CLSep 4, 2023
Prompting or Fine-tuning? A Comparative Study of Large Language Models for Taxonomy ConstructionBoqi Chen, Fandi Yi, Dániel Varró
Taxonomies represent hierarchical relations between entities, frequently applied in various software modeling and natural language processing (NLP) activities. They are typically subject to a set of structural constraints restricting their content. However, manual taxonomy construction can be time-consuming, incomplete, and costly to maintain. Recent studies of large language models (LLMs) have demonstrated that appropriate user inputs (called prompting) can effectively guide LLMs, such as GPT-3, in diverse NLP tasks without explicit (re-)training. However, existing approaches for automated taxonomy construction typically involve fine-tuning a language model by adjusting model parameters. In this paper, we present a general framework for taxonomy construction that takes into account structural constraints. We subsequently conduct a systematic comparison between the prompting and fine-tuning approaches performed on a hypernym taxonomy and a novel computer science taxonomy dataset. Our result reveals the following: (1) Even without explicit training on the dataset, the prompting approach outperforms fine-tuning-based approaches. Moreover, the performance gap between prompting and fine-tuning widens when the training dataset is small. However, (2) taxonomies generated by the fine-tuning approach can be easily post-processed to satisfy all the constraints, whereas handling violations of the taxonomies produced by the prompting approach can be challenging. These evaluation findings provide guidance on selecting the appropriate method for taxonomy construction and highlight potential enhancements for both approaches.
CVApr 26, 2022
Differentiable Zooming for Multiple Instance Learning on Whole-Slide ImagesKevin Thandiackal, Boqi Chen, Pushpak Pati et al.
Multiple Instance Learning (MIL) methods have become increasingly popular for classifying giga-pixel sized Whole-Slide Images (WSIs) in digital pathology. Most MIL methods operate at a single WSI magnification, by processing all the tissue patches. Such a formulation induces high computational requirements, and constrains the contextualization of the WSI-level representation to a single scale. A few MIL methods extend to multiple scales, but are computationally more demanding. In this paper, inspired by the pathological diagnostic process, we propose ZoomMIL, a method that learns to perform multi-level zooming in an end-to-end manner. ZoomMIL builds WSI representations by aggregating tissue-context information from multiple magnifications. The proposed method outperforms the state-of-the-art MIL methods in WSI classification on two large datasets, while significantly reducing the computational demands with regard to Floating-Point Operations (FLOPs) and processing time by up to 40x.
CVMay 29
Benchmarking and Enhancing Text-to-Image Models for Generating Visual Representations in Early Arithmetic EducationJunling Wang, Boqi Chen, Heejin Do et al.
AI systems are increasingly used to support educational content creation, yet it remains unclear whether they can generate outputs that faithfully represent the pedagogical concepts they are intended to teach. Thus, we introduce equation-to-visual generation, a task that, in contrast to conventional image generation, requires producing pedagogically meaningful visuals from arithmetic equations while precisely preserving their numerical and relational structure. Informed by interviews with teachers and an analysis of educational materials, we construct E2V-Bench, a benchmark spanning four pedagogically grounded visual types, along with automatic metrics for evaluating visual correctness. Our evaluation reveals that recent text-to-image (T2I) models frequently fail on this task, with errors dominated by incorrect object counts and broken relational structure. Building on this, we explore benchmark-guided enhancement strategies. These strategies improve representative models, while the remaining gap calls for stronger numerical and relational grounding in future T2I models.
CVJan 3, 2023
Generative appearance replay for continual unsupervised domain adaptationBoqi Chen, Kevin Thandiackal, Pushpak Pati et al.
