Publications (48)
Matching in the Wild: Learning Anatomical Embeddings for Multi-Modality Images
Xiaoyu Bai, Fan Bai, Xiaofei Huo +10
Radiotherapists require accurate registration of MR/CT images to effectively use information from both modalities. In a typical registration pipeline, rigid or affine transformatio…
Task Matters: Knowledge Requirements Shape LLM Responses to Context-Memory Conflict
Kaiser Sun, Fan Bai, Mark Dredze
Large language models (LLMs) draw on both contextual information and parametric memory, yet these sources can conflict. Prior studies have largely examined this issue in contextual…
One Polyp Identifies All: One-Shot Polyp Segmentation with SAM via Cascaded Priors and Iterative Prompt Evolution
Xinyu Mao, Xiaohan Xing, Fei Meng +4
Polyp segmentation is vital for early colorectal cancer detection, yet traditional fully supervised methods struggle with morphological variability and domain shifts, requiring fre…
Process-Level Representation of Scientific Protocols with Interactive Annotation
Ronen Tamari, Fan Bai, Alan Ritter +1
We develop Process Execution Graphs (PEG), a document-level representation of real-world wet lab biochemistry protocols, addressing challenges such as cross-sentence relations, lon…
Schema-Driven Information Extraction from Heterogeneous Tables
Fan Bai, Junmo Kang, Gabriel Stanovsky +3
In this paper, we explore the question of whether large language models can support cost-efficient information extraction from tables. We introduce schema-driven information extrac…
Air cold atmospheric plasma with patterns for anaplastic squamous cell carcinoma treatment
Fan Bai, Yingjie Lu, Yujie Zhi +8
In recent years, cold atmospheric plasma (CAP) using inert gas has been successfully applied for biomedicine, such as sterilization, wound healing, skin diseases, and tumor treatme…
Label Propagation on K-partite Graphs with Heterophily
Dingxiong Deng, Fan Bai, Yiqi Tang +3
In this paper, for the first time, we study label propagation in heterogeneous graphs under heterophily assumption. Homophily label propagation (i.e., two connected nodes share sim…
Entity Tracking via Effective Use of Multi-Task Learning Model and Mention-guided Decoding
Janvijay Singh, Fan Bai, Zhen Wang
Cross-task knowledge transfer via multi-task learning has recently made remarkable progress in general NLP tasks. However, entity tracking on the procedural text has not benefited…
Structured Minimally Supervised Learning for Neural Relation Extraction
Fan Bai, Alan Ritter
We present an approach to minimally supervised relation extraction that combines the benefits of learned representations and structured learning, and accurately predicts sentence-l…
PromptAgent: Strategic Planning with Language Models Enables Expert-level Prompt Optimization
Xinyuan Wang, Chenxi Li, Zhen Wang +6
Highly effective, task-specific prompts are often heavily engineered by experts to integrate detailed instructions and domain insights based on a deep understanding of both instinc…
Reading, Not Thinking: Understanding and Bridging the Modality Gap When Text Becomes Pixels in Multimodal LLMs
Kaiser Sun, Xiaochuang Yuan, Hongjun Liu +4
Multimodal large language models (MLLMs) can process text presented as images, yet they often perform worse than when the same content is provided as textual tokens. We systematica…
SegVol: Universal and Interactive Volumetric Medical Image Segmentation
Yuxin Du, Fan Bai, Tiejun Huang +1
Precise image segmentation provides clinical study with instructive information. Despite the remarkable progress achieved in medical image segmentation, there is still an absence o…
Solving some Navier-Stokes Equations with the initial conditions being some complex-valued periodic functions on
Tao Zhang, Alatancang Chen, Fan Bai
In this paper, we utilize some series and an iterative method to solve some Navier-Stokes equations with the initial conditions being some complex-valued periodic functions on $R^3…
Edit Probability for Scene Text Recognition
Fan Bai, Zhanzhan Cheng, Yi Niu +2
We consider the scene text recognition problem under the attention-based encoder-decoder framework, which is the state of the art. The existing methods usually employ a frame-wise…
Spatial clustering and common regulatory elements correlate with coordinated gene expression
Jingyu Zhang, Hengyu Chen, Ruoyan Li +4
Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes. In prokaryotic cells, a single-input-module motif with one tr…
