Boqi Chen

Boqi 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.

Kevin 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.

Boqi 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.

Boqi 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.

Da 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.

Boqi 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}.

Boqi 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.

Boqi 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.

Boqi 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.

Dzung 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.

Boqi 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.

Isidora 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.

Boqi 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.