling

Automatic subphenotyping from electronic health records (EHRs)provides numerous opportunities to understand diseases with unique subgroups and enhance personalized medicine for patients. However, existing machine learning algorithms either focus on specific diseases for better interpretability or produce coarse-grained phenotype topics without considering nuanced disease patterns. In this study, we propose a guided topic model, MixEHR-Nest, to infer sub-phenotype topics from thousands of disease using multi-modal EHR data. Specifically, MixEHR-Nest detects multiple subtopics from each phenotype topic, whose prior is guided by the expert-curated phenotype concepts such as Phenotype Codes (PheCodes) or Clinical Classification Software (CCS) codes. We evaluated MixEHR-Nest on two EHR datasets: (1) the MIMIC-III dataset consisting of over 38 thousand patients from intensive care unit (ICU) from Beth Israel Deaconess Medical Center (BIDMC) in Boston, USA; (2) the healthcare administrative database PopHR, comprising 1.3 million patients from Montreal, Canada. Experimental results demonstrate that MixEHR-Nest can identify subphenotypes with distinct patterns within each phenotype, which are predictive for disease progression and severity. Consequently, MixEHR-Nest distinguishes between type 1 and type 2 diabetes by inferring subphenotypes using CCS codes, which do not differentiate these two subtype concepts. Additionally, MixEHR-Nest not only improved the prediction accuracy of short-term mortality of ICU patients and initial insulin treatment in diabetic patients but also revealed the contributions of subphenotypes. For longitudinal analysis, MixEHR-Nest identified subphenotypes of distinct age prevalence under the same phenotypes, such as asthma, leukemia, epilepsy, and depression. The MixEHR-Nest software is available at GitHub: https://github.com/li-lab-mcgill/MixEHR-Nest.

cs.LG↗

arXiv2024

Anti-jamming Transmission of Downlink Cell Free Millimeter-Wave MIMO System

In this letter, the maximization of resistible jamming power is studied for multi-user downlink millimeter-wave cell-free multiple-input-multiple-output (CF-MIMO) systems. We propose an alternate optimization-based anti-jamming hybrid beamforming (AO-AJHBF) scheme. For receiving beamforming, more practical prior about the jamming channel, i.e., second-order statistics rather than instantaneous information, is exploited via maximizing the generalized Rayleigh quotient. For transmitting beamforming, we use the max-min fairness principle and propose a low-complexity projected gradient ascent-based method to circumvent the excessive computation of semi-definite relaxation (SDR). Simulations verify the performance advantage of proposed AO-AJHBF over schemes based on weighted minimum mean square error and SDR methods.

eess.SP↗

arXiv2024

DualStreamFoveaNet: A Dual Stream Fusion Architecture with Anatomical Awareness for Robust Fovea Localization

Accurate fovea localization is essential for analyzing retinal diseases to prevent irreversible vision loss. While current deep learning-based methods outperform traditional ones, they still face challenges such as the lack of local anatomical landmarks around the fovea, the inability to robustly handle diseased retinal images, and the variations in image conditions. In this paper, we propose a novel transformer-based architecture called DualStreamFoveaNet (DSFN) for multi-cue fusion. This architecture explicitly incorporates long-range connections and global features using retina and vessel distributions for robust fovea localization. We introduce a spatial attention mechanism in the dual-stream encoder to extract and fuse self-learned anatomical information, focusing more on features distributed along blood vessels and significantly reducing computational costs by decreasing token numbers. Our extensive experiments show that the proposed architecture achieves state-of-the-art performance on two public datasets and one large-scale private dataset. Furthermore, we demonstrate that the DSFN is more robust on both normal and diseased retina images and has better generalization capacity in cross-dataset experiments.

cs.CV↗

arXiv2024

Retrieval Augmented Generation (RAG) and Beyond: A Comprehensive Survey on How to Make your LLMs use External Data More Wisely