M3D: Advancing 3D Medical Image Analysis with Multi-Modal Large Language Models
Fan Bai, Yuxin Du, Tiejun Huang +2
Medical image analysis is essential to clinical diagnosis and treatment, which is increasingly supported by multi-modal large language models (MLLMs). However, previous research ha…
Discrepancy-based Active Learning for Weakly Supervised Bleeding Segmentation in Wireless Capsule Endoscopy Images
Fan Bai, Xiaohan Xing, Yutian Shen +2
Weakly supervised methods, such as class activation maps (CAM) based, have been applied to achieve bleeding segmentation with low annotation efforts in Wireless Capsule Endoscopy (…
Low Temperature Dependence in 1H CRAMPS & 13C CP/MAS ssNMR Spectra of Alanine Enantiomers
Miao Zhang, Fan Bai, Wenqing Wang +1
1H RAMPS solid state NMR and 13C CP/MAS spectra of D- and L- alanine crystals were measured at temperature ranging from 220K to 295K. Some major points are as follows: (1)alpha-H a…
LLMs are Better Than You Think: Label-Guided In-Context Learning for Named Entity Recognition
Fan Bai, Hamid Hassanzadeh, Ardavan Saeedi +1
In-context learning (ICL) enables large language models (LLMs) to perform new tasks using only a few demonstrations. However, in Named Entity Recognition (NER), existing ICL method…
UAE: Universal Anatomical Embedding on Multi-modality Medical Images
Xiaoyu Bai, Fan Bai, Xiaofei Huo +5
Identifying specific anatomical structures (\textit{e.g.}, lesions or landmarks) in medical images plays a fundamental role in medical image analysis. Exemplar-based landmark detec…
SLPT: Selective Labeling Meets Prompt Tuning on Label-Limited Lesion Segmentation
Fan Bai, Ke Yan, Xiaoyu Bai +6
Medical image analysis using deep learning is often challenged by limited labeled data and high annotation costs. Fine-tuning the entire network in label-limited scenarios can lead…
Coupling between switching regulation and torque generation in bacterial flagellar motor
Fan Bai, Tohru Minamino, Zhanghan Wu +2
The bacterial flagellar motor plays a crucial role in both bacterial locomotion and chemotaxis. Recent experiments reveal that the switching dynamics of the motor depends on the mo…
Prediction of vaccination coverage level in the heterogeneous mixing population
Fan Bai, Qianyu Chen, Yizhuo Xu
Heterogeneity of population is a key factor in modeling the transmission of disease among the population and has huge impact on the outcome of the transmission. In order to investi…
Pre-train or Annotate? Domain Adaptation with a Constrained Budget
Fan Bai, Alan Ritter, Wei Xu
Recent work has demonstrated that pre-training in-domain language models can boost performance when adapting to a new domain. However, the costs associated with pre-training raise…
An age-of-infection model with both symptomatic and asymptomatic infections
Fan Bai
We formulate a general age-of-infection epidemic model with two pathways: the symptomatic infections and the asymptomatic infections. We then calculate the basic reproduction numbe…
Hierarchical Policy for Non-prehensile Multi-object Rearrangement with Deep Reinforcement Learning and Monte Carlo Tree Search
Fan Bai, Fei Meng, Jianbang Liu +2
Non-prehensile multi-object rearrangement is a robotic task of planning feasible paths and transferring multiple objects to their predefined target poses without grasping. It needs…
A Review of Salam Phase Transition in Protein Amino Acids: Implication for Biomolecular Homochirality
Fan Bai, Wenqing Wang
The origin of chirality, closely related to the evolution of life on the earth, has long been debated. In 1991, Abdus Salam suggested a novel approach to achieve biomolecular homoc…
Bacterial stress granule protects mRNA through ribonucleases exclusion
Linsen Pei, Yujia Xian, Xiaodan Yan +7
Membraneless droplets formed through liquid-liquid phase separation (LLPS) play a crucial role in mRNA storage, enabling organisms to swiftly respond to environmental changes. Howe…
Search for the Parity-Violating Effects between D- and L-alanine
Wenqing Wang, Fan Bai, Zhi Liang
The contribution of parity-violating effects to the phase transition of the D-/L-alanine crystals was confirmed by 1H CRAMPS solid state NMR, DC-magnetic susceptibilities and ultra…
Text Recognition in Real Scenarios with a Few Labeled Samples
Jinghuang Lin, Zhanzhan Cheng, Fan Bai +3
Scene text recognition (STR) is still a hot research topic in computer vision field due to its various applications. Existing works mainly focus on learning a general model with a…
Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation?
