398,231 results on '"A. Shih"'
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2. Bridging the PLC Binary Analysis Gap: A Cross-Compiler Dataset and Neural Framework for Industrial Control Systems
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Achamyeleh, Yonatan Gizachew, Yu, Shih-Yuan, Araya, Gustavo Quirós, and Faruque, Mohammad Abdullah Al
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Computer Science - Software Engineering ,Computer Science - Machine Learning - Abstract
Industrial Control Systems (ICS) rely heavily on Programmable Logic Controllers (PLCs) to manage critical infrastructure, yet analyzing PLC executables remains challenging due to diverse proprietary compilers and limited access to source code. To bridge this gap, we introduce PLC-BEAD, a comprehensive dataset containing 2431 compiled binaries from 700+ PLC programs across four major industrial compilers (CoDeSys, GEB, OpenPLC-V2, OpenPLC-V3). This novel dataset uniquely pairs each binary with its original Structured Text source code and standardized functionality labels, enabling both binary-level and source-level analysis. We demonstrate the dataset's utility through PLCEmbed, a transformer-based framework for binary code analysis that achieves 93\% accuracy in compiler provenance identification and 42\% accuracy in fine-grained functionality classification across 22 industrial control categories. Through comprehensive ablation studies, we analyze how compiler optimization levels, code patterns, and class distributions influence model performance. We provide detailed documentation of the dataset creation process, labeling taxonomy, and benchmark protocols to ensure reproducibility. Both PLC-BEAD and PLCEmbed are released as open-source resources to foster research in PLC security, reverse engineering, and ICS forensics, establishing new baselines for data-driven approaches to industrial cybersecurity.
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- 2025
3. Zero Echo Time Functional MRI in Humans
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Özen, Ali Caglar, Liu, Shuai, Ilbey, Serhat, Bock, Michael, Emir, Uzay, and Shih, Yen-Yu Ian
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Physics - Medical Physics ,Quantitative Biology - Neurons and Cognition - Abstract
Motivation: Conventional echo planar imaging(EPI) based functional MRI(fMRI) uses the BOLD contrast to map activity changes in human brains. Introducing an efficient ZTE sequence for functional brain mapping can help address limitations of EPI and demonstrate the feasibility of using T1 related changes as a surrogate marker of brain activity. Goals: To test and optimize ZTE sequence for fMRI. Methods: A ZTE sequence with radial inside out spokes was used to prepare a dynamic imaging protocol that matches conventional EPI time course. Temporal SNR and sensitivity to susceptibility differences of ZTE were evaluated and the sequence was benchmarked against BOLD EPI in a task based visual fMRI study with healthy volunteers at 3T. Results: Phantom measurements confirmed sensitivity of the ZTE protocol to the oxygen concentration. Functional activation in primary visual cortex could be detected using ZTE. Resting state networks could also be identified using independent component analysis. Discussion: ZTE-based fMRI is proposed for mapping functional activation in human brain. ZTE is robust against susceptibility artefacts and significantly reduces acoustic noise. Radial sampling pattern allows for high undersampling rates to increase temporal resolution., Comment: 20 pages, 8 figures
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- 2025
4. Strength Estimation and Human-Like Strength Adjustment in Games
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Chen, Chun Jung, Shih, Chung-Chin, and Wu, Ti-Rong
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Computer Science - Artificial Intelligence ,Computer Science - Human-Computer Interaction ,Computer Science - Machine Learning - Abstract
Strength estimation and adjustment are crucial in designing human-AI interactions, particularly in games where AI surpasses human players. This paper introduces a novel strength system, including a strength estimator (SE) and an SE-based Monte Carlo tree search, denoted as SE-MCTS, which predicts strengths from games and offers different playing strengths with human styles. The strength estimator calculates strength scores and predicts ranks from games without direct human interaction. SE-MCTS utilizes the strength scores in a Monte Carlo tree search to adjust playing strength and style. We first conduct experiments in Go, a challenging board game with a wide range of ranks. Our strength estimator significantly achieves over 80% accuracy in predicting ranks by observing 15 games only, whereas the previous method reached 49% accuracy for 100 games. For strength adjustment, SE-MCTS successfully adjusts to designated ranks while achieving a 51.33% accuracy in aligning to human actions, outperforming a previous state-of-the-art, with only 42.56% accuracy. To demonstrate the generality of our strength system, we further apply SE and SE-MCTS to chess and obtain consistent results. These results show a promising approach to strength estimation and adjustment, enhancing human-AI interactions in games. Our code is available at https://rlg.iis.sinica.edu.tw/papers/strength-estimator., Comment: Accepted by the Thirteenth International Conference on Learning Representations (ICLR 2025)
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- 2025
5. Robust Super-Moir\'e in Large Angle Single-Twist Bilayers
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Li, Yanxing, Shi, Chuqiao, Zhang, Fan, Liu, Xiaohui, Xue, Yuan, Ha, Viet-Anh, Gao, Qiang, Dong, Chengye, Lin, Yu-chuan, Holtzman, Luke N, Morales-Durán, Nicolas, Kim, Hyunsue, Jiang, Yi, Holbrook, Madisen, Hone, James, Barmak, Katayun, Robinson, Joshua, Li, Xiaoqin, Giustino, Feliciano, Khalaf, Eslam, Han, Yimo, and Shih, Chih-Kang
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Condensed Matter - Materials Science - Abstract
Forming long wavelength moir\'e superlattices (MSL) at small-angle twist van der Waals (vdW) bilayers has been a key approach to creating moir\'e flat bands. The small-angle twist, however, leads to strong lattice reconstruction, causing domain walls and moir\'e disorders, which pose considerable challenges in engineering such platforms. At large twist angles, the rigid lattices render a more robust, but shorter wavelength MSL, making it difficult to engineer flat bands. Here, we depict a novel approach to tailoring robust super-moir\'e (SM) structures that combines the advantages of both small-twist and large-twist transition metal dichalcogenides (TMDs) bilayers using only a single twist angle near a commensurate angle. Structurally, we unveil the spontaneous formation of a periodic arrangement of three inequivalent commensurate moir\'e (CM) stacking, where the angle deviation from the commensurate angle can tune the periodicity. Electronically, we reveal a large set of van Hove singularities (VHSs) that indicate strong band hybridization, leading to flat bands near the valence band maximum. Our study paves the way for a new platform of robust SM bilayers with structural rigidity and controllable wavelength, extending the investigation of the interplay among band topology, quantum geometry, and moir\'e superconductivity to the large twist angle regime.
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- 2025
6. The JCMT BISTRO Survey: Magnetic Fields Align with Orbital Structure in the Galactic Center
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Karoly, Janik, Ward-Thompson, Derek, Pattle, Kate, Longmore, Steven N., Di Francesco, James, Whitworth, Anthony, Johnstone, Doug, Sadavoy, Sarah, Koch, Patrick M., Yang, Meng-Zhe, Furuya, Ray, Lu, Xing, Tamura, Motohide, Debattista, Victor, Eden, David, Hwang, Jihye, Poidevin, Frederick, Najimudeen, Bijas, Chen, Szu-Ting, Chung, Eun Jung, Coude, Simon, Lin, Sheng-Jun, Doi, Yasuo, Onaka, Takashi, Fanciullo, Lapo, Liu, Tie, Li, Guangxing, Bastien, Pierre, Hasegawa, Tetsuo, Kwon, Woojin, Lai, Shih-Ping, and Qiu, Keping
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Astrophysics - Astrophysics of Galaxies - Abstract
We present the magnetic field in the dense material of the Central Molecular Zone (CMZ) of the Milky Way, traced in 850 $\mu$m polarized dust emission as part of the James Clerk Maxwell Telescope (JCMT) B-fields In STar-forming Region Observations (BISTRO) Survey. We observe a highly ordered magnetic field across the CMZ between Sgr B2 and Sgr C, which is strongly preferentially aligned with the orbital gas flows within the clouds of the CMZ. We find that the observed relative orientations are non-random at a $>$99% confidence level and are consistent with models in which the magnetic field vectors are aligned within 30$^{o}$ to the gas flows in 3D. The deviations from aligned magnetic fields are most prominent at positive Galactic longitudes, where the CMZ clouds are more massive, denser, and more actively forming stars. Our observed strongly preferentially parallel magnetic field morphology leads us to hypothesize that in the absence of star formation, the magnetic field in the CMZ is entrained in the orbital gas flows around Sgr A$^{*}$, while gravitational collapse and feedback in star-forming regions can locally reorder the field. This magnetic field behavior is similar to that observed in the CMZ of the nuclear starburst galaxy NGC 253. This suggests that despite its current low star formation rate, the CMZ of the Milky Way is analogous to those of more distant, actively star-forming, galaxies., Comment: Submitted to ApJL. 15 pages, 8 figures (4 in main text, 4 in appendices), 5 appendices
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- 2025
7. Human-Centric Community Detection in Hybrid Metaverse Networks with Integrated AI Entities
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Chiu, Shih-Hsuan, Teng, Ya-Wen, Yang, De-Nian, and Chen, Ming-Syan
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Computer Science - Social and Information Networks ,Computer Science - Artificial Intelligence - Abstract
Community detection is a cornerstone problem in social network analysis (SNA), aimed at identifying cohesive communities with minimal external links. However, the rise of generative AI and Metaverse introduce complexities by creating hybrid human-AI social networks (denoted by HASNs), where traditional methods fall short, especially in human-centric settings. This paper introduces a novel community detection problem in HASNs (denoted by MetaCD), which seeks to enhance human connectivity within communities while reducing the presence of AI nodes. Effective processing of MetaCD poses challenges due to the delicate trade-off between excluding certain AI nodes and maintaining community structure. To address this, we propose CUSA, an innovative framework incorporating AI-aware clustering techniques that navigate this trade-off by selectively retaining AI nodes that contribute to community integrity. Furthermore, given the scarcity of real-world HASNs, we devise four strategies for synthesizing these networks under various hypothetical scenarios. Empirical evaluations on real social networks, reconfigured as HASNs, demonstrate the effectiveness and practicality of our approach compared to traditional non-deep learning and graph neural network (GNN)-based methods., Comment: 15 pages, Accepted for publication in the ACM WWW 2025
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- 2025
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8. On K\'ahler-Einstein Currents
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Chen, Yifan, Chiu, Shih-Kai, Hallgren, Max, Székelyhidi, Gábor, Tô, Tat Dat, and Tong, Freid
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Mathematics - Differential Geometry ,53C25 - Abstract
We show that a general class of singular K\"ahler metrics with Ricci curvature bounded below define K\"ahler currents. In particular the result applies to singular K\"ahler-Einstein metrics on klt pairs, and an analogous result holds for K\"ahler-Ricci solitons. In addition we show that if a singular K\"ahler-Einstein metric can be approximated by smooth metrics on a resolution whose Ricci curvature has negative part that is bounded uniformly in $L^p$ for $p > \frac{2n-1}{n}$, then the metric defines an RCD space., Comment: 20 pages
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- 2025
9. YNote: A Novel Music Notation for Fine-Tuning LLMs in Music Generation
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Lu, Shao-Chien, Yeh, Chen-Chen, Cho, Hui-Lin, Hsu, Chun-Chieh, Hsu, Tsai-Ling, Wu, Cheng-Han, Shih, Timothy K., and Lin, Yu-Cheng
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Computer Science - Sound ,Computer Science - Artificial Intelligence ,Electrical Engineering and Systems Science - Audio and Speech Processing - Abstract
The field of music generation using Large Language Models (LLMs) is evolving rapidly, yet existing music notation systems, such as MIDI, ABC Notation, and MusicXML, remain too complex for effective fine-tuning of LLMs. These formats are difficult for both machines and humans to interpret due to their variability and intricate structure. To address these challenges, we introduce YNote, a simplified music notation system that uses only four characters to represent a note and its pitch. YNote's fixed format ensures consistency, making it easy to read and more suitable for fine-tuning LLMs. In our experiments, we fine-tuned GPT-2 (124M) on a YNote-encoded dataset and achieved BLEU and ROUGE scores of 0.883 and 0.766, respectively. With just two notes as prompts, the model was able to generate coherent and stylistically relevant music. We believe YNote offers a practical alternative to existing music notations for machine learning applications and has the potential to significantly enhance the quality of music generation using LLMs.