Large language models (LLMs) augmented with external data have demonstrated remarkable capabilities in completing real-world tasks. Techniques for integrating external data into LLMs, such as Retrieval-Augmented Generation (RAG) and fine-tuning, are gaining increasing attention and widespread application. Nonetheless, the effective deployment of data-augmented LLMs across various specialized fields presents substantial challenges. These challenges encompass a wide range of issues, from retrieving relevant data and accurately interpreting user intent to fully harnessing the reasoning capabilities of LLMs for complex tasks. We believe that there is no one-size-fits-all solution for data-augmented LLM applications. In practice, underperformance often arises from a failure to correctly identify the core focus of a task or because the task inherently requires a blend of multiple capabilities that must be disentangled for better resolution. In this survey, we propose a RAG task categorization method, classifying user queries into four levels based on the type of external data required and primary focus of the task: explicit fact queries, implicit fact queries, interpretable rationale queries, and hidden rationale queries. We define these levels of queries, provide relevant datasets, and summarize the key challenges and most effective techniques for addressing these challenges. Finally, we discuss three main forms of integrating external data into LLMs: context, small model, and fine-tuning, highlighting their respective strengths, limitations, and the types of problems they are suited to solve. This work aims to help readers thoroughly understand and decompose the data requirements and key bottlenecks in building LLM applications, offering solutions to the different challenges and serving as a guide to systematically developing such applications.

cs.CL↗

arXiv2024

EnJa: Ensemble Jailbreak on Large Language Models

As Large Language Models (LLMs) are increasingly being deployed in safety-critical applications, their vulnerability to potential jailbreaks -- malicious prompts that can disable the safety mechanism of LLMs -- has attracted growing research attention. While alignment methods have been proposed to protect LLMs from jailbreaks, many have found that aligned LLMs can still be jailbroken by carefully crafted malicious prompts, producing content that violates policy regulations. Existing jailbreak attacks on LLMs can be categorized into prompt-level methods which make up stories/logic to circumvent safety alignment and token-level attack methods which leverage gradient methods to find adversarial tokens. In this work, we introduce the concept of Ensemble Jailbreak and explore methods that can integrate prompt-level and token-level jailbreak into a more powerful hybrid jailbreak attack. Specifically, we propose a novel EnJa attack to hide harmful instructions using prompt-level jailbreak, boost the attack success rate using a gradient-based attack, and connect the two types of jailbreak attacks via a template-based connector. We evaluate the effectiveness of EnJa on several aligned models and show that it achieves a state-of-the-art attack success rate with fewer queries and is much stronger than any individual jailbreak.

cs.CR↗

arXiv2024

OfficeBench: Benchmarking Language Agents across Multiple Applications for Office Automation

Office automation significantly enhances human productivity by automatically finishing routine tasks in the workflow. Beyond the basic information extraction studied in much of the prior document AI literature, the office automation research should be extended to more realistic office tasks which require to integrate various information sources in the office system and produce outputs through a series of decision-making processes. We introduce OfficeBench, one of the first office automation benchmarks for evaluating current LLM agents' capability to address office tasks in realistic office workflows. OfficeBench requires LLM agents to perform feasible long-horizon planning, proficiently switch between applications in a timely manner, and accurately ground their actions within a large combined action space, based on the contextual demands of the workflow. Applying our customized evaluation methods on each task, we find that GPT-4 Omni achieves the highest pass rate of 47.00%, demonstrating a decent performance in handling office tasks. However, this is still far below the human performance and accuracy standards required by real-world office workflows. We further observe that most issues are related to operation redundancy and hallucinations, as well as limitations in switching between multiple applications, which may provide valuable insights for developing effective agent frameworks for office automation.