Pedro R. A. S. Bassi, Wenxuan Li, Yucheng Tang +50
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…
RASEC: Rescaling Acquisition Strategy with Energy Constraints under SE-OU Fusion Kernel for Active Trachea Palpation and Incision Recommendation in Laryngeal Region
Wenchao Yue, Fan Bai, Jianbang Liu +4
A novel palpation-based incision detection strategy in the laryngeal region, potentially for robotic tracheotomy, is proposed in this letter. A tactile sensor is introduced to meas…
C3-STISR: Scene Text Image Super-resolution with Triple Clues
Minyi Zhao, Miao Wang, Fan Bai +3
Scene text image super-resolution (STISR) has been regarded as an important pre-processing task for text recognition from low-resolution scene text images. Most recent approaches u…
Few-Shot Anaphora Resolution in Scientific Protocols via Mixtures of In-Context Experts
Nghia T. Le, Fan Bai, Alan Ritter
Anaphora resolution is an important task for information extraction across a range of languages, text genres, and domains, motivating the need for methods that do not require large…
Give me Some Hard Questions: Synthetic Data Generation for Clinical QA
Fan Bai, Keith Harrigian, Joel Stremmel +3
Clinical Question Answering (QA) systems enable doctors to quickly access patient information from electronic health records (EHRs). However, training these systems requires signif…
Temperature dependence of optical rotation study on parity-violating phase transition of D-, L-, and DL-alanine
Fan Bai, Miao Zhang, Wenqing Wang
Chiral molecules are characterized by a specific optical rotation angle. An experimental method was presented to dissect the temperature dependence of the optical rotation angle wi…
A Consumer-tier based Visual-Brain Machine Interface for Augmented Reality Glasses Interactions
Yuying Jiang, Fan Bai, Zicheng Zhang +9
Objective.Visual-Brain Machine Interface(V-BMI) has provide a novel interaction technique for Augmented Reality (AR) industries. Several state-of-arts work has demonstates its high…
Federated Face Recognition
Fan Bai, Jiaxiang Wu, Pengcheng Shen +2
Face recognition has been extensively studied in computer vision and artificial intelligence communities in recent years. An important issue of face recognition is data privacy, wh…
SynKB: Semantic Search for Synthetic Procedures
Fan Bai, Alan Ritter, Peter Madrid +2
In this paper we present SynKB, an open-source, automatically extracted knowledge base of chemical synthesis protocols. Similar to proprietary chemistry databases such as Reaxsys,…
Membraneless organelles formed by liquid-liquid phase separation increase bacterial fitness
Xin Jin, Ji-Eun Lee, Charley Schaefer +10
Liquid-liquid phase separation is emerging as a crucial phenomenon in several fundamental cell processes. A range of eukaryotic systems exhibit liquid condensates. However, their f…
Online Learning for Wireless Distributed Computing
Yi-Hsuan Kao, Kwame Wright, Bhaskar Krishnamachari +1
There has been a growing interest for Wireless Distributed Computing (WDC), which leverages collaborative computing over multiple wireless devices. WDC enables complex applications…
Demystifying Training-Time Augmentation for Data-Constrained Language Model Pretraining
Michael K. Chen, Xikun Zhang, Fan Bai +2
As AI labs approach a data ceiling where compute capacity outpaces the rate of new high-quality text generation, language model pretraining is shifting toward a data-constrained, c…
FIRE-Bench: Evaluating AI Agents on the Rediscovery of Scientific Insights
Zhen Wang, Fan Bai, Zhongyan Luo +9
Autonomous agents powered by large language models (LLMs) promise to accelerate scientific discovery end-to-end, but rigorously evaluating their capacity for verifiable discovery r…
EPD-Serve: A Flexible Multimodal EPD Disaggregation Inference Serving System On Ascend
Fan Bai, Pai Peng, Zhengzhi Tang +8
With the widespread adoption of large multimodal models, efficient inference across text, image, audio, and video modalities has become critical. However, existing multimodal infer…
Steps and bumps: precision extraction of discrete states of molecular machines using physically-based, high-throughput time series analysis
Max A. Little, Bradley C. Steel, Fan Bai +5
We report new statistical time-series analysis tools providing significant improvements in the rapid, precision extraction of discrete state dynamics from large databases of experi…
AON: Towards Arbitrarily-Oriented Text Recognition
Zhanzhan Cheng, Yangliu Xu, Fan Bai +3
Recognizing text from natural images is a hot research topic in computer vision due to its various applications. Despite the enduring research of several decades on optical charact…
Agent-as-Peer-Debriefer: A Multi-Agent Framework with Perspective-Based Refinement for Qualitative Analysis
Zhimin Lin, Kun Cheng, Zhiyao Shu +4
Large language models (LLMs) are increasingly used for qualitative data analysis (QDA), yet their outputs often miss the depth and nuance of human analysis. We argue this gap refle…
Focusing Attention: Towards Accurate Text Recognition in Natural Images
Zhanzhan Cheng, Fan Bai, Yunlu Xu +3
Scene text recognition has been a hot research topic in computer vision due to its various applications. The state of the art is the attention-based encoder-decoder framework that…