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- 2025
10. Hookpad Aria: A Copilot for Songwriters
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Donahue, Chris, Wu, Shih-Lun, Kim, Yewon, Carlton, Dave, Miyakawa, Ryan, and Thickstun, John
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Computer Science - Sound ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning - Abstract
We present Hookpad Aria, a generative AI system designed to assist musicians in writing Western pop songs. Our system is seamlessly integrated into Hookpad, a web-based editor designed for the composition of lead sheets: symbolic music scores that describe melody and harmony. Hookpad Aria has numerous generation capabilities designed to assist users in non-sequential composition workflows, including: (1) generating left-to-right continuations of existing material, (2) filling in missing spans in the middle of existing material, and (3) generating harmony from melody and vice versa. Hookpad Aria is also a scalable data flywheel for music co-creation -- since its release in March 2024, Aria has generated 318k suggestions for 3k users who have accepted 74k into their songs. More information about Hookpad Aria is available at https://www.hooktheory.com/hookpad/aria, Comment: Extended abstract presented in the Late-Breaking Demo Session at ISMIR 2024 (ISMIR LBD 2024)
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- 2025
11. RAILS: Risk-Aware Iterated Local Search for Joint SLA Decomposition and Service Provider Management in Multi-Domain Networks
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Hsu, Cyril Shih-Huan, Papagianni, Chrysa, and Grosso, Paola
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Computer Science - Networking and Internet Architecture ,Computer Science - Machine Learning - Abstract
The emergence of the fifth generation (5G) technology has transformed mobile networks into multi-service environments, necessitating efficient network slicing to meet diverse Service Level Agreements (SLAs). SLA decomposition across multiple network domains, each potentially managed by different service providers, poses a significant challenge due to limited visibility into real-time underlying domain conditions. This paper introduces Risk-Aware Iterated Local Search (RAILS), a novel risk model-driven meta-heuristic framework designed to jointly address SLA decomposition and service provider selection in multi-domain networks. By integrating online risk modeling with iterated local search principles, RAILS effectively navigates the complex optimization landscape, utilizing historical feedback from domain controllers. We formulate the joint problem as a Mixed-Integer Nonlinear Programming (MINLP) problem and prove its NP-hardness. Extensive simulations demonstrate that RAILS achieves near-optimal performance, offering an efficient, real-time solution for adaptive SLA management in modern multi-domain networks., Comment: The paper has been submitted to IEEE HPSR 2025
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- 2025
12. Probing Large Language Models in Reasoning and Translating Complex Linguistic Puzzles
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Lin, Zheng-Lin, Shih, Yu-Fei, and Hsieh, Shu-Kai
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Computer Science - Computation and Language - Abstract
This paper investigates the utilization of Large Language Models (LLMs) for solving complex linguistic puzzles, a domain requiring advanced reasoning and adept translation capabilities akin to human cognitive processes. We explore specific prompting techniques designed to enhance ability of LLMs to reason and elucidate their decision-making pathways, with a focus on Input-Output Prompting (IO), Chain-of-Thought Prompting (CoT), and Solo Performance Prompting (SPP). Utilizing datasets from the Puzzling Machine Competition and various Linguistics Olympiads, we employ a comprehensive set of metrics to assess the performance of GPT-4 0603, a prominent LLM, across these prompting methods. Our findings illuminate the potential of LLMs in linguistic reasoning and complex translation tasks, highlighting their capabilities and identifying limitations in the context of linguistic puzzles. This research contributes significantly to the broader field of Natural Language Processing (NLP) by providing insights into the optimization of LLM applications for improved reasoning and translation accuracy, thereby enriching the ongoing dialogue in NLP advancements., Comment: 8 pages, 8 figures
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- 2025
13. Imitation Game for Adversarial Disillusion with Multimodal Generative Chain-of-Thought Role-Play
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Chang, Ching-Chun, Chen, Fan-Yun, Gu, Shih-Hong, Gao, Kai, Wang, Hanrui, and Echizen, Isao
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Computer Science - Artificial Intelligence ,Computer Science - Cryptography and Security ,Computer Science - Computer Vision and Pattern Recognition - Abstract
As the cornerstone of artificial intelligence, machine perception confronts a fundamental threat posed by adversarial illusions. These adversarial attacks manifest in two primary forms: deductive illusion, where specific stimuli are crafted based on the victim model's general decision logic, and inductive illusion, where the victim model's general decision logic is shaped by specific stimuli. The former exploits the model's decision boundaries to create a stimulus that, when applied, interferes with its decision-making process. The latter reinforces a conditioned reflex in the model, embedding a backdoor during its learning phase that, when triggered by a stimulus, causes aberrant behaviours. The multifaceted nature of adversarial illusions calls for a unified defence framework, addressing vulnerabilities across various forms of attack. In this study, we propose a disillusion paradigm based on the concept of an imitation game. At the heart of the imitation game lies a multimodal generative agent, steered by chain-of-thought reasoning, which observes, internalises and reconstructs the semantic essence of a sample, liberated from the classic pursuit of reversing the sample to its original state. As a proof of concept, we conduct experimental simulations using a multimodal generative dialogue agent and evaluates the methodology under a variety of attack scenarios.
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- 2025
14. The Influence of V-Defects, Leakage, and Random Alloy Fluctuations on the Carrier Transport in Red InGaN MQW LEDs
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Huang, Huai-Chin, Chen, Shih-Min, Weisbuch, Claude, Speck, James S., and Wu, Yuh-Renn
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Physics - Applied Physics ,Condensed Matter - Mesoscale and Nanoscale Physics - Abstract
Red InGaN-based light-emitting diodes (LEDs) exhibit lower internal quantum efficiencies (IQEs) than violet, blue, and green InGaN LEDs due to a reduction in radiative recombination rates relative to non-radiative recombination rates as the indium composition increases. Additionally, the larger polarization and band offset barriers between high indium content InGaN quantum wells and GaN quantum barriers increase the forward voltage. In blue and green LEDs, random alloy fluctuations and V-defects play a key role in reducing the forward voltage. When V-defects are present, either naturally or intentionally introduced, they create an alternative path for carrier injection into the MQWs through the V-defect sidewalls. This injection mechanism explains the turn-on voltages of green LEDs. However, in InGaN red LEDs, these two phenomena do not reduce the forward voltage as effectively as in blue and green LEDs, and consequently, the computed forward voltage remains significantly higher than the measured one. Furthermore, currents are observed at low voltages before the turn-on voltage (\(V < \hbar\omega/e = 2.0 \, \text{V}\)) of red LEDs. To address this, we introduce dislocation-induced tail states in the modeling, suggesting that leakage current through these states may play a significant role both below and at turn-on voltages. The simulation also indicates that leakage carriers below turn-on accumulate, partially diffuse in the QWs, screen the polarization-induced barrier in the low injection regime, and further reduce the forward voltage. Despite these beneficial effects, a drawback of dislocation-induced tail states is the enhanced nonradiative recombination in the dislocation line region. This study provides a detailed analysis of device injection physics in InGaN QW red LEDs and outlines potential optimization strategies., Comment: 8 pages, 8 figures
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- 2025
15. Reasoning Over the Glyphs: Evaluation of LLM's Decipherment of Rare Scripts
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Shih, Yu-Fei, Lin, Zheng-Lin, and Hsieh, Shu-Kai
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Computer Science - Computation and Language ,Computer Science - Machine Learning ,J.5 ,I.2.7 - Abstract
We explore the capabilities of LVLMs and LLMs in deciphering rare scripts not encoded in Unicode. We introduce a novel approach to construct a multimodal dataset of linguistic puzzles involving such scripts, utilizing a tokenization method for language glyphs. Our methods include the Picture Method for LVLMs and the Description Method for LLMs, enabling these models to tackle these challenges. We conduct experiments using prominent models, GPT-4o, Gemini, and Claude 3.5 Sonnet, on linguistic puzzles. Our findings reveal the strengths and limitations of current AI methods in linguistic decipherment, highlighting the impact of Unicode encoding on model performance and the challenges of modeling visual language tokens through descriptions. Our study advances understanding of AI's potential in linguistic decipherment and underscores the need for further research., Comment: 7 pages, 3 figures
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- 2025
16. PuzzleGPT: Emulating Human Puzzle-Solving Ability for Time and Location Prediction
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Ayyubi, Hammad, Feng, Xuande, Liu, Junzhang, Lin, Xudong, Wang, Zhecan, and Chang, Shih-Fu
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning - Abstract
The task of predicting time and location from images is challenging and requires complex human-like puzzle-solving ability over different clues. In this work, we formalize this ability into core skills and implement them using different modules in an expert pipeline called PuzzleGPT. PuzzleGPT consists of a perceiver to identify visual clues, a reasoner to deduce prediction candidates, a combiner to combinatorially combine information from different clues, a web retriever to get external knowledge if the task can't be solved locally, and a noise filter for robustness. This results in a zero-shot, interpretable, and robust approach that records state-of-the-art performance on two datasets -- TARA and WikiTilo. PuzzleGPT outperforms large VLMs such as BLIP-2, InstructBLIP, LLaVA, and even GPT-4V, as well as automatically generated reasoning pipelines like VisProg, by at least 32% and 38%, respectively. It even rivals or surpasses finetuned models., Comment: NAACL 2025 Findings
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- 2025
17. ENTER: Event Based Interpretable Reasoning for VideoQA
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Ayyubi, Hammad, Liu, Junzhang, Asgarov, Ali, Hakim, Zaber Ibn Abdul, Sarker, Najibul Haque, Wang, Zhecan, Tang, Chia-Wei, Alomari, Hani, Atabuzzaman, Md., Lin, Xudong, Dyava, Naveen Reddy, Chang, Shih-Fu, and Thomas, Chris
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence - Abstract
In this paper, we present ENTER, an interpretable Video Question Answering (VideoQA) system based on event graphs. Event graphs convert videos into graphical representations, where video events form the nodes and event-event relationships (temporal/causal/hierarchical) form the edges. This structured representation offers many benefits: 1) Interpretable VideoQA via generated code that parses event-graph; 2) Incorporation of contextual visual information in the reasoning process (code generation) via event graphs; 3) Robust VideoQA via Hierarchical Iterative Update of the event graphs. Existing interpretable VideoQA systems are often top-down, disregarding low-level visual information in the reasoning plan generation, and are brittle. While bottom-up approaches produce responses from visual data, they lack interpretability. Experimental results on NExT-QA, IntentQA, and EgoSchema demonstrate that not only does our method outperform existing top-down approaches while obtaining competitive performance against bottom-up approaches, but more importantly, offers superior interpretability and explainability in the reasoning process.