Deep learning models can achieve high accuracy when trained on large amounts of labeled data. However, real-world scenarios often involve several challenges: Training data may become available in installments, may originate from multiple different domains, and may not contain labels for training. Certain settings, for instance medical applications, often involve further restrictions that prohibit retention of previously seen data due to privacy regulations. In this work, to address such challenges, we study unsupervised segmentation in continual learning scenarios that involve domain shift. To that end, we introduce GarDA (Generative Appearance Replay for continual Domain Adaptation), a generative-replay based approach that can adapt a segmentation model sequentially to new domains with unlabeled data. In contrast to single-step unsupervised domain adaptation (UDA), continual adaptation to a sequence of domains enables leveraging and consolidation of information from multiple domains. Unlike previous approaches in incremental UDA, our method does not require access to previously seen data, making it applicable in many practical scenarios. We evaluate GarDA on two datasets with different organs and modalities, where it substantially outperforms existing techniques.
SEMay 28
Projectional Decoding: Towards Semantic-Aware LLM GenerationBoqi Chen, José Antonio Hernández López, Aren A. Babikian
Large language models (LLMs) are increasingly used to generate software artifacts across many software engineering (SE) tasks, yet ensuring the semantic validity of these artifacts remains a fundamental challenge. Existing constrained decoding techniques can enforce syntactic correctness and, in some cases, specific semantic rules, but lack a general representation that bridges LLM-generated text with the reasoning required for semantic validation in SE. In this paper, we propose projectional decoding, a novel conceptual framework that integrates domain semantics directly into the generation process by maintaining, alongside text, a partial graph model as the primary artifact representation throughout generation. This abstract representation enables incremental semantic validation by explicitly capturing uncertainty and natively supporting error detection, while guiding generation toward semantically valid outputs with provable guarantees. We present preliminary results on a program generation task which demonstrate the potential of this approach to improve the semantic validity of LLM-generated artifacts. We also discuss how projectional decoding can enable verifiable automation with LLMs across various SE activities.
IVMar 17, 2023
MRIS: A Multi-modal Retrieval Approach for Image Synthesis on Diverse ModalitiesBoqi Chen, Marc Niethammer
Multiple imaging modalities are often used for disease diagnosis, prediction, or population-based analyses. However, not all modalities might be available due to cost, different study designs, or changes in imaging technology. If the differences between the types of imaging are small, data harmonization approaches can be used; for larger changes, direct image synthesis approaches have been explored. In this paper, we develop an approach based on multi-modal metric learning to synthesize images of diverse modalities. We use metric learning via multi-modal image retrieval, resulting in embeddings that can relate images of different modalities. Given a large image database, the learned image embeddings allow us to use k-nearest neighbor (k-NN) regression for image synthesis. Our driving medical problem is knee osteoarthritis (KOA), but our developed method is general after proper image alignment. We test our approach by synthesizing cartilage thickness maps obtained from 3D magnetic resonance (MR) images using 2D radiographs. Our experiments show that the proposed method outperforms direct image synthesis and that the synthesized thickness maps retain information relevant to downstream tasks such as progression prediction and Kellgren-Lawrence grading (KLG). Our results suggest that retrieval approaches can be used to obtain high-quality and meaningful image synthesis results given large image databases.
CLFeb 25Code
MEDSYN: Benchmarking Multi-EviDence SYNthesis in Complex Clinical Cases for Multimodal Large Language ModelsBoqi Chen, Xudong Liu, Jiachuan Peng et al.
Multimodal large language models (MLLMs) have shown great potential in medical applications, yet existing benchmarks inadequately capture real-world clinical complexity. We introduce MEDSYN, a multilingual, multimodal benchmark of highly complex clinical cases with up to 7 distinct visual clinical evidence (CE) types per case. Mirroring clinical workflow, we evaluate 18 MLLMs on differential diagnosis (DDx) generation and final diagnosis (FDx) selection. While top models often match or even outperform human experts on DDx generation, all MLLMs exhibit a much larger DDx--FDx performance gap compared to expert clinicians, indicating a failure mode in synthesis of heterogeneous CE types. Ablations attribute this failure to (i) overreliance on less discriminative textual CE ($\it{e.g.}$, medical history) and (ii) a cross-modal CE utilization gap. We introduce Evidence Sensitivity to quantify the latter and show that a smaller gap correlates with higher diagnostic accuracy. Finally, we demonstrate how it can be used to guide interventions to improve model performance. We will open-source our benchmark and code.
