Haoyu Dong

Maciej A. Mazurowski, Haoyu Dong, Hanxue Gu et al.

Training segmentation models for medical images continues to be challenging due to the limited availability of data annotations. Segment Anything Model (SAM) is a foundation model that is intended to segment user-defined objects of interest in an interactive manner. While the performance on natural images is impressive, medical image domains pose their own set of challenges. Here, we perform an extensive evaluation of SAM's ability to segment medical images on a collection of 19 medical imaging datasets from various modalities and anatomies. We report the following findings: (1) SAM's performance based on single prompts highly varies depending on the dataset and the task, from IoU=0.1135 for spine MRI to IoU=0.8650 for hip X-ray. (2) Segmentation performance appears to be better for well-circumscribed objects with prompts with less ambiguity and poorer in various other scenarios such as the segmentation of brain tumors. (3) SAM performs notably better with box prompts than with point prompts. (4) SAM outperforms similar methods RITM, SimpleClick, and FocalClick in almost all single-point prompt settings. (5) When multiple-point prompts are provided iteratively, SAM's performance generally improves only slightly while other methods' performance improves to the level that surpasses SAM's point-based performance. We also provide several illustrations for SAM's performance on all tested datasets, iterative segmentation, and SAM's behavior given prompt ambiguity. We conclude that SAM shows impressive zero-shot segmentation performance for certain medical imaging datasets, but moderate to poor performance for others. SAM has the potential to make a significant impact in automated medical image segmentation in medical imaging, but appropriate care needs to be applied when using it.

Ao Liu, Haoyu Dong, Naoaki Okazaki et al.

Logical table-to-text generation is a task that involves generating logically faithful sentences from tables, which requires models to derive logical level facts from table records via logical inference. It raises a new challenge on the logical-level content planning of table-to-text models. However, directly learning the logical inference knowledge from table-text pairs is very difficult for neural models because of the ambiguity of natural language and the scarcity of parallel data. Hence even large-scale pre-trained language models present low logical fidelity on logical table-to-text. In this work, we propose a PLOG (Pretrained Logical Form Generator) framework to improve the generation fidelity. Specifically, PLOG is first pretrained on a table-to-logic-form generation (table-to-logic) task, then finetuned on downstream table-to-text tasks. The formal definition of logical forms enables us to collect large amount of accurate logical forms from tables without human annotation. In addition, PLOG can learn logical inference from table-logic pairs much more definitely than from table-text pairs. To evaluate our model, we further collect a controlled logical table-to-text dataset CONTLOG based on an existing dataset. On two benchmarks, LOGICNLG and CONTLOG, PLOG outperforms strong baselines by a large margin on the logical fidelity, demonstrating the effectiveness of table-to-logic pretraining.

Haochen Wang, Kai Hu, Haoyu Dong et al.

We study a new problem setting of question answering (QA), referred to as DocTabQA. Within this setting, given a long document, the goal is to respond to questions by organizing the answers into structured tables derived directly from the document's content. Unlike traditional QA approaches which predominantly rely on unstructured text to formulate responses, DocTabQA aims to leverage structured tables as answers to convey information clearly and systematically, thereby enhancing user comprehension and highlighting relationships between data points. To the best of our knowledge, this problem has not been previously explored. In this paper, we introduce the QTabA dataset, encompassing 300 financial documents, accompanied by manually annotated 1.5k question-table pairs. Initially, we leverage Large Language Models (LLMs) such as GPT-4 to establish a baseline. However, it is widely acknowledged that LLMs encounter difficulties when tasked with generating intricate, structured outputs from long input sequences. To overcome these challenges, we present a two-stage framework, called DocTabTalk, which initially retrieves relevant sentences from extensive documents and subsequently generates hierarchical tables based on these identified sentences. DocTabTalk incorporates two key technological innovations: AlignLLaMA and TabTalk, which are specifically tailored to assist GPT-4 in tackling DocTabQA, enabling it to generate well-structured, hierarchical tables with improved organization and clarity. Comprehensive experimental evaluations conducted on both QTabA and RotoWire datasets demonstrate that our DocTabTalk significantly enhances the performances of the GPT-4 in our proposed DocTabQA task and the table generation task. The code and dataset are available at https://github.com/SmileWHC/DocTabQA for further research.

Haoyu Dong, Jianbo Zhao, Yuzhang Tian et al.