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- 2025
18. A2SB: Audio-to-Audio Schrodinger Bridges
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Kong, Zhifeng, Shih, Kevin J, Nie, Weili, Vahdat, Arash, Lee, Sang-gil, Santos, Joao Felipe, Jukic, Ante, Valle, Rafael, and Catanzaro, Bryan
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Computer Science - Sound ,Computer Science - Machine Learning ,Electrical Engineering and Systems Science - Audio and Speech Processing - Abstract
Audio in the real world may be perturbed due to numerous factors, causing the audio quality to be degraded. The following work presents an audio restoration model tailored for high-res music at 44.1kHz. Our model, Audio-to-Audio Schrodinger Bridges (A2SB), is capable of both bandwidth extension (predicting high-frequency components) and inpainting (re-generating missing segments). Critically, A2SB is end-to-end without need of a vocoder to predict waveform outputs, able to restore hour-long audio inputs, and trained on permissively licensed music data. A2SB is capable of achieving state-of-the-art bandwidth extension and inpainting quality on several out-of-distribution music test sets. Our demo website is https: //research.nvidia.com/labs/adlr/A2SB/.
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- 2025
19. Kilometer-Scale E3SM Land Model Simulation over North America
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Wang, Dali, Wang, Chen, Cao, Qinglei, Schwartz, Peter, Yuan, Fengming, Krishna, Jayesh, Wu, Danqing, Ricciuto, Danial, Thornton, Peter, Kao, Shih-Chieh, Thornton, Michele, and Mohror, Kathryn
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Computer Science - Computational Engineering, Finance, and Science - Abstract
The development of a kilometer-scale E3SM Land Model (km-scale ELM) is an integral part of the E3SM project, which seeks to advance energy-related Earth system science research with state-of-the-art modeling and simulation capabilities on exascale computing systems. Through the utilization of high-fidelity data products, such as atmospheric forcing and soil properties, the km-scale ELM plays a critical role in accurately modeling geographical characteristics and extreme weather occurrences. The model is vital for enhancing our comprehension and prediction of climate patterns, as well as their effects on ecosystems and human activities. This study showcases the first set of full-capability, km-scale ELM simulations over various computational domains, including simulations encompassing 21.6 million land gridcells, reflecting approximately 21.5 million square kilometers of North America at a 1 km x 1 km resolution. We present the largest km-scale ELM simulation using up to 100,800 CPU cores across 2,400 nodes. This continental-scale simulation is 300 times larger than any previous studies, and the computational resources used are about 400 times larger than those used in prior efforts. Both strong and weak scaling tests have been conducted, revealing exceptional performance efficiency and resource utilization. The km-scale ELM uses the common E3SM modeling infrastructure and a general data toolkit known as KiloCraft. Consequently, it can be readily adapted for both fully-coupled E3SM simulations and data-driven simulations over specific areas, ranging from a single gridcell to the entire North America.
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- 2025
20. In Vivo Study of Bone Growth Around Additively Manufactured Implants with Ti-6Al-4V and Bioactive Glass Powder Composites
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Lee, Chih-Yu, Kung, Pei-Ching, Huang, Chih-Chieh, Shih, Shao-Ju, Huang, E-Wen, Chen, San-Yuan, Wu, Meng-Huang, and Tsou, Nien-Ti
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Physics - Medical Physics ,Quantitative Biology - Tissues and Organs - Abstract
Osseointegration is crucial to the success of biomedical implants. Additive manufacturing of implants offers a high degree of design freedom, enabling precise control over implant geometry and material composition. Bioactive glass (BG) can substantially enhance bone binding and bioactivity; however, limited research has been conducted on its incorporation into additively manufactured implants. The performance of BG varies depending on the incorporation method, and the spatial and temporal evolution of its integration remains unclear. In this study, we synthesized Ti-6Al-4V/58S BG composites by using the selective laser melting method and systematically compared the effects of BG coating and doping in additively manufactured implants. In vivo histological results from animal tests were statistically analyzed and discussed in terms of osseointegration over 4- and 12-week periods. Bone-to-implant contact (BIC) and bone density (BD) were used as quantitative metrics to evaluate interactions between the implants and surrounding bone. Our findings indicate that both BG-doped and BG-coated implants accelerated bone ingrowth during the early stages of healing. BG-coated implants demonstrated a greater improvement than did pure 3D-printed Ti-6Al-4V implants. However, the effects of BG became nonsignificant during the later healing stage (12 weeks). This study provides a foundation for systematically investigating BG incorporation methods in 3D-printed biomedical implants and their effect on osseointegration.
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- 2025
21. Matrix Ordering through Spectral and Nilpotent Structures in Totally Ordered Complex Number Fields
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Chang, Shih-Yu
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Mathematics - Functional Analysis ,Mathematics - Operator Algebras ,Quantum Physics - Abstract
Matrix inequalities play a pivotal role in mathematics, generalizing scalar inequalities and providing insights into linear operator structures. However, the widely used L\"owner ordering, which relies on real-valued eigenvalues, is limited to Hermitian matrices, restricting its applicability to non-Hermitian systems increasingly relevant in fields like non-Hermitian physics. To overcome this, we develop a total ordering relation for complex numbers, enabling comparisons of the spectral components of general matrices with complex eigenvalues. Building on this, we introduce the Spectral and Nilpotent Ordering (SNO), a partial order for arbitrary matrices of the same dimensions. We further establish a theoretical framework for majorization ordering with complex-valued functions, which aids in refining SNO and analyzing spectral components. An additional result is the extension of the Schur--Ostrowski criterion to the complex domain. Moreover, we characterize Jordan blocks of matrix functions using a generalized dominance order for nilpotent components, facilitating systematic analysis of non-diagonalizable matrices. Finally, we derive monotonicity and convexity conditions for functions under the SNO framework, laying a new mathematical foundation for advancing matrix analysis.
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- 2025
22. Evidence for the gravity-driven and magnetically-regularized gas flows feeding the massive protostellar cluster in Cep A
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Sandhyarani, Panigrahy, Eswaraiah, Chakali, Vázquez-Semadeni, Enrique, Gómez, Gilberto C., Thieme, Travis J., Samal, Manash R., Li, Di, Wang, Jia-Wei, Lai, Shih-Ping, Chen, Wen-Ping, and Ojha, D. K.
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Astrophysics - Astrophysics of Galaxies - Abstract
The hierarchical interplay among gravity, magnetic fields, and turbulent gas flows in delivering the necessary material to form massive protostellar clusters remains enigmatic. We have performed high-resolution (beam size $\sim$14 arcsec $\simeq$ 0.05 pc at a distance 725 pc) 850 $\mu$m dust polarization and C$^{18}$O molecular line observations of Cepheus A (Cep A), the second closest massive star-forming region, using the 15-meter James Clerk Maxwell Telescope (JCMT) along with the SCUBA-2/POL-2 and HARP instruments. Our key analyses reveal that (i) morphologically, all three fields--gravitational (G), magnetic (B), and kinetic (K) fields--are aligned with each other, and (ii) energetically, they exhibit a hierarchical relationship with gravitational ($E_{\mathrm{G}}$) > magnetic ($E_{\mathrm{B}}$) > kinetic ($E_{\mathrm{K}}$). Gravity dominates in Cep A clump and, as a primary active player, dictates the other two agents. Consequently, gravity plays two active roles: (i) induces gas flows and (ii) drags B-field lines toward the gravitational trough. Since magnetic energy dominates kinetic energy, $E_{\mathrm{B}}$ > $E_{\mathrm{K}}$, the "dragged-in" B-field as a secondary active player can mitigate turbulence and instabilities, thereby regularizing gas flows into a more ordered configuration. At the $\sim$0.60 pc clump scale, these flows deliver material at a substantially high rate of $\sim$ 2.1$\times$10$^{-4}$ M$_{\odot}$ yr$^{-1}$ toward the cluster center. Our study, for the first time, presents new insights into how B-fields and turbulent gas flows passively assist the active role of gravity in the formation of a protostellar cluster, contrasting with the standard notion that these agents primarily oppose gravitational collapse., Comment: 33 pages, 6 figures in the main text and 8 figures in the supplementary material, Submitted, and comments are welcome
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- 2025
23. Local Existence of a Classical Solution for Quasi-Linear Hyperbolic Systems
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Chou, Shih-Wei, Lin, Ying-Chieh, and Tsuge, Naoki
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Mathematics - Analysis of PDEs - Abstract
In this paper, we study quasi-linear hyperbolic systems. Our goal in this paper is to provide a new proof of local existence of a classical solution for the system. Most difficult point is to prove the convergence of the derivative of approximate solutions by the Arzela-Ascoli theorem.