CLJan 13
Evaluating Implicit Regulatory Compliance in LLM Tool Invocation via Logic-Guided SynthesisDa Song, Yuheng Huang, Boqi Chen et al.
The integration of large language models (LLMs) into autonomous agents has enabled complex tool use, yet in high-stakes domains, these systems must strictly adhere to regulatory standards beyond simple functional correctness. However, existing benchmarks often overlook implicit regulatory compliance, thus failing to evaluate whether LLMs can autonomously enforce mandatory safety constraints. To fill this gap, we introduce LogiSafetyGen, a framework that converts unstructured regulations into Linear Temporal Logic oracles and employs logic-guided fuzzing to synthesize valid, safety-critical traces. Building on this framework, we construct LogiSafetyBench, a benchmark comprising 240 human-verified tasks that require LLMs to generate Python programs that satisfy both functional objectives and latent compliance rules. Evaluations of 13 state-of-the-art (SOTA) LLMs reveal that larger models, despite achieving better functional correctness, frequently prioritize task completion over safety, which results in non-compliant behavior.
CVNov 10, 2025
YoNoSplat: You Only Need One Model for Feedforward 3D Gaussian SplattingBotao Ye, Boqi Chen, Haofei Xu et al.
Fast and flexible 3D scene reconstruction from unstructured image collections remains a significant challenge. We present YoNoSplat, a feedforward model that reconstructs high-quality 3D Gaussian Splatting representations from an arbitrary number of images. Our model is highly versatile, operating effectively with both posed and unposed, calibrated and uncalibrated inputs. YoNoSplat predicts local Gaussians and camera poses for each view, which are aggregated into a global representation using either predicted or provided poses. To overcome the inherent difficulty of jointly learning 3D Gaussians and camera parameters, we introduce a novel mixing training strategy. This approach mitigates the entanglement between the two tasks by initially using ground-truth poses to aggregate local Gaussians and gradually transitioning to a mix of predicted and ground-truth poses, which prevents both training instability and exposure bias. We further resolve the scale ambiguity problem by a novel pairwise camera-distance normalization scheme and by embedding camera intrinsics into the network. Moreover, YoNoSplat also predicts intrinsic parameters, making it feasible for uncalibrated inputs. YoNoSplat demonstrates exceptional efficiency, reconstructing a scene from 100 views (at 280x518 resolution) in just 2.69 seconds on an NVIDIA GH200 GPU. It achieves state-of-the-art performance on standard benchmarks in both pose-free and pose-dependent settings. Our project page is at https://botaoye.github.io/yonosplat/.
CVNov 7, 2024Code
Generalizable Single-Source Cross-modality Medical Image Segmentation via Invariant Causal MechanismsBoqi Chen, Yuanzhi Zhu, Yunke Ao et al.
Single-source domain generalization (SDG) aims to learn a model from a single source domain that can generalize well on unseen target domains. This is an important task in computer vision, particularly relevant to medical imaging where domain shifts are common. In this work, we consider a challenging yet practical setting: SDG for cross-modality medical image segmentation. We combine causality-inspired theoretical insights on learning domain-invariant representations with recent advancements in diffusion-based augmentation to improve generalization across diverse imaging modalities. Guided by the ``intervention-augmentation equivariant'' principle, we use controlled diffusion models (DMs) to simulate diverse imaging styles while preserving the content, leveraging rich generative priors in large-scale pretrained DMs to comprehensively perturb the multidimensional style variable. Extensive experiments on challenging cross-modality segmentation tasks demonstrate that our approach consistently outperforms state-of-the-art SDG methods across three distinct anatomies and imaging modalities. The source code is available at \href{https://github.com/ratschlab/ICMSeg}{https://github.com/ratschlab/ICMSeg}.