Spreadsheets are characterized by their extensive two-dimensional grids, flexible layouts, and varied formatting options, which pose significant challenges for large language models (LLMs). In response, we introduce SpreadsheetLLM, pioneering an efficient encoding method designed to unleash and optimize LLMs' powerful understanding and reasoning capability on spreadsheets. Initially, we propose a vanilla serialization approach that incorporates cell addresses, values, and formats. However, this approach was limited by LLMs' token constraints, making it impractical for most applications. To tackle this challenge, we develop SheetCompressor, an innovative encoding framework that compresses spreadsheets effectively for LLMs. It comprises three modules: structural-anchor-based compression, inverse index translation, and data-format-aware aggregation. It significantly improves performance in the spreadsheet table detection task, outperforming the vanilla approach by 25.6% in GPT4's in-context learning setting. Moreover, fine-tuned LLM with SheetCompressor has an average compression ratio of 25 times, and achieves a state-of-the-art 78.9% F1 score, surpassing the best existing models by 12.3%. Finally, we propose Chain of Spreadsheet for downstream tasks of spreadsheet understanding and validate it in a new and demanding spreadsheet QA task. We methodically leverage the inherent layout and structure of spreadsheets, demonstrating that SpreadsheetLLM is highly effective across a variety of spreadsheet tasks.

Fan Zhou, Haoyu Dong, Qian Liu et al.

Numerical reasoning over natural language has been a long-standing goal for the research community. However, cutting-edge language models have proven difficult to reliably generalize to a broad range of numbers, although they have shown proficiency in reasoning over common and simple numbers. In this paper, we propose a novel method to elicit and exploit the numerical reasoning knowledge hidden in pre-trained language models using simple anchor numbers. Concretely, we first leverage simple numbers as anchors to probe the implicitly inferred arithmetic expressions from language models, and then explicitly apply the expressions on complex numbers to get corresponding answers. To inversely elicit arithmetic expressions, we transform and formulate the task as an analytically solvable linear system. Experimental results on several numerical reasoning benchmarks demonstrate that our approach significantly improves numerical reasoning capabilities of existing LMs. More importantly, our approach is training-free and simply works in the inference phase, making it highly portable and achieving consistent performance benefits across a variety of language models (GPT-3, T5, BART, etc) in all zero-shot, few-shot, and fine-tuning scenarios.

Pedro R. A. S. Bassi, Wenxuan Li, Yucheng Tang et al.

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across various out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms on three test sets. In addition, we also evaluated pre-existing AI frameworks--which, differing from algorithms, are more flexible and can support different algorithms--including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

Mengkang Hu, Haoyu Dong, Ping Luo et al.

Due to the concise and structured nature of tables, the knowledge contained therein may be incomplete or missing, posing a significant challenge for table question answering (TableQA) and data analysis systems. Most existing datasets either fail to address the issue of external knowledge in TableQA or only utilize unstructured text as supplementary information for tables. In this paper, we propose to use a knowledge base (KB) as the external knowledge source for TableQA and construct a dataset KET-QA with fine-grained gold evidence annotation. Each table in the dataset corresponds to a sub-graph of the entire KB, and every question requires the integration of information from both the table and the sub-graph to be answered. To extract pertinent information from the vast knowledge sub-graph and apply it to TableQA, we design a retriever-reasoner structured pipeline model. Experimental results demonstrate that our model consistently achieves remarkable relative performance improvements ranging from 1.9 to 6.5 times and absolute improvements of 11.66% to 44.64% on EM scores across three distinct settings (fine-tuning, zero-shot, and few-shot), in comparison with solely relying on table information in the traditional TableQA manner. However, even the best model achieves a 60.23% EM score, which still lags behind the human-level performance, highlighting the challenging nature of KET-QA for the question-answering community. We also provide a human evaluation of error cases to analyze further the aspects in which the model can be improved. Project page: https://ketqa.github.io/.

Yihao Liu, Shuocheng Li, Lang Cao et al.

Large language models are increasingly used for complex reasoning tasks where high-quality offline data such as expert-annotated solutions and distilled reasoning traces are often available. However, in environments with sparse rewards, reinforcement learning struggles to sample successful trajectories, leading to inefficient learning. At the same time, these offline trajectories that represent correct reasoning paths are not utilized by standard on-policy reinforcement learning methods. We introduce SuperRL, a unified training framework that adaptively alternates between RL and SFT. Whenever every rollout for a given instance receives zero reward, indicating the absence of a learning signal, SuperRL falls back to SFT on the curated offline data. Extensive experiments across diverse reasoning benchmarks show that SuperRL surpasses vanilla RL by delivering higher sample efficiency, stronger generalization, and improved robustness under sparse rewards.

Wei Zhao, Zhitao Hou, Siyuan Wu et al.