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- 2025
24. An Efficiency Firmware Verification Framework for Public Key Infrastructure with Smart Grid and Energy Storage System
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Shih, Jhih-Zen, Chuang, Cheng-Che, Huang, Hong-Sheng, Chen, Hsuan-Tung, and Sun, Hung-Min
- Subjects
Computer Science - Cryptography and Security - Abstract
As a critical component of electrical energy infrastructure, the smart grid system has become indispensable to the energy sector. However, the rapid evolution of smart grids has attracted numerous nation-state actors seeking to disrupt the power infrastructure of adversarial nations. This development underscores the urgent need to establish secure mechanisms for firmware updates, with firmware signing and verification serving as pivotal elements in safeguarding system integrity. In this work, we propose a digital signing and verification framework grounded in Public Key Infrastructure (PKI), specifically tailored for resource-constrained devices such as smart meters. The framework utilizes the Concise Binary Object Representation (CBOR) and Object Signing and Encryption (COSE) formats to achieve efficient da-ta encapsulation and robust security features. Our approach not only en-sures the secure deployment of firmware updates against the convergence of information technology (IT) and operational technology (OT) attacks but also addresses performance bottlenecks stemming from device limitations, thereby enhancing the overall reliability and stability of the smart grid sys-tem., Comment: 10pages, 5 figures
- Published
- 2025
25. A CT Image Classification Network Framework for Lung Tumors Based on Pre-trained MobileNetV2 Model and Transfer learning, And Its Application and Market Analysis in the Medical field
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Gao, Ziyang, Tian, Yong, Lin, Shih-Chi, and Lin, Junghua
- Subjects
Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition - Abstract
In the medical field, accurate diagnosis of lung cancer is crucial for treatment. Traditional manual analysis methods have significant limitations in terms of accuracy and efficiency. To address this issue, this paper proposes a deep learning network framework based on the pre-trained MobileNetV2 model, initialized with weights from the ImageNet-1K dataset (version 2). The last layer of the model (the fully connected layer) is replaced with a new fully connected layer, and a softmax activation function is added to efficiently classify three types of lung cancer CT scan images. Experimental results show that the model achieves an accuracy of 99.6% on the test set, with significant improvements in feature extraction compared to traditional models.With the rapid development of artificial intelligence technologies, deep learning applications in medical image processing are bringing revolutionary changes to the healthcare industry. AI-based lung cancer detection systems can significantly improve diagnostic efficiency, reduce the workload of doctors, and occupy an important position in the global healthcare market. The potential of AI to improve diagnostic accuracy, reduce medical costs, and promote precision medicine will have a profound impact on the future development of the healthcare industry.
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- 2025
26. Track reconstruction as a service for collider physics
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Zhao, Haoran, Chou, Yuan-Tang, Yao, Yao, Ju, Xiangyang, Feng, Yongbin, McCormack, William Patrick, Cochran-Branson, Miles, Schulte, Jan-Frederik, Liu, Miaoyuan, Duarte, Javier, Harris, Philip, Hsu, Shih-Chieh, Pedro, Kevin, and Tran, Nhan
- Subjects
Physics - Instrumentation and Detectors ,Computer Science - Distributed, Parallel, and Cluster Computing ,High Energy Physics - Experiment - Abstract
Optimizing charged-particle track reconstruction algorithms is crucial for efficient event reconstruction in Large Hadron Collider (LHC) experiments due to their significant computational demands. Existing track reconstruction algorithms have been adapted to run on massively parallel coprocessors, such as graphics processing units (GPUs), to reduce processing time. Nevertheless, challenges remain in fully harnessing the computational capacity of coprocessors in a scalable and non-disruptive manner. This paper proposes an inference-as-a-service approach for particle tracking in high energy physics experiments. To evaluate the efficacy of this approach, two distinct tracking algorithms are tested: Patatrack, a rule-based algorithm, and Exa$.$TrkX, a machine learning-based algorithm. The as-a-service implementations show enhanced GPU utilization and can process requests from multiple CPU cores concurrently without increasing per-request latency. The impact of data transfer is minimal and insignificant compared to running on local coprocessors. This approach greatly improves the computational efficiency of charged particle tracking, providing a solution to the computing challenges anticipated in the High-Luminosity LHC era., Comment: 19 pages, 8 figures, submitted to JINST
- Published
- 2025
27. Enhancing Virtual Try-On with Synthetic Pairs and Error-Aware Noise Scheduling
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Li, Nannan, Shih, Kevin J., and Plummer, Bryan A.
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Given an isolated garment image in a canonical product view and a separate image of a person, the virtual try-on task aims to generate a new image of the person wearing the target garment. Prior virtual try-on works face two major challenges in achieving this goal: a) the paired (human, garment) training data has limited availability; b) generating textures on the human that perfectly match that of the prompted garment is difficult, often resulting in distorted text and faded textures. Our work explores ways to tackle these issues through both synthetic data as well as model refinement. We introduce a garment extraction model that generates (human, synthetic garment) pairs from a single image of a clothed individual. The synthetic pairs can then be used to augment the training of virtual try-on. We also propose an Error-Aware Refinement-based Schr\"odinger Bridge (EARSB) that surgically targets localized generation errors for correcting the output of a base virtual try-on model. To identify likely errors, we propose a weakly-supervised error classifier that localizes regions for refinement, subsequently augmenting the Schr\"odinger Bridge's noise schedule with its confidence heatmap. Experiments on VITON-HD and DressCode-Upper demonstrate that our synthetic data augmentation enhances the performance of prior work, while EARSB improves the overall image quality. In user studies, our model is preferred by the users in an average of 59% of cases.
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- 2025
28. Proton Radiation Damage and Annealing of COSI p-type Cross-strip HPGe Detectors
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Haight, Sophia E., Boggs, Steven E., Brewster, Gabriel, Pike, Sean N., Roberts, Jarred M., Shih, Albert Y., Szornel, Joanna M., Tomsick, John A., Valluvan, Aravind B., and Zoglauer, Andreas
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Physics - Instrumentation and Detectors ,Astrophysics - Instrumentation and Methods for Astrophysics ,Nuclear Experiment - Abstract
In order to understand the effects of a space radiation environment on cross-strip germanium detectors, we investigated the effects of high-energy proton damage on a COSI detector and the capabilities of high-temperature annealing in repairing detector spectral resolution. We irradiated a COSI-balloon cross-strip high-purity germanium (HPGe) detector with a high-energy proton fluence corresponding to ~10 years in a space radiation environment. We repaired the resulting degradation in spectral resolution within 16% of its preradiation value through a series of high-temperature anneals. We characterize the repair of charge traps with time spent under high-temperature anneal to inform an annealing procedure for long-term maintenance of COSI's spectral resolution., Comment: 22 pages, 7 figures, 2 tables, to be published in NIM A
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- 2025
29. Generating Multimodal Images with GAN: Integrating Text, Image, and Style
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Tan, Chaoyi, Zhang, Wenqing, Qi, Zhen, Shih, Kowei, Li, Xinshi, and Xiang, Ao
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Computer Science - Computer Vision and Pattern Recognition - Abstract
In the field of computer vision, multimodal image generation has become a research hotspot, especially the task of integrating text, image, and style. In this study, we propose a multimodal image generation method based on Generative Adversarial Networks (GAN), capable of effectively combining text descriptions, reference images, and style information to generate images that meet multimodal requirements. This method involves the design of a text encoder, an image feature extractor, and a style integration module, ensuring that the generated images maintain high quality in terms of visual content and style consistency. We also introduce multiple loss functions, including adversarial loss, text-image consistency loss, and style matching loss, to optimize the generation process. Experimental results show that our method produces images with high clarity and consistency across multiple public datasets, demonstrating significant performance improvements compared to existing methods. The outcomes of this study provide new insights into multimodal image generation and present broad application prospects.
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- 2025
30. Constrained Pricing in Choice-based Revenue Management
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Shao, Qian, Mai, Tien, and Cheng, Shih-Fen
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Mathematics - Optimization and Control - Abstract
We consider a dynamic pricing problem in network revenue management where customer behavior is predicted by a choice model, i.e., the multinomial logit (MNL) model. The problem, even in the static setting (i.e., customer demand remains unchanged over time), is highly non-concave in prices. Existing studies mostly rely on the observation that the objective function is concave in terms of purchasing probabilities, implying that the static pricing problem with linear constraints on purchasing probabilities can be efficiently solved. However, this approach is limited in handling constraints on prices, noting that such constraints could be highly relevant in some real business considerations. To address this limitation, in this work, we consider a general pricing problem that involves constraints on both prices and purchasing probabilities. To tackle the non-concavity challenge, we develop an approximation mechanism that allows solving the constrained static pricing problem through bisection and mixed-integer linear programming (MILP). We further extend the approximation method to the dynamic pricing context. Our approach involves a resource decomposition method to address the curse of dimensionality of the dynamic problem, as well as a MILP approach to solving sub-problems to near-optimality. Numerical results based on generated instances of various sizes indicate the superiority of our approximation approach in both static and dynamic settings.