CVMar 12
Controllable Egocentric Video Generation via Occlusion-Aware Sparse 3D Hand JointsChenyangguang Zhang, Botao Ye, Boqi Chen et al.
Motion-controllable video generation is crucial for egocentric applications in virtual reality and embodied AI. However, existing methods often struggle to achieve 3D-consistent fine-grained hand articulation. By adopting on 2D trajectories or implicit poses, they collapse 3D geometry into spatially ambiguous signals or over rely on human-centric priors. Under severe egocentric occlusions, this causes motion inconsistencies and hallucinated artifacts, as well as preventing cross-embodiment generalization to robotic hands. To address these limitations, we propose a novel framework that generates egocentric videos from a single reference frame, leveraging sparse 3D hand joints as embodiment-agnostic control signals with clear semantic and geometric structures. We introduce an efficient control module that resolves occlusion ambiguities while fully preserving 3D information. Specifically, it extracts occlusion-aware features from the source reference frame by penalizing unreliable visual signals from hidden joints, and employs a 3D-based weighting mechanism to robustly handle dynamically occluded target joints during motion propagation. Concurrently, the module directly injects 3D geometric embeddings into the latent space to strictly enforce structural consistency. To facilitate robust training and evaluation, we develop an automated annotation pipeline that yields over one million high-quality egocentric video clips paired with precise hand trajectories. Additionally, we register humanoid kinematic and camera data to construct a cross-embodiment benchmark. Extensive experiments demonstrate that our approach significantly outperforms state-of-the-art baselines, generating high-fidelity egocentric videos with realistic interactions and exhibiting exceptional cross-embodiment generalization to robotic hands.
SEMar 31
Structure- and Event-Driven Frameworks for State Machine Modeling with Large Language ModelsSamer Abdulkarim, Evan Boyd, Karl Bridi et al.
UML state machine design is a critical process in software engineering. Traditionally, state machines are manually crafted by experienced engineers based on natural language requirements-a time-consuming and error-prone procedure. Many automated approaches exist but they require structured NL requirements. In this paper, we investigate the capabilities of current Large Language Models to fully automate UML state machine generation via specialized State Machine Frameworks (SMFs) from non-structured NL requirements. We evaluate two types of state-of-the-art LLMs using single-step and multi-step prompting approaches: a non-reasoning LLM GPT-4o and a reasoning-focused LLM Claude 3.5 Sonnet, and introduce a novel Hybrid Approach that uses the output from a Single-Prompt Baseline as an initial draft state machine, which is then refined through an SMF. In our study, two distinct SMFs are developed based on human approaches: (i) a Structure-Driven SMF, in which state machine components (states, transitions, guards, actions, etc.) are generated in sequential steps, and (ii) an Event-Driven SMF, where identified events iteratively guide state machine construction. Our experiments indicate that while LLMs demonstrate a promising ability to generate state machine models from the Single-Prompt Baseline (e.g., F1-scores of 0.90 for states and 0.75 for transitions using Claude 3.5 Sonnet), their performance is not yet fully sufficient for a fully automated solution (e.g., F1-scores of 0.23 for guards and 0.00 for actions for GPT-4o). Our proposed Hybrid Approach improves the performance of the non-reasoning LLM (GPT-4o) to a similar level as the reasoning LLM (Claude 3.5 Sonnet) but does not further improve the reasoning LLM. Our evaluation highlights both the potential and the limitations of current LLMs for automated state machine design, providing a baseline for future research in this domain.
LGAug 11, 2025Code
WeChat-YATT: A Scalable, Simple, Efficient, and Production Ready Training LibraryJunyu Wu, Weiming Chang, Xiaotao Liu et al.