Writing formulas on spreadsheets, such as Microsoft Excel and Google Sheets, is a widespread practice among users performing data analysis. However, crafting formulas on spreadsheets remains a tedious and error-prone task for many end-users, particularly when dealing with complex operations. To alleviate the burden associated with writing spreadsheet formulas, this paper introduces a novel benchmark task called NL2Formula, with the aim to generate executable formulas that are grounded on a spreadsheet table, given a Natural Language (NL) query as input. To accomplish this, we construct a comprehensive dataset consisting of 70,799 paired NL queries and corresponding spreadsheet formulas, covering 21,670 tables and 37 types of formula functions. We realize the NL2Formula task by providing a sequence-to-sequence baseline implementation called fCoder. Experimental results validate the effectiveness of fCoder, demonstrating its superior performance compared to the baseline models. Furthermore, we also compare fCoder with an initial GPT-3.5 model (i.e., text-davinci-003). Lastly, through in-depth error analysis, we identify potential challenges in the NL2Formula task and advocate for further investigation.

Xinyi He, Yihao Liu, Mengyu Zhou et al.

Tabular data are crucial in many fields and their understanding by large language models (LLMs) under high parameter efficiency paradigm is important. However, directly applying parameter-efficient fine-tuning (PEFT) techniques to tabular tasks presents significant challenges, particularly in terms of better table serialization and the representation of two-dimensional structured information within a one-dimensional sequence. To address this, we propose TableLoRA, a module designed to improve LLMs' understanding of table structure during PEFT. It incorporates special tokens for serializing tables with special token encoder and uses 2D LoRA to encode low-rank information on cell positions. Experiments on four tabular-related datasets demonstrate that TableLoRA consistently outperforms vanilla LoRA and surpasses various table encoding methods tested in control experiments. These findings reveal that TableLoRA, as a table-specific LoRA, enhances the ability of LLMs to process tabular data effectively, especially in low-parameter settings, demonstrating its potential as a robust solution for handling table-related tasks.

Hanbing Liu, Lang Cao, Yuanyi Ren et al.

Large language models have demonstrated impressive reasoning capabilities, yet they often suffer from inefficiencies due to unnecessarily verbose or redundant outputs. While many works have explored reinforcement learning (RL) to enhance reasoning abilities, most primarily focus on improving accuracy, with limited attention to reasoning efficiency. Some existing approaches introduce direct length-based rewards to encourage brevity, but this often leads to noticeable drops in accuracy. In this paper, we propose Bingo, an RL framework that advances length-based reward design to boost efficient reasoning. Bingo incorporates two key mechanisms: a significance-aware length reward, which gradually guides the model to reduce only insignificant tokens, and a dynamic length reward, which initially encourages elaborate reasoning for hard questions but decays over time to improve overall efficiency. Experiments across multiple reasoning benchmarks show that Bingo improves both accuracy and efficiency. It outperforms the vanilla reward and several other length-based reward baselines in RL, achieving a favorable trade-off between accuracy and efficiency. These results underscore the potential of training LLMs explicitly for efficient reasoning.

Yaqian Chen, Hanxue Gu, Haoyu Dong et al.

Accurately registering breast MR images from different time points enables the alignment of anatomical structures and tracking of tumor progression, supporting more effective breast cancer detection, diagnosis, and treatment planning. However, the complexity of dense tissue and its highly non-rigid nature pose challenges for conventional registration methods, which primarily focus on aligning general structures while overlooking intricate internal details. To address this, we propose \textbf{GuidedMorph}, a novel two-stage registration framework designed to better align dense tissue. In addition to a single-scale network for global structure alignment, we introduce a framework that utilizes dense tissue information to track breast movement. The learned transformation fields are fused by introducing the Dual Spatial Transformer Network (DSTN), improving overall alignment accuracy. A novel warping method based on the Euclidean distance transform (EDT) is also proposed to accurately warp the registered dense tissue and breast masks, preserving fine structural details during deformation. The framework supports paradigms that require external segmentation models and with image data only. It also operates effectively with the VoxelMorph and TransMorph backbones, offering a versatile solution for breast registration. We validate our method on ISPY2 and internal dataset, demonstrating superior performance in dense tissue, overall breast alignment, and breast structural similarity index measure (SSIM), with notable improvements by over 13.01% in dense tissue Dice, 3.13% in breast Dice, and 1.21% in breast SSIM compared to the best learning-based baseline.

Deyin Yi, Yihao Liu, Lang Cao et al.