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- 2025
31. ASKCOS: an open source software suite for synthesis planning
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Tu, Zhengkai, Choure, Sourabh J., Fong, Mun Hong, Roh, Jihye, Levin, Itai, Yu, Kevin, Joung, Joonyoung F., Morgan, Nathan, Li, Shih-Cheng, Sun, Xiaoqi, Lin, Huiqian, Murnin, Mark, Liles, Jordan P., Struble, Thomas J., Fortunato, Michael E., Liu, Mengjie, Green, William H., Jensen, Klavs F., and Coley, Connor W.
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Computer Science - Artificial Intelligence - Abstract
The advancement of machine learning and the availability of large-scale reaction datasets have accelerated the development of data-driven models for computer-aided synthesis planning (CASP) in the past decade. Here, we detail the newest version of ASKCOS, an open source software suite for synthesis planning that makes available several research advances in a freely available, practical tool. Four one-step retrosynthesis models form the basis of both interactive planning and automatic planning modes. Retrosynthetic planning is complemented by other modules for feasibility assessment and pathway evaluation, including reaction condition recommendation, reaction outcome prediction, and auxiliary capabilities such as solubility prediction and quantum mechanical descriptor prediction. ASKCOS has assisted hundreds of medicinal, synthetic, and process chemists in their day-to-day tasks, complementing expert decision making. It is our belief that CASP tools like ASKCOS are an important part of modern chemistry research, and that they offer ever-increasing utility and accessibility.
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- 2025
32. LTCXNet: Advancing Chest X-Ray Analysis with Solutions for Long-Tailed Multi-Label Classification and Fairness Challenges
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Huang, Chin-Wei, Shen, Mu-Yi, Shih, Kuan-Chang, Lin, Shih-Chih, Chen, Chi-Yu, and Kuo, Po-Chih
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence - Abstract
Chest X-rays (CXRs) often display various diseases with disparate class frequencies, leading to a long-tailed, multi-label data distribution. In response to this challenge, we explore the Pruned MIMIC-CXR-LT dataset, a curated collection derived from the MIMIC-CXR dataset, specifically designed to represent a long-tailed and multi-label data scenario. We introduce LTCXNet, a novel framework that integrates the ConvNeXt model, ML-Decoder, and strategic data augmentation, further enhanced by an ensemble approach. We demonstrate that LTCXNet improves the performance of CXR interpretation across all classes, especially enhancing detection in rarer classes like `Pneumoperitoneum' and `Pneumomediastinum' by 79\% and 48\%, respectively. Beyond performance metrics, our research extends into evaluating fairness, highlighting that some methods, while improving model accuracy, could inadvertently affect fairness across different demographic groups negatively. This work contributes to advancing the understanding and management of long-tailed, multi-label data distributions in medical imaging, paving the way for more equitable and effective diagnostic tools., Comment: 8 pages, 5 figures
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- 2024
33. Dynamic-SUPERB Phase-2: A Collaboratively Expanding Benchmark for Measuring the Capabilities of Spoken Language Models with 180 Tasks
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Huang, Chien-yu, Chen, Wei-Chih, Yang, Shu-wen, Liu, Andy T., Li, Chen-An, Lin, Yu-Xiang, Tseng, Wei-Cheng, Diwan, Anuj, Shih, Yi-Jen, Shi, Jiatong, Chen, William, Chen, Xuanjun, Hsiao, Chi-Yuan, Peng, Puyuan, Wang, Shih-Heng, Kuan, Chun-Yi, Lu, Ke-Han, Chang, Kai-Wei, Yang, Chih-Kai, Ritter-Gutierrez, Fabian, Chuang, Ming To, Huang, Kuan-Po, Arora, Siddhant, Lin, You-Kuan, Yeo, Eunjung, Chang, Kalvin, Chien, Chung-Ming, Choi, Kwanghee, Hsieh, Cheng-Hsiu, Lin, Yi-Cheng, Yu, Chee-En, Chiu, I-Hsiang, Guimarães, Heitor R., Han, Jionghao, Lin, Tzu-Quan, Lin, Tzu-Yuan, Chang, Homu, Chang, Ting-Wu, Chen, Chun Wei, Chen, Shou-Jen, Chen, Yu-Hua, Cheng, Hsi-Chun, Dhawan, Kunal, Fang, Jia-Lin, Fang, Shi-Xin, Chiang, Kuan-Yu Fang, Fu, Chi An, Hsiao, Hsien-Fu, Hsu, Ching Yu, Huang, Shao-Syuan, Wei, Lee Chen, Lin, Hsi-Che, Lin, Hsuan-Hao, Lin, Hsuan-Ting, Lin, Jian-Ren, Liu, Ting-Chun, Lu, Li-Chun, Pai, Tsung-Min, Pasad, Ankita, Kuan, Shih-Yun Shan, Shon, Suwon, Tang, Yuxun, Tsai, Yun-Shao, Wei, Jui-Chiang, Wei, Tzu-Chieh, Wu, Chengxi, Wu, Dien-Ruei, Yang, Chao-Han Huck, Yang, Chieh-Chi, Yip, Jia Qi, Yuan, Shao-Xiang, Noroozi, Vahid, Chen, Zhehuai, Wu, Haibin, Livescu, Karen, Harwath, David, Watanabe, Shinji, and Lee, Hung-yi
- Subjects
Computer Science - Computation and Language ,Electrical Engineering and Systems Science - Audio and Speech Processing - Abstract
Multimodal foundation models, such as Gemini and ChatGPT, have revolutionized human-machine interactions by seamlessly integrating various forms of data. Developing a universal spoken language model that comprehends a wide range of natural language instructions is critical for bridging communication gaps and facilitating more intuitive interactions. However, the absence of a comprehensive evaluation benchmark poses a significant challenge. We present Dynamic-SUPERB Phase-2, an open and evolving benchmark for the comprehensive evaluation of instruction-based universal speech models. Building upon the first generation, this second version incorporates 125 new tasks contributed collaboratively by the global research community, expanding the benchmark to a total of 180 tasks, making it the largest benchmark for speech and audio evaluation. While the first generation of Dynamic-SUPERB was limited to classification tasks, Dynamic-SUPERB Phase-2 broadens its evaluation capabilities by introducing a wide array of novel and diverse tasks, including regression and sequence generation, across speech, music, and environmental audio. Evaluation results indicate that none of the models performed well universally. SALMONN-13B excelled in English ASR, while WavLLM demonstrated high accuracy in emotion recognition, but current models still require further innovations to handle a broader range of tasks. We will soon open-source all task data and the evaluation pipeline.
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- 2024
34. CaloChallenge 2022: A Community Challenge for Fast Calorimeter Simulation
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Krause, Claudius, Giannelli, Michele Faucci, Kasieczka, Gregor, Nachman, Benjamin, Salamani, Dalila, Shih, David, Zaborowska, Anna, Amram, Oz, Borras, Kerstin, Buckley, Matthew R., Buhmann, Erik, Buss, Thorsten, Cardoso, Renato Paulo Da Costa, Caterini, Anthony L., Chernyavskaya, Nadezda, Corchia, Federico A. G., Cresswell, Jesse C., Diefenbacher, Sascha, Dreyer, Etienne, Ekambaram, Vijay, Eren, Engin, Ernst, Florian, Favaro, Luigi, Franchini, Matteo, Gaede, Frank, Gross, Eilam, Hsu, Shih-Chieh, Jaruskova, Kristina, Käch, Benno, Kalagnanam, Jayant, Kansal, Raghav, Kim, Taewoo, Kobylianskii, Dmitrii, Korol, Anatolii, Korcari, William, Krücker, Dirk, Krüger, Katja, Letizia, Marco, Li, Shu, Liu, Qibin, Liu, Xiulong, Loaiza-Ganem, Gabriel, Madula, Thandikire, McKeown, Peter, Melzer-Pellmann, Isabell-A., Mikuni, Vinicius, Nguyen, Nam, Ore, Ayodele, Schweitzer, Sofia Palacios, Pang, Ian, Pedro, Kevin, Plehn, Tilman, Pokorski, Witold, Qu, Huilin, Raikwar, Piyush, Raine, John A., Reyes-Gonzalez, Humberto, Rinaldi, Lorenzo, Ross, Brendan Leigh, Scham, Moritz A. W., Schnake, Simon, Shimmin, Chase, Shlizerman, Eli, Soybelman, Nathalie, Srivatsa, Mudhakar, Tsolaki, Kalliopi, Vallecorsa, Sofia, Yeo, Kyongmin, and Zhang, Rui
- Subjects
Physics - Instrumentation and Detectors ,Computer Science - Machine Learning ,High Energy Physics - Experiment ,High Energy Physics - Phenomenology - Abstract
We present the results of the "Fast Calorimeter Simulation Challenge 2022" - the CaloChallenge. We study state-of-the-art generative models on four calorimeter shower datasets of increasing dimensionality, ranging from a few hundred voxels to a few tens of thousand voxels. The 31 individual submissions span a wide range of current popular generative architectures, including Variational AutoEncoders (VAEs), Generative Adversarial Networks (GANs), Normalizing Flows, Diffusion models, and models based on Conditional Flow Matching. We compare all submissions in terms of quality of generated calorimeter showers, as well as shower generation time and model size. To assess the quality we use a broad range of different metrics including differences in 1-dimensional histograms of observables, KPD/FPD scores, AUCs of binary classifiers, and the log-posterior of a multiclass classifier. The results of the CaloChallenge provide the most complete and comprehensive survey of cutting-edge approaches to calorimeter fast simulation to date. In addition, our work provides a uniquely detailed perspective on the important problem of how to evaluate generative models. As such, the results presented here should be applicable for other domains that use generative AI and require fast and faithful generation of samples in a large phase space., Comment: 204 pages, 100+ figures, 30+ tables
- Published
- 2024
35. Effect of Visual Programming Instruction on Students' Flow Experience, Programming Self-Efficacy, and Sustained Willingness to Learn
- Author
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Chiao Ling Huang, Lianzi Fu, Shih-Chieh Hung, and Shu Ching Yang
- Abstract
Background: Many studies have highlighted the positive effects of visual programming instruction (VPI) on students' learning experiences, programming self-efficacy and flow experience. However, there is a notable gap in the research on how these factors specifically impact programming achievement and learning intentions. Our study addresses this gap by focusing on flowchart-based programming--a relatively underexplored area in educational research. To ensure relevance to the educational context, AbilixChart and Ability Storm SK902 were specifically selected for their alignment with the curriculum of the target school, where these tools are widely utilised in both teaching and extracurricular activities. This alignment allowed for a seamless integration of these tools into regular classroom practices after the study's conclusion, ensuring continued application and maximising the study's practical impact. Furthermore, integrating educational robots enhanced student engagement and provided a practical means to evaluate the accuracy of their programming skills. By doing so, our study not only contributes to filling a gap in the literature but also has the potential to influence educational practices by demonstrating the value of incorporating flowchart-based programming and robotics into the curriculum. Objectives: The present study aims to conduct an instructional experiment utilising VPI with flowchart-based programming tools. The main objective is to investigate how these tools influence 219 high school students' flow experience, programming self-efficacy, and sustained learning willingness. Methods: This study employed a pre- and post-test design with a single group and conducted an 11-week instructional experiment. The students used the Abilix Chart software and the Ability Storm SK902 kit to build an intelligent car and learn about visual programming. They were tasked with independently designing programs to solve practical problems in different scenarios. Research tools included Scales of Flow Experience, Computer Programming Self-Efficacy, Sustained Learning Willingness and Program Achievement. Results: The findings revealed that VPI effectively improved students' programming achievement, flow experience and programming self-efficacy. Students with programming learning experience surpassed their inexperienced peers in willingness to engage in sustained learning. Conversely, 4.57% of the group with lower pre-test scores and no learning experience showed more positive emotional experience than those with learning experience. Conclusions: The results indicated that VPI positively affected programming achievement, self-efficacy and flow experience. Regardless of prior programming experience, all students benefited from VPI. Additionally, self-efficacy and flow experience were key factors influencing sustained learning motivation and achievement.