Reinforcement Learning from Human Feedback (RLHF) has emerged as a prominent paradigm for training large language models and multimodal systems. Despite the notable advances enabled by existing RLHF training frameworks, significant challenges remain to scale to complex multimodal workflows and adapt to dynamic workloads. In particular, current systems often encounter limitations related to controller scalability when managing large models, as well as inefficiencies in orchestrating intricate RLHF pipelines, especially in scenarios that require dynamic sampling and resource allocation. In this paper, we introduce WeChat-YATT Yet Another Transformer Trainer in WeChat, a simple, scalable, and balanced RLHF training framework specifically designed to address these challenges. WeChat-YATT features a parallel controller programming model that enables flexible and efficient orchestration of complex RLHF workflows, effectively mitigating bottlenecks associated with centralized controller architectures and facilitating scalability in large-scale data scenarios. In addition, we propose a dynamic placement schema that adaptively partitions computational resources and schedules workloads, thereby significantly reducing hardware idle time and improving GPU utilization under variable training conditions. We evaluate WeChat-YATT across diverse experimental scenarios, demonstrating its substantial throughput improvements over state-of-the-art RLHF training frameworks. Furthermore, WeChat-YATT has been successfully deployed to train models that support WeChat product features for a large-scale user base, underscoring its effectiveness and robustness in real-world applications. We have made WeChat-YATT publicly available at https://www.github.com/tencent/WeChat-YATT.
SEAug 1, 2025Code
Accurate and Consistent Graph Model Generation from Text with Large Language ModelsBoqi Chen, Ou Wei, Bingzhou Zheng et al.
Graph model generation from natural language description is an important task with many applications in software engineering. With the rise of large language models (LLMs), there is a growing interest in using LLMs for graph model generation. Nevertheless, LLM-based graph model generation typically produces partially correct models that suffer from three main issues: (1) syntax violations: the generated model may not adhere to the syntax defined by its metamodel, (2) constraint inconsistencies: the structure of the model might not conform to some domain-specific constraints, and (3) inaccuracy: due to the inherent uncertainty in LLMs, the models can include inaccurate, hallucinated elements. While the first issue is often addressed through techniques such as constraint decoding or filtering, the latter two remain largely unaddressed. Motivated by recent self-consistency approaches in LLMs, we propose a novel abstraction-concretization framework that enhances the consistency and quality of generated graph models by considering multiple outputs from an LLM. Our approach first constructs a probabilistic partial model that aggregates all candidate outputs and then refines this partial model into the most appropriate concrete model that satisfies all constraints. We evaluate our framework on several popular open-source and closed-source LLMs using diverse datasets for model generation tasks. The results demonstrate that our approach significantly improves both the consistency and quality of the generated graph models.
SEMay 4
LLM-Assisted Repository-Level Generation with Structured Spec-Driven EngineeringShuzhao Feng, Boqi Chen, Brett H Meyer et al.
State-of-the-art Large Language Models (LLMs) excel in code generation at the function level. However, the output quality significantly declines when scaling to repository-level systems. Current workflows relying only on natural language prompts suffer from inherent ambiguity and a lack of verifiability. To address this, we propose structured spec-driven engineering (SSDE), a paradigm that leverages structured artifacts to guide LLM generation. We argue that structured specifications as LLM inputs make high-quality, repository-level code generation a tangible goal, while at the same time offering superior verifiability, leading to significant potential for improvement. We first investigate the feasibility of this vision through a pilot study generating Model-View-Controller (MVC) business logic for three software systems using five LLMs, and then highlight the potential, challenges, and future roadmap for SSDE.
CLApr 25
Revisiting Greedy Decoding for Visual Question Answering: A Calibration PerspectiveBoqi Chen, Xudong Liu, Yunke Ao et al.