Tabular data analysis is crucial in many scenarios, yet efficiently identifying the most relevant data analysis queries and results for a new table remains a significant challenge. The complexity of tabular data, diverse analytical operations, and the demand for high-quality analysis make the process tedious. To address these challenges, we aim to recommend query-code-result triplets tailored for new tables in tabular data analysis workflows. In this paper, we present TablePilot, a pioneering tabular data analysis framework leveraging large language models to autonomously generate comprehensive and superior analytical results without relying on user profiles or prior interactions. The framework incorporates key designs in analysis preparation and analysis optimization to enhance accuracy. Additionally, we propose Rec-Align, a novel method to further improve recommendation quality and better align with human preferences. Experiments on DART, a dataset specifically designed for comprehensive tabular data analysis recommendation, demonstrate the effectiveness of our framework. Based on GPT-4o, the tuned TablePilot achieves 77.0% top-5 recommendation recall. Human evaluations further highlight its effectiveness in optimizing tabular data analysis workflows.

Lang Cao, Jingxian Xu, Hanbing Liu et al.

Tables are a fundamental structure for organizing and analyzing data, making effective table understanding a critical capability for intelligent systems. While large language models (LMs) demonstrate strong general reasoning abilities, they continue to struggle with accurate numerical or symbolic reasoning over tabular data, especially in complex scenarios. Spreadsheet formulas provide a powerful and expressive medium for representing executable symbolic operations, encoding rich reasoning patterns that remain largely underutilized. In this paper, we propose Formula Tuning (Fortune), a reinforcement learning (RL) framework that trains LMs to generate executable spreadsheet formulas for question answering over general tabular data. Formula Tuning reduces the reliance on supervised formula annotations by using binary answer correctness as a reward signal, guiding the model to learn formula derivation through reasoning. We provide a theoretical analysis of its advantages and demonstrate its effectiveness through extensive experiments on seven table reasoning benchmarks. Formula Tuning substantially enhances LM performance, particularly on multi-step numerical and symbolic reasoning tasks, enabling a 7B model to outperform OpenAI o1 on table understanding. This highlights the potential of formula-driven RL to advance symbolic table reasoning in LMs.

Nicholas Konz, Haoyu Dong, Maciej A. Mazurowski

Automated tumor detection in Digital Breast Tomosynthesis (DBT) is a difficult task due to natural tumor rarity, breast tissue variability, and high resolution. Given the scarcity of abnormal images and the abundance of normal images for this problem, an anomaly detection/localization approach could be well-suited. However, most anomaly localization research in machine learning focuses on non-medical datasets, and we find that these methods fall short when adapted to medical imaging datasets. The problem is alleviated when we solve the task from the image completion perspective, in which the presence of anomalies can be indicated by a discrepancy between the original appearance and its auto-completion conditioned on the surroundings. However, there are often many valid normal completions given the same surroundings, especially in the DBT dataset, making this evaluation criterion less precise. To address such an issue, we consider pluralistic image completion by exploring the distribution of possible completions instead of generating fixed predictions. This is achieved through our novel application of spatial dropout on the completion network during inference time only, which requires no additional training cost and is effective at generating diverse completions. We further propose minimum completion distance (MCD), a new metric for detecting anomalies, thanks to these stochastic completions. We provide theoretical as well as empirical support for the superiority over existing methods of using the proposed method for anomaly localization. On the DBT dataset, our model outperforms other state-of-the-art methods by at least 10\% AUROC for pixel-level detection.

Haoyu Dong, Zhoujun Cheng, Xinyi He et al.

Since a vast number of tables can be easily collected from web pages, spreadsheets, PDFs, and various other document types, a flurry of table pre-training frameworks have been proposed following the success of text and images, and they have achieved new state-of-the-arts on various tasks such as table question answering, table type recognition, column relation classification, table search, formula prediction, etc. To fully use the supervision signals in unlabeled tables, a variety of pre-training objectives have been designed and evaluated, for example, denoising cell values, predicting numerical relationships, and implicitly executing SQLs. And to best leverage the characteristics of (semi-)structured tables, various tabular language models, particularly with specially-designed attention mechanisms, have been explored. Since tables usually appear and interact with free-form text, table pre-training usually takes the form of table-text joint pre-training, which attracts significant research interests from multiple domains. This survey aims to provide a comprehensive review of different model designs, pre-training objectives, and downstream tasks for table pre-training, and we further share our thoughts and vision on existing challenges and future opportunities.

Zhoujun Cheng, Haoyu Dong, Ran Jia et al.