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- 2025
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36. Self-Gated Radial Free-Breathing Liver MR Elastography: Assessment of Technical Performance in Children at 3 T.
- Author
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Kafali, Sevgi, Bolster, Bradley, Shih, Shu-Fu, Delgado, Timoteo, Deshpande, Vibhas, Zhong, Xiaodong, Adamos, Timothy, Ghahremani, Shahnaz, Calkins, Kara, and Wu, Holden
- Subjects
children ,fibrosis ,free‐breathing ,liver MR elastography ,liver stiffness ,radial sampling ,Humans ,Female ,Elasticity Imaging Techniques ,Male ,Child ,Liver ,Prospective Studies ,Reproducibility of Results ,Adolescent ,Respiration ,Magnetic Resonance Imaging ,Artifacts ,Image Processing ,Computer-Assisted ,Motion ,Breath Holding - Abstract
BACKGROUND: Conventional liver magnetic resonance elastography (MRE) requires breath-holding (BH) to avoid motion artifacts, which is challenging for children. While radial free-breathing (FB)-MRE is an alternative for quantifying liver stiffness (LS), previous methods had limitations of long scan times, acquiring two slices in 5 minutes, and not resolving motion during reconstruction. PURPOSE: To reduce FB-MRE scan time to 4 minutes for four slices and to investigate the impact of self-gated (SG) motion compensation on FB-MRE LS quantification in terms of agreement, intrasession repeatability, and technical quality compared to conventional BH-MRE. STUDY TYPE: Prospective. POPULATION: Twenty-six children without fibrosis (median age: 12.9 years, 15 females). FIELD STRENGTH/SEQUENCE: 3 T; Cartesian gradient-echo (GRE) BH-MRE, research application radial GRE FB-MRE. ASSESSMENT: Participants were scanned twice to measure repeatability, without moving the table or changing the participants position. LS was measured in areas of the liver with numerical confidence ≥90%. Technical quality was examined using measurable liver area (%). STATISTICAL TESTS: Agreement of LS between BH-MRE and FB-MRE was evaluated using Bland-Altman analysis for SG acceptance rates of 40%, 60%, 80%, and 100%. LS repeatability was assessed using within-subject coefficient of variation (wCV). The differences in LS and measurable liver area were examined using Kruskal-Wallis and Wilcoxon signed-rank tests. P
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- 2025
37. Polygenic height prediction for the Han Chinese in Taiwan.
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Chang, Chih-Hao, Chou, Che-Yu, Raben, Timothy, Chen, Shih-Ann, Jong, Yuh-Jyh, Wu, Jeng-Yih, Yang, Shun-Fa, Chen, Hsiang-Cheng, Chen, Yen-Lin, Chen, Ming, Ma, Gwo-Chin, Huang, Chih-Yang, Wang, Tso-Fu, Lee, Sing-Lian, Hung, Chen-Fang, Pang, See-Tong, Widen, Erik, Chang, Yao-Ming, Yeh, Erh-Chan, Wei, Chun-Yu, Chen, Chien-Hsiun, Hsu, Stephen, and Kwok, Pui-Yan
- Abstract
Human height prediction based on genetic factors alone shows positive correlation, but predictors developed for one population perform less well when applied to population of different ancestries. In this study, we evaluated the utility of incorporating non-genetic factors in height predictors for the Han Chinese population in Taiwan. We analyzed data from 78,719 Taiwan Biobank (TWB) participants and 40,641 Taiwan Precision Medicine Initiative (TPMI) participants using genome-wide association study and multivariable linear regression least absolute shrinkage and selection operator (LASSO) methods to incorporate genetic and non-genetic factors for height prediction. Our findings establish that combining birth year (as a surrogate for nutritional status), age at measurement (to account for age-associated effects on height), and genetic profile data improves the accuracy of height prediction. This method enhances the correlation between predicted and actual height and significantly reduces the discrepancies between predicted and actual height in both males and females.
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- 2025
38. Inhibition of Galectin-1 and Androgen Receptor Axis Enhances Enzalutamide Treatment in Enzalutamide Resistant Prostate Cancer.
- Author
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Wang, Hsiao-Chi, Gao, Allen, Xia, Roger, Wu, Chun-Te, Hsu, Ssu-Wei, Chen, Ching-Hsien, and Shih, Tsung-Chieh
- Subjects
Galectin-1 ,LLS30 ,prostate cancer - Abstract
BACKGROUND/OBJECTIVE: Prostate cancer (PCa) remains a prevalent and deadly disease, particularly in its advanced stages. Despite various available treatments, resistance to drugs like enzalutamide continues to present significant challenges. This study aimed to investigate the role of Galectin-1 (Gal-1) in enzalutamide-resistant PCa and assess its potential as a therapeutic target to overcome resistance. METHODS: The study utilized specific siRNA-mediated knockdown of Gal-1 in enzalutamide-resistant PCa cells to evaluate its effects on cell proliferation and response to enzalutamide treatment. An orthotopic mouse model was employed to examine the in vivo impact of Gal-1 knockdown. Pharmacological targeting of Gal-1 was conducted using LLS30, and its effects were assessed both in vitro and in vivo. RNA sequencing (RNA-seq) analysis was performed to explore the molecular mechanisms underlying the observed effects. RESULTS: The findings demonstrated significant upregulation of Gal-1 in enzalutamide-resistant PCa cells. Gal-1 knockdown inhibited cell proliferation and resensitized resistant cells to enzalutamide treatment in the orthotopic mouse model. Elevated levels of androgen receptor full-length and AR-V7 are key mechanisms under-lying resistance to enzalutamide in PCa. Gal-1 knockdown suppressed AR and AR-V7 expression and their transcriptional activity. Treatment with LLS30 significantly suppressed the growth of enzalutamide-resistant PCa cells and exhibited synergistic effects when combined with enzalutamide. Notably, this combination therapy significantly inhibited the growth of enzalutamide-resistant xenografts in vivo. RNA-seq analysis revealed that LLS30 modulates AR and AR-V7 signaling through the inhibition of associated target genes. CONCLUSION: These findings highlight Gal-1 as a promising therapeutic target for overcoming enzalutamide resistance in PCa. Targeting the Gal-1/AR/AR-V7 axis with LLS30 presents a novel strategy to enhance enzalutamide efficacy and address drug resistance in advanced PCa.
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- 2025
39. A map of the rubisco biochemical landscape.
- Author
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Prywes, Noam, Phillips, Naiya, Oltrogge, Luke, Lindner, Sebastian, Taylor-Kearney, Leah, Tsai, Yi-Chin, de Pins, Benoit, Cowan, Aidan, Chang, Hana, Wang, Renee, Hall, Laina, Bellieny-Rabelo, Daniel, Nisonoff, Hunter, Weissman, Rachel, Flamholz, Avi, Ding, David, Bhatt, Abhishek, Mueller-Cajar, Oliver, Shih, Patrick, Milo, Ron, and Savage, David
- Abstract
Rubisco is the primary CO2-fixing enzyme of the biosphere1, yet it has slow kinetics2. The roles of evolution and chemical mechanism in constraining its biochemical function remain debated3,4. Engineering efforts aimed at adjusting the biochemical parameters of rubisco have largely failed5, although recent results indicate that the functional potential of rubisco has a wider scope than previously known6. Here we developed a massively parallel assay, using an engineered Escherichia coli7 in which enzyme activity is coupled to growth, to systematically map the sequence-function landscape of rubisco. Composite assay of more than 99% of single-amino acid mutants versus CO2 concentration enabled inference of enzyme velocity and apparent CO2 affinity parameters for thousands of substitutions. This approach identified many highly conserved positions that tolerate mutation and rare mutations that improve CO2 affinity. These data indicate that non-trivial biochemical changes are readily accessible and that the functional distance between rubiscos from diverse organisms can be traversed, laying the groundwork for further enzyme engineering efforts.