Stochastic sampling strategies are widely adopted in large language models (LLMs) to balance output coherence and diversity. These heuristics are often inherited in Multimodal LLMs (MLLMs) without task-specific justification. However, we contend that stochastic decoding can be suboptimal for Visual Question Answering (VQA). VQA is a closed-ended task with head-heavy answer distributions where uncertainty is usually epistemic, arising from missing or ambiguous visual evidence rather than plausible continuations. In this work, we provide a theoretical formalization of the relationship between model calibration and predictive accuracy, and derive the sufficient conditions for greedy decoding optimality. Extensive experiments provide empirical evidence for the superiority of greedy decoding over stochastic sampling across multiple benchmarks. Furthermore, we propose Greedy Decoding for Reasoning Models, which outperforms both stochastic sampling and standard greedy decoding in multimodal reasoning scenarios. Overall, our results caution against naively inheriting LLMs decoding heuristics in MLLMs and demonstrate that greedy decoding can be an efficient yet strong default for VQA.
CVMar 18, 2024
A Unified Model for Longitudinal Multi-Modal Multi-View Prediction with MissingnessBoqi Chen, Junier Oliva, Marc Niethammer
Medical records often consist of different modalities, such as images, text, and tabular information. Integrating all modalities offers a holistic view of a patient's condition, while analyzing them longitudinally provides a better understanding of disease progression. However, real-world longitudinal medical records present challenges: 1) patients may lack some or all of the data for a specific timepoint, and 2) certain modalities or views might be absent for all patients during a particular period. In this work, we introduce a unified model for longitudinal multi-modal multi-view prediction with missingness. Our method allows as many timepoints as desired for input, and aims to leverage all available data, regardless of their availability. We conduct extensive experiments on the knee osteoarthritis dataset from the Osteoarthritis Initiative for pain and Kellgren-Lawrence grade prediction at a future timepoint. We demonstrate the effectiveness of our method by comparing results from our unified model to specific models that use the same modality and view combinations during training and evaluation. We also show the benefit of having extended temporal data and provide post-hoc analysis for a deeper understanding of each modality/view's importance for different tasks.
AIAug 29, 2025
SHERPA: A Model-Driven Framework for Large Language Model ExecutionBoqi Chen, Kua Chen, José Antonio Hernández López et al.
Recently, large language models (LLMs) have achieved widespread application across various fields. Despite their impressive capabilities, LLMs suffer from a lack of structured reasoning ability, particularly for complex tasks requiring domain-specific best practices, which are often unavailable in the training data. Although multi-step prompting methods incorporating human best practices, such as chain-of-thought and tree-of-thought, have gained popularity, they lack a general mechanism to control LLM behavior. In this paper, we propose SHERPA, a model-driven framework to improve the LLM performance on complex tasks by explicitly incorporating domain-specific best practices into hierarchical state machines. By structuring the LLM execution processes using state machines, SHERPA enables more fine-grained control over their behavior via rules or decisions driven by machine learning-based approaches, including LLMs. We show that SHERPA is applicable to a wide variety of tasks-specifically, code generation, class name generation, and question answering-replicating previously proposed approaches while further improving the performance. We demonstrate the effectiveness of SHERPA for the aforementioned tasks using various LLMs. Our systematic evaluation compares different state machine configurations against baseline approaches without state machines. Results show that integrating well-designed state machines significantly improves the quality of LLM outputs, and is particularly beneficial for complex tasks with well-established human best practices but lacking data used for training LLMs.
CVMar 24, 2025
Revisiting Automatic Data Curation for Vision Foundation Models in Digital PathologyBoqi Chen, Cédric Vincent-Cuaz, Lydia A. Schoenpflug et al.
Vision foundation models (FMs) are accelerating the development of digital pathology algorithms and transforming biomedical research. These models learn, in a self-supervised manner, to represent histological features in highly heterogeneous tiles extracted from whole-slide images (WSIs) of real-world patient samples. The performance of these FMs is significantly influenced by the size, diversity, and balance of the pre-training data. However, data selection has been primarily guided by expert knowledge at the WSI level, focusing on factors such as disease classification and tissue types, while largely overlooking the granular details available at the tile level. In this paper, we investigate the potential of unsupervised automatic data curation at the tile-level, taking into account 350 million tiles. Specifically, we apply hierarchical clustering trees to pre-extracted tile embeddings, allowing us to sample balanced datasets uniformly across the embedding space of the pretrained FM. We further identify these datasets are subject to a trade-off between size and balance, potentially compromising the quality of representations learned by FMs, and propose tailored batch sampling strategies to mitigate this effect. We demonstrate the effectiveness of our method through improved performance on a diverse range of clinically relevant downstream tasks.