cs.CL↗

arXiv2024

LMDX: Language Model-based Document Information Extraction and Localization

Large Language Models (LLM) have revolutionized Natural Language Processing (NLP), improving state-of-the-art and exhibiting emergent capabilities across various tasks. However, their application in extracting information from visually rich documents, which is at the core of many document processing workflows and involving the extraction of key entities from semi-structured documents, has not yet been successful. The main obstacles to adopting LLMs for this task include the absence of layout encoding within LLMs, which is critical for high quality extraction, and the lack of a grounding mechanism to localize the predicted entities within the document. In this paper, we introduce Language Model-based Document Information Extraction and Localization (LMDX), a methodology to reframe the document information extraction task for a LLM. LMDX enables extraction of singular, repeated, and hierarchical entities, both with and without training data, while providing grounding guarantees and localizing the entities within the document. Finally, we apply LMDX to the PaLM 2-S and Gemini Pro LLMs and evaluate it on VRDU and CORD benchmarks, setting a new state-of-the-art and showing how LMDX enables the creation of high quality, data-efficient parsers.

cs.CL↗

arXiv2024

Debug like a Human: A Large Language Model Debugger via Verifying Runtime Execution Step-by-step

Large language models (LLMs) are leading significant progress in code generation. Beyond one-pass code generation, recent works further integrate unit tests and program verifiers into LLMs to iteratively refine the generated programs. However, these works consider the generated programs as an indivisible entity, which falls short for LLMs in debugging the programs, especially when the programs contain complex logic flows and data operations. In contrast, when human developers debug programs, they typically set breakpoints and selectively examine runtime execution information. The execution flow and the intermediate variables play a crucial role in the debugging process, yet they are underutilized in the existing literature on code generation. In this study, we introduce Large Language Model Debugger (LDB), a novel debugging framework that enables LLMs to refine their generated programs with the runtime execution information. Specifically, LDB segments the programs into basic blocks and tracks the values of intermediate variables after each block throughout the runtime execution. This allows LLMs to concentrate on simpler code units within the overall execution flow, verify their correctness against the task description block by block, and efficiently pinpoint any potential errors. Experiments demonstrate that LDB consistently enhances the baseline performance by up to 9.8% across the HumanEval, MBPP, and TransCoder benchmarks, archiving new state-of-the-art performance in code debugging for various LLM selections.

cs.SE↗

arXiv2024

Parts-per-billion Trace Element Detection in Anhydrous Minerals by Micro-scale Quantitative NMR

Nominally anhydrous minerals (NAMs) composing Earth's and planetary rocks incorporate microscopic amounts of volatiles. However, volatile distribution in NAMs and their effect on physical properties of rocks remain controversial. Thus, constraining trace volatile concentrations in NAMs is tantamount to our understanding of the evolution of rocky planets and planetesimals. Here, we present a novel approach of trace-element quantification using micro-scale Nuclear Magnetic Resonance (NMR) spectroscopy. This approach employs the principle of enhanced mass-sensitivity in NMR microcoils formerly used in \textit{in-situ} high pressure experiments. We were able to demonstrate that this method is in excellent agreement with standard methods across their respective detection capabilities. We show that by simultaneous detection of internal reference nuclei, the quantification sensitivity can be substantially increased, leading to quantifiable trace volatile element amounts of about $50$ wt-ppb measured in a micro-meter sized single anorthitic mineral grain, greatly enhancing detection capabilities of volatiles in geologically important systems.

physics.geo-ph↗

arXiv2024

LLM-RadJudge: Achieving Radiologist-Level Evaluation for X-Ray Report Generation

Evaluating generated radiology reports is crucial for the development of radiology AI, but existing metrics fail to reflect the task's clinical requirements. This study proposes a novel evaluation framework using large language models (LLMs) to compare radiology reports for assessment. We compare the performance of various LLMs and demonstrate that, when using GPT-4, our proposed metric achieves evaluation consistency close to that of radiologists. Furthermore, to reduce costs and improve accessibility, making this method practical, we construct a dataset using LLM evaluation results and perform knowledge distillation to train a smaller model. The distilled model achieves evaluation capabilities comparable to GPT-4. Our framework and distilled model offer an accessible and efficient evaluation method for radiology report generation, facilitating the development of more clinically relevant models. The model will be further open-sourced and accessible.

cs.CL↗