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- 2025
40. Reevaluating Propensity to Support Sustainability
- Author
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Theisz, Alec Andrew, Min, Aehong, and Shih, Patrick C
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Built Environment and Design - Abstract
In a world faced with ever-growing crises of climate change, economic inequality, and social injustice, sustainability has become a catch-all term to address these challenges and more. However, efforts to measure the social, environmental, and economic factors of sustainability are undermined by inconsistent understandings of the term. This research seeks to address this gap in sustainability research by constructing a wide-reaching propensity instrument that incorporates the different constructs of sustainability. A literature review informed propensity instrument construction. The first version of the instrument included 269 items, which were narrowed to 100 after an iterative process of merging, refinement, and elimination. The 100 scale items were deployed through an online survey, where 162 responses were collected to inform data analysis. Principal component analysis revealed two primary factors of Sustainable Behavior and Sustainability Attitude. After further refinement based on items’ factor-loading scores and communalities, 13 items remained that described sustainability as environmentally and socially conscious behaviors and attitudes. The third construct of sustainability, economics, was not present after such refinements, suggesting that purely economic behaviors and attitudes are disparate from individuals’ sustainability propensity. This new propensity instrument informs the understanding of sustainability and provides a tool for measuring sustainability with more breadth.
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- 2025
41. Characterizing hole trap production due to proton irradiation in germanium cross-strip detectors.
- Author
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Pike, Sean, Boggs, Steven, Brewster, Gabriel, Haight, Sophia, Roberts, Jarred, Shih, Albert, Szornel, Joanna, Tomsick, John, and Zoglauer, Andreas
- Subjects
Charge trapping ,Gamma-ray spectroscopy ,Germanium semiconductor detectors ,Radiation damage - Abstract
We present an investigation into the effects of high-energy proton damage on charge trapping in germanium cross-strip detectors with the goal of accomplishing three important measurements. First, we calibrated and characterized the spectral resolution of a spare COSI-balloon detector in order to determine the effects of intrinsic trapping, finding that electron trapping due to impurities dominates over hole trapping in the undamaged detector. Second, we performed two rounds of proton irradiation of the detector in order to quantify, for the first time, the rate at which charge traps are produced by proton irradiation. We find that the product of the hole trap density and cross-sectional area, [ n σ ] h , follows a linear relationship with the proton fluence, F p , with a slope of ( 5.4 ± 0.4 ) × 10 - 11 cm / p + . Third, by utilizing our measurements of physical trapping parameters, we performed calibrations which corrected for the effects of trapping and mitigated degradation to the spectral resolution of the detector.
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- 2025
42. Toward a Computable Phenotype for Determining Eligibility of Lung Cancer Screening Using Electronic Health Records.
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Yang, Shuang, Huang, Yu, Lou, Xiwei, Lyu, Tianchen, Wei, Ruoqi, Mehta, Hiren, Wu, Yonghui, Alvarado, Michelle, Salloum, Ramzi, Braithwaite, Dejana, Huo, Jinhai, Shih, Ya-Chen, Guo, Yi, and Bian, Jiang
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Humans ,Electronic Health Records ,Lung Neoplasms ,Early Detection of Cancer ,Female ,Middle Aged ,Male ,Aged ,Algorithms ,Phenotype ,Tomography ,X-Ray Computed ,Natural Language Processing ,Eligibility Determination - Abstract
PURPOSE: Lung cancer screening (LCS) has the potential to reduce mortality and detect lung cancer at its early stages, but the high false-positive rate associated with low-dose computed tomography (LDCT) for LCS acts as a barrier to its widespread adoption. This study aims to develop computable phenotype (CP) algorithms on the basis of electronic health records (EHRs) to identify individuals eligibility for LCS, thereby enhancing LCS utilization in real-world settings. MATERIALS AND METHODS: The study cohort included 5,778 individuals who underwent LDCT for LCS from 2012 to 2022, as recorded in the University of Florida Health Integrated Data Repository. CP rules derived from LCS guidelines were used to identify potential candidates, incorporating both structured EHR and clinical notes analyzed via natural language processing. We then conducted manual reviews of 453 randomly selected charts to refine and validate these rules, assessing CP performance using metrics, for example, F1 score, specificity, and sensitivity. RESULTS: We developed an optimal CP rule that integrates both structured and unstructured data, adhering to the US Preventive Services Task Force 2013 and 2020 guidelines. This rule focuses on age (55-80 years for 2013 and 50-80 years for 2020), smoking status (current, former, and others), and pack-years (≥30 for 2013 and ≥20 for 2020), achieving F1 scores of 0.75 and 0.84 for the respective guidelines. Including unstructured data improved the F1 score performance by up to 9.2% for 2013 and 12.9% for 2020, compared with using structured data alone. CONCLUSION: Our findings underscore the critical need for improved documentation of smoking information in EHRs, demonstrate the value of artificial intelligence techniques in enhancing CP performance, and confirm the effectiveness of EHR-based CP in identifying LCS-eligible individuals. This supports its potential to aid clinical decision making and optimize patient care.
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- 2025
43. Studying tech adoption with “text-as-data”: Opportunities, pitfalls, and complementarities in the case of transportation
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Chiu, Shih-Hung, Han, Tianyu, Post, Alison E, Ratan, Ishana, and Soga, Kenichi
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Built Environment and Design ,Architecture ,Urban and Regional Planning ,Big data ,planning processes ,smart cities ,urban analytics ,urban transportation - Abstract
The rapid digitization and publication of local government records presents researchers with an unprecedented chance to study governance processes. In tandem, advances in computer science and statistics—alongside significant increases in computational power—have led to the development of “text-as-data” methods and their application to social science and policy research. This paper evaluates the potential utility of digitized public meeting minutes and video recordings for studying decision-making about technology adoption by local public agencies, using survey data on the same topic as a benchmark. Focusing on transit agencies in California, we evaluate surveys and digitized meeting records with respect to overall data availability, bias in data availability, and the types of information about technology adoption contained. We find that meeting minutes and video recordings are available for more than twice as many agencies than for a state transit agency-sponsored survey, and that the availability of digitized records is not skewed toward larger agencies, as is the case for survey data. Meanwhile, we find important complementarities with respect to the type of information available about technology adoption in these three data sources.
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- 2025
44. Exploiting Domain-Specific Parallel Data on Multilingual Language Models for Low-resource Language Translation
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Ranathungaa, Surangika, Nayak, Shravan, Huang, Shih-Ting Cindy, Mao, Yanke, Su, Tong, Chan, Yun-Hsiang Ray, Yuan, Songchen, Rinaldi, Anthony, and Lee, Annie En-Shiun
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Computer Science - Computation and Language - Abstract
Neural Machine Translation (NMT) systems built on multilingual sequence-to-sequence Language Models (msLMs) fail to deliver expected results when the amount of parallel data for a language, as well as the language's representation in the model are limited. This restricts the capabilities of domain-specific NMT systems for low-resource languages (LRLs). As a solution, parallel data from auxiliary domains can be used either to fine-tune or to further pre-train the msLM. We present an evaluation of the effectiveness of these two techniques in the context of domain-specific LRL-NMT. We also explore the impact of domain divergence on NMT model performance. We recommend several strategies for utilizing auxiliary parallel data in building domain-specific NMT models for LRLs.
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- 2024
45. A Tale of Three: Magnetic Fields along the Orion Integral-Shaped Filament as Revealed by JCMT BISTRO survey
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Wu, Jintai, Qiu, Keping, Poidevin, Frederick, Bastien, Pierre, Liu, Junhao, Ching, Tao-Chung, Bourke, Tyler L., Ward-Thompson, Derek, Pattle, Kate, Johnstone, Doug, Koch, Patrick M., Arzoumanian, Doris, Lee, Chang Won, Fanciullo, Lapo, Onaka, Takashi, Hwang, Jihye, Gouellec, Valentin J. M. Le, Soam, Archana, Tamura, Motohide, Tahani, Mehrnoosh, Eswaraiah, Chakali, Li, Hua-Bai, Berry, David, Furuya, Ray S., Coude, Simon, Kwon, Woojin, Lin, Sheng-Jun, Wang, Jia-Wei, Hasegawa, Tetsuo, Lai, Shih-Ping, Byun, Do-Young, Chen, Zhiwei, Chen, Huei-Ru Vivien, Chen, Wen Ping, Chen, Mike, Cho, Jungyeon, Choi, Youngwoo, Choi, Yunhee, Choi, Minho, Chrysostomou, Antonio, Chung, Eun Jung, Dai, Sophia, Di Francesco, James, Diep, Pham Ngoc, Doi, Yasuo, Duan, Hao-Yuan, Duan, Yan, Eden, David, Fiege, Jason, Fissel, Laura M., Franzmann, Erica, Friberg, Per, Friesen, Rachel, Fuller, Gary, Gledhill, Tim, Graves, Sarah, Greaves, Jane, Griffin, Matt, Gu, Qilao, Han, Ilseung, Hayashi, Saeko, Hoang, Thiem, Houde, Martin, Inoue, Tsuyoshi, Inutsuka, Shu-ichiro, Iwasaki, Kazunari, Jeong, Il-Gyo, Konyves, Vera, Kang, Ji-hyun, Kang, Miju, Karoly, Janik, Kataoka, Akimasa, Kawabata, Koji, Kim, Shinyoung, Kim, Mi-Ryang, Kim, Kyoung Hee, Kim, Kee-Tae, Kim, Jongsoo, Kim, Hyosung, Kim, Gwanjeong, Kirchschlager, Florian, Kirk, Jason, Kobayashi, Masato I. N., Kusune, Takayoshi, Kwon, Jungmi, Lacaille, Kevin, Law, Chi-Yan, Lee, Hyeseung, Lee, Chin-Fei, Lee, Sang-Sung, Lee, Jeong-Eun, Li, Dalei, Li, Di, Li, Guangxing, Liu, Sheng-Yuan, Liu, Tie, Liu, Hong-Li, Lu, Xing, Lyo, A-Ran, Mairs, Steve, Matsumura, Masafumi, Matthews, Brenda, Moriarty-Schieven, Gerald, Nagata, Tetsuya, Nakamura, Fumitaka, Nakanishi, Hiroyuki, Ngoc, Nguyen Bich, Ohashi, Nagayoshi, Park, Geumsook, Parsons, Harriet, Peretto, Nicolas, Priestley, Felix, Pyo, Tae-Soo, Qian, Lei, Rao, Ramprasad, Rawlings, Jonathan, Rawlings, Mark, Retter, Brendan, Richer, John, Rigby, Andrew, Sadavoy, Sarah, Saito, Hiro, Savini, Giorgio, Seta, Masumichi, Sharma, Ekta, Shimajiri, Yoshito, Shinnaga, Hiroko, Tang, Ya-Wen, Tang, Xindi, Thuong, Hoang Duc, Tomisaka, Kohji, Tram, Le Ngoc, Tsukamoto, Yusuke, Viti, Serena, Wang, Hongchi, Whitworth, Anthony, Xie, Jinjin, Yang, Meng-Zhe, Yen, Hsi-Wei, Yoo, Hyunju, Yuan, Jinghua, Yun, Hyeong-Sik, Zenko, Tetsuya, Zhang, Guoyin, Zhang, Chuan-Peng, Zhang, Yapeng, Zhou, Jianjun, Zhu, Lei, de Looze, Ilse, Andre, Philippe, Dowell, C. Darren, Eyres, Stewart, Falle, Sam, Robitaille, Jean-Francois, and van Loo, Sven
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Astrophysics - Astrophysics of Galaxies ,Astrophysics - Solar and Stellar Astrophysics - Abstract
As part of the BISTRO survey, we present JCMT 850 $\mu$m polarimetric observations towards the Orion Integral-Shaped Filament (ISF) that covers three portions known as OMC-1, OMC-2, and OMC-3. The magnetic field threading the ISF seen in the JCMT POL-2 map appears as a tale of three: pinched for OMC-1, twisted for OMC-2, and nearly uniform for OMC-3. A multi-scale analysis shows that the magnetic field structure in OMC-3 is very consistent at all the scales, whereas the field structure in OMC-2 shows no correlation across different scales. In OMC-1, the field retains its mean orientation from large to small scales, but shows some deviations at small scales. Histograms of relative orientations between the magnetic field and filaments reveal a bimodal distribution for OMC-1, a relatively random distribution for OMC-2, and a distribution with a predominant peak at 90$^\circ$ for OMC-3. Furthermore, the magnetic fields in OMC-1 and OMC-3 both appear to be aligned perpendicular to the fibers, which are denser structures within the filament, but the field in OMC-2 is aligned along with the fibers. All these suggest that gravity, turbulence, and magnetic field are each playing a leading role in OMC-1, 2, and 3, respectively. While OMC-2 and 3 have almost the same gas mass, density, and non-thermal velocity dispersion, there are on average younger and fewer young stellar objects in OMC-3, providing evidence that a stronger magnetic field will induce slower and less efficient star formation in molecular clouds., Comment: published in the ApJ Letters
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- 2024
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46. How soap bubbles change shape while maintaining a fixed volume of air?