CVFeb 12
Mask What Matters: Mitigating Object Hallucinations in Multimodal Large Language Models with Object-Aligned Visual Contrastive DecodingBoqi Chen, Xudong Liu, Jianing Qiu
We study object hallucination in Multimodal Large Language Models (MLLMs) and improve visual contrastive decoding (VCD) by constructing an object-aligned auxiliary view. We leverage object-centric attention in self-supervised Vision Transformers. In particular, we remove the most salient visual evidence to construct an auxiliary view that disrupts unsupported tokens and produces a stronger contrast signal. Our method is prompt-agnostic, model-agnostic, and can be seamlessly plugged into the existing VCD pipeline with little computation overhead, i.e., a single cacheable forward pass. Empirically, our method demonstrates consistent gains on two popular object hallucination benchmarks across two MLLMs.
LGJul 16, 2025
NOCTA: Non-Greedy Objective Cost-Tradeoff Acquisition for Longitudinal DataDzung Dinh, Boqi Chen, Marc Niethammer et al.
In many critical applications, resource constraints limit the amount of information that can be gathered to make predictions. For example, in healthcare, patient data often spans diverse features ranging from lab tests to imaging studies. Each feature may carry different information and must be acquired at a respective cost of time, money, or risk to the patient. Moreover, temporal prediction tasks, where both instance features and labels evolve over time, introduce additional complexity in deciding when or what information is important. In this work, we propose NOCTA, a Non-Greedy Objective Cost-Tradeoff Acquisition method that sequentially acquires the most informative features at inference time while accounting for both temporal dynamics and acquisition cost. We first introduce a cohesive estimation target for our NOCTA setting, and then develop two complementary estimators: 1) a non-parametric method based on nearest neighbors to guide the acquisition (NOCTA-NP), and 2) a parametric method that directly predicts the utility of potential acquisitions (NOCTA-P). Experiments on synthetic and real-world medical datasets demonstrate that both NOCTA variants outperform existing baselines.
IVMar 21, 2025
Downstream Analysis of Foundational Medical Vision Models for Disease ProgressionBasar Demir, Soumitri Chattopadhyay, Thomas Hastings Greer et al.
Medical vision foundational models are used for a wide variety of tasks, including medical image segmentation and registration. This work evaluates the ability of these models to predict disease progression using a simple linear probe. We hypothesize that intermediate layer features of segmentation models capture structural information, while those of registration models encode knowledge of change over time. Beyond demonstrating that these features are useful for disease progression prediction, we also show that registration model features do not require spatially aligned input images. However, for segmentation models, spatial alignment is essential for optimal performance. Our findings highlight the importance of spatial alignment and the utility of foundation model features for image registration.
ROMar 17, 2025
MIXPINN: Mixed-Material Simulations by Physics-Informed Neural NetworkXintian Yuan, Yunke Ao, Boqi Chen et al.
Simulating the complex interactions between soft tissues and rigid anatomy is critical for applications in surgical training, planning, and robotic-assisted interventions. Traditional Finite Element Method (FEM)-based simulations, while accurate, are computationally expensive and impractical for real-time scenarios. Learning-based approaches have shown promise in accelerating predictions but have fallen short in modeling soft-rigid interactions effectively. We introduce MIXPINN, a physics-informed Graph Neural Network (GNN) framework for mixed-material simulations, explicitly capturing soft-rigid interactions using graph-based augmentations. Our approach integrates Virtual Nodes (VNs) and Virtual Edges (VEs) to enhance rigid body constraint satisfaction while preserving computational efficiency. By leveraging a graph-based representation of biomechanical structures, MIXPINN learns high-fidelity deformations from FEM-generated data and achieves real-time inference with sub-millimeter accuracy. We validate our method in a realistic clinical scenario, demonstrating superior performance compared to baseline GNN models and traditional FEM methods. Our results show that MIXPINN reduces computational cost by an order of magnitude while maintaining high physical accuracy, making it a viable solution for real-time surgical simulation and robotic-assisted procedures.