Tables store rich numerical data, but numerical reasoning over tables is still a challenge. In this paper, we find that the spreadsheet formula, which performs calculations on numerical values in tables, is naturally a strong supervision of numerical reasoning. More importantly, large amounts of spreadsheets with expert-made formulae are available on the web and can be obtained easily. FORTAP is the first method for numerical-reasoning-aware table pretraining by leveraging large corpus of spreadsheet formulae. We design two formula pretraining tasks to explicitly guide FORTAP to learn numerical reference and calculation in semi-structured tables. FORTAP achieves state-of-the-art results on two representative downstream tasks, cell type classification and formula prediction, showing great potential of numerical-reasoning-aware pretraining.

Zhoujun Cheng, Haoyu Dong, Zhiruo Wang et al.

Tables are often created with hierarchies, but existing works on table reasoning mainly focus on flat tables and neglect hierarchical tables. Hierarchical tables challenge existing methods by hierarchical indexing, as well as implicit relationships of calculation and semantics. This work presents HiTab, a free and open dataset to study question answering (QA) and natural language generation (NLG) over hierarchical tables. HiTab is a cross-domain dataset constructed from a wealth of statistical reports (analyses) and Wikipedia pages, and has unique characteristics: (1) nearly all tables are hierarchical, and (2) both target sentences for NLG and questions for QA are revised from original, meaningful, and diverse descriptive sentences authored by analysts and professions of reports. (3) to reveal complex numerical reasoning in statistical analyses, we provide fine-grained annotations of entity and quantity alignment. HiTab provides 10,686 QA pairs and descriptive sentences with well-annotated quantity and entity alignment on 3,597 tables with broad coverage of table hierarchies and numerical reasoning types. Targeting hierarchical structure, we devise a novel hierarchy-aware logical form for symbolic reasoning over tables, which shows high effectiveness. Targeting complex numerical reasoning, we propose partially supervised training given annotations of entity and quantity alignment, which helps models to largely reduce spurious predictions in the QA task. In the NLG task, we find that entity and quantity alignment also helps NLG models to generate better results in a conditional generation setting. Experiment results of state-of-the-art baselines suggest that this dataset presents a strong challenge and a valuable benchmark for future research.

Yixin Wang, Zihao Lin, Zhe Xu et al.

Medical imaging plays a pivotal role in diagnosis and treatment in clinical practice. Inspired by the significant progress in automatic image captioning, various deep learning (DL)-based methods have been proposed to generate radiology reports for medical images. Despite promising results, previous works overlook the uncertainties of their models and are thus unable to provide clinicians with the reliability/confidence of the generated radiology reports to assist their decision-making. In this paper, we propose a novel method to explicitly quantify both the visual uncertainty and the textual uncertainty for DL-based radiology report generation. Such multi-modal uncertainties can sufficiently capture the model confidence degree at both the report level and the sentence level, and thus they are further leveraged to weight the losses for more comprehensive model optimization. Experimental results have demonstrated that the proposed method for model uncertainty characterization and estimation can produce more reliable confidence scores for radiology report generation, and the modified loss function, which takes into account the uncertainties, leads to better model performance on two public radiology report datasets. In addition, the quality of the automatically generated reports was manually evaluated by human raters and the results also indicate that the proposed uncertainties can reflect the variance of clinical diagnosis.

Haoyu Dong, Ze Wang, Qiang Qiu et al.

Image retrieval relies heavily on the quality of the data modeling and the distance measurement in the feature space. Building on the concept of image manifold, we first propose to represent the feature space of images, learned via neural networks, as a graph. Neighborhoods in the feature space are now defined by the geodesic distance between images, represented as graph vertices or manifold samples. When limited images are available, this manifold is sparsely sampled, making the geodesic computation and the corresponding retrieval harder. To address this, we augment the manifold samples with geometrically aligned text, thereby using a plethora of sentences to teach us about images. In addition to extensive results on standard datasets illustrating the power of text to help in image retrieval, a new public dataset based on CLEVR is introduced to quantify the semantic similarity between visual data and text data. The experimental results show that the joint embedding manifold is a robust representation, allowing it to be a better basis to perform image retrieval given only an image and a textual instruction on the desired modifications over the image

Yifan Xu, Kening Zhang, Haoyu Dong et al.

Exposure bias describes the phenomenon that a language model trained under the teacher forcing schema may perform poorly at the inference stage when its predictions are conditioned on its previous predictions unseen from the training corpus. Recently, several generative adversarial networks (GANs) and reinforcement learning (RL) methods have been introduced to alleviate this problem. Nonetheless, a common issue in RL and GANs training is the sparsity of reward signals. In this paper, we adopt two simple strategies, multi-range reinforcing, and multi-entropy sampling, to amplify and denoise the reward signal. Our model produces an improvement over competing models with regards to BLEU scores and road exam, a new metric we designed to measure the robustness against exposure bias in language models.