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Li, Wei-Chih, Shih, Chih-Yao, Chang, Tzu-Liang, and Hong, Tzay-Ming
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Physics - Fluid Dynamics - Abstract
We combine experiments and theoretical derivations to study the evolution of a stretched soap bubble and compare it with an open film to highlight the effect of volume conservation. We identify a critical length for both surfaces, beyond which a bottleneck develops in the middle and begins to shrink irreversibly, ultimately pinching off into multiple compartments. Before leaving the equilibrium regime, surface energy minimization governs the shape, which can be addressed theoretically via the variational method. In contrast to open films, soap bubble volume conservation introduces a Lagrange multiplier, analogous to a pressure difference, mediating long-range shape evolution. By examining how boundary constraints influence deformation, we contrast the bubble's convex-to-concave transition with the behavior of soap films under similar conditions. Our analysis of equilibrium and breakup regimes reveals critical differences between bubble and film stability profiles, shedding light on universal behaviors in non-equilibrium fluid mechanics, with implications for biological and material sciences., Comment: 9 pages
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- 2024
47. Mapping Dark Matter Through the Dust of the Milky Way Part I: Dust Correction and Phase Space Density
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Putney, Eric, Shih, David, Lim, Sung Hak, and Buckley, Matthew R.
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Astrophysics - Astrophysics of Galaxies ,High Energy Physics - Phenomenology - Abstract
The Boltzmann equation relates the equilibrium phase space distribution of stars in the Milky Way to the Galaxy's gravitational potential. However, observations of stellar populations are biased by extinction from foreground dust, which complicates measurements of the potential in the disk and towards the Galactic center. Using the kinematics of Red Clump and Red Branch stars in Gaia DR3, we use machine learning to simultaneously estimate both the unbiased stellar phase space density and the gravitational potential. The unbiased phase space density is obtained through a learned "dust efficiency factor" -- an observational selection function that accounts for dust extinction. The potential and the dust efficiency are parameterized by fully connected neural networks and are completely data driven. We validate the dust efficiency using a recent three-dimensional dust map in this work, and examine the potential in a companion paper., Comment: 27 pages, 12 figures
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- 2024
48. Experience of Training a 1.7B-Parameter LLaMa Model From Scratch
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Li, Miles Q., Fung, Benjamin C. M., and Huang, Shih-Chia
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence - Abstract
Pretraining large language models is a complex endeavor influenced by multiple factors, including model architecture, data quality, training continuity, and hardware constraints. In this paper, we share insights gained from the experience of training DMaS-LLaMa-Lite, a fully open source, 1.7-billion-parameter, LLaMa-based model, on approximately 20 billion tokens of carefully curated data. We chronicle the full training trajectory, documenting how evolving validation loss levels and downstream benchmarks reflect transitions from incoherent text to fluent, contextually grounded output. Beyond pretraining, we extend our analysis to include a post-training phase focused on instruction tuning, where the model was refined to produce more contextually appropriate, user-aligned responses. We highlight practical considerations such as the importance of restoring optimizer states when resuming from checkpoints, and the impact of hardware changes on training stability and throughput. While qualitative evaluation provides an intuitive understanding of model improvements, our analysis extends to various performance benchmarks, demonstrating how high-quality data and thoughtful scaling enable competitive results with significantly fewer training tokens. By detailing these experiences and offering training logs, checkpoints, and sample outputs, we aim to guide future researchers and practitioners in refining their pretraining strategies. The training script is available on Github at https://github.com/McGill-DMaS/DMaS-LLaMa-Lite-Training-Code. The model checkpoints are available on Huggingface at https://huggingface.co/collections/McGill-DMaS/dmas-llama-lite-6761d97ba903f82341954ceb.
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- 2024
49. The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods
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Yaniv, Ziv, Anidi, Ifeanyichukwu U., Arakkal, Leanne, Arroyo-Mejías, Armando J., Beuschel, Rebecca T., Börner, Katy, Chu, Colin J., Clark, Beatrice, Clatworthy, Menna R., Colautti, Jake, Coscia, Fabian, Croteau, Joshua, Denha, Saven, Dever, Rose, Dutra, Walderez O., Fritzsche, Sonja, Fullam, Spencer, Gerner, Michael Y., Gola, Anita, Gollob, Kenneth J., Hernandez, Jonathan M., Hor, Jyh Liang, Ichise, Hiroshi, Jing, Zhixin, Jonigk, Danny, Kandov, Evelyn, Kastenmüller, Wolfgang, Koenig, Joshua F. E., Kothurkar, Aanandita, Kortekaas, Rosa K., Kreins, Alexandra Y., Lamborn, Ian T., Lin, Yuri, Morais, Katia Luciano Pereira, Lunich, Aleksandra, Luz, Jean C. S., MacDonald, Ryan B., Makranz, Chen, Maltez, Vivien I., McDonough, John E., Moriarty, Ryan V., Ocampo-Godinez, Juan M., Olyntho, Vitoria M., Oxenius, Annette, Padhan, Kartika, Remmert, Kirsten, Richoz, Nathan, Schrom, Edward C., Shang, Wanjing, Shi, Lihong, Shih, Rochelle M., Speranza, Emily, Stierli, Salome, Teichmann, Sarah A., Veres, Tibor Z., Vierhout, Megan, Wachter, Brianna T., Williams, Margaret, Zangger, Nathan, Germain, Ronald N., and Radtke, Andrea J.
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Quantitative Biology - Tissues and Organs ,Electrical Engineering and Systems Science - Image and Video Processing - Abstract
The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the open-source software community and includes three facets: a development platform (GitHub), static website, and service for data archiving. The Knowledge-Base facilitates the practice of open science throughout the research life cycle by providing validation data for recommended and non-recommended reagents, e.g., primary and secondary antibodies. In addition to reporting negative data, the Knowledge-Base empowers method adoption and evolution by providing a venue for sharing protocols, videos, datasets, software, and publications. A dedicated discussion forum fosters a sense of community among researchers while addressing questions not covered in published manuscripts. Together, scientists from around the world are advancing scientific discovery at a faster pace, reducing wasted time and effort, and instilling greater confidence in the resulting data.
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- 2024
50. Entanglement induced by Heisenberg exchange between an electron in a nested quantum dot and a qubit with relative motion
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Lin, Lee-Che, Tan, Seng Ghee, Chang, Ching-Ray, Sun, Shih-Jye, and Chen, Son-Hsien
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Condensed Matter - Mesoscale and Nanoscale Physics ,Quantum Physics - Abstract
We propose a nested quantum dot structure for improved control of entanglement induced by the Heisenberg exchange between an electron and a qubit with relative motion. The entanglement is quantified by the mutual information (MI). The electron, initially prepared in the ground state, generally produces greater entanglement when excited to the scattering state compared to remaining in the bound state. In the bound state, the final entanglement oscillates as a function of the qubit speed and can be tuned accordingly. In the case of long-range interaction, the normalized exchange distribution leads to substantial final entanglement, independent of the qubit moving direction, indicating that even very weak but prolonged exchange can still generate significant entanglement. In the case of short-range interaction, different moving directions lead to varying MI values. We also consider the scenario without the nested dot and find that the same maximum (among all times) MI is pre-determined solely by the initial angle between the spins. In this case, the entanglement exhibits different growth characteristics during different phases. The saturation of the MI mimics that of a strict zero-dimensional quantum dot, where exchange and time are combined into a single parameter, the amount of interaction., Comment: 7 pages, 3 figures
- Published
- 2024
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