SENov 22, 2024
The Power of Types: Exploring the Impact of Type Checking on Neural Bug Detection in Dynamically Typed LanguagesBoqi Chen, José Antonio Hernández López, Gunter Mussbacher et al.
Motivation: Automated bug detection in dynamically typed languages such as Python is essential for maintaining code quality. The lack of mandatory type annotations in such languages can lead to errors that are challenging to identify early with traditional static analysis tools. Recent progress in deep neural networks has led to increased use of neural bug detectors. In statically typed languages, a type checker is integrated into the compiler and thus taken into consideration when the neural bug detector is designed for these languages. Problem: However, prior studies overlook this aspect during the training and testing of neural bug detectors for dynamically typed languages. When an optional type checker is used, assessing existing neural bug detectors on bugs easily detectable by type checkers may impact their performance estimation. Moreover, including these bugs in the training set of neural bug detectors can shift their detection focus toward the wrong type of bugs. Contribution: We explore the impact of type checking on various neural bug detectors for variable misuse bugs, a common type targeted by neural bug detectors. Existing synthetic and real-world datasets are type-checked to evaluate the prevalence of type-related bugs. Then, we investigate how type-related bugs influence the training and testing of the neural bug detectors. Findings: Our findings indicate that existing bug detection datasets contain a significant proportion of type-related bugs. Building on this insight, we discover integrating the neural bug detector with a type checker can be beneficial, especially when the code is annotated with types. Further investigation reveals neural bug detectors perform better on type-related bugs than other bugs. Moreover, removing type-related bugs from the training data helps improve neural bug detectors' ability to identify bugs beyond the scope of type checkers.
CLJun 25, 2024
Detecting Frames in News Headlines and Lead Images in U.S. Gun Violence CoverageIsidora Chara Tourni, Lei Guo, Hengchang Hu et al.
News media structure their reporting of events or issues using certain perspectives. When describing an incident involving gun violence, for example, some journalists may focus on mental health or gun regulation, while others may emphasize the discussion of gun rights. Such perspectives are called \say{frames} in communication research. We study, for the first time, the value of combining lead images and their contextual information with text to identify the frame of a given news article. We observe that using multiple modes of information(article- and image-derived features) improves prediction of news frames over any single mode of information when the images are relevant to the frames of the headlines. We also observe that frame image relevance is related to the ease of conveying frames via images, which we call frame concreteness. Additionally, we release the first multimodal news framing dataset related to gun violence in the U.S., curated and annotated by communication researchers. The dataset will allow researchers to further examine the use of multiple information modalities for studying media framing.
LGMay 14, 2024
Certifying Robustness of Graph Convolutional Networks for Node Perturbation with Polyhedra Abstract InterpretationBoqi Chen, Kristóf Marussy, Oszkár Semeráth et al.
Graph convolutional neural networks (GCNs) are powerful tools for learning graph-based knowledge representations from training data. However, they are vulnerable to small perturbations in the input graph, which makes them susceptible to input faults or adversarial attacks. This poses a significant problem for GCNs intended to be used in critical applications, which need to provide certifiably robust services even in the presence of adversarial perturbations. We propose an improved GCN robustness certification technique for node classification in the presence of node feature perturbations. We introduce a novel polyhedra-based abstract interpretation approach to tackle specific challenges of graph data and provide tight upper and lower bounds for the robustness of the GCN. Experiments show that our approach simultaneously improves the tightness of robustness bounds as well as the runtime performance of certification. Moreover, our method can be used during training to further improve the robustness of GCNs.