arXiv subjects

Si Chen

Publications and source records attributed to Si Chen.

At least 37 records · Page 2Linked to original sources

arXiv2026

Single-frame super-resolution via Sparse Point Optimization

Fluorescence microscopy is essential in biological and medical research, providing critical insights into cellular structures. However, limited by optical diffraction and background noise, a substantial amount of hidden information is still unexploited. To address these challenges, we introduce a novel computational method, termed Sparse Point Optimization Theory (SPOT), which accurately localizes fluorescent emitters by solving an optimization problem. Our results demonstrate that SPOT successfully resolves 30 nm fluorescent line pairs, reveals structural details beyond the diffraction limit in both Airyscan and structured illumination microscopy, and outperforms established algorithms in single-molecule localization tasks. This generic method effectively pushes the resolution limit in the presence of noise, and holds great promise for advancing fluorescence microscopy and analysis in cell biology.

physics.bio-ph↗

arXiv2026

BioChemInsight: An Online Platform for Automated Extraction of Chemical Structures and Activity Data from Patents

The automated extraction of chemical structures and their corresponding bioactivity data is essential for accelerating drug discovery and enabling data-driven research. Current optical chemical structure recognition tools lack the capability to autonomously link molecular structures with their bioactivity profiles, posing a significant bottleneck in structure-activity relationship analysis. To address this, we present BioChemInsight, an open-source pipeline that integrates DECIMER Segmentation with MolNexTR for chemical structure recognition, GLM-4.5V for compound identifier association, and PaddleOCR combined with GLM-4.6 for bioactivity extraction and unit normalization. We evaluated BioChemInsight on 181 patents covering 15 therapeutic targets. The system achieved an average extraction accuracy of above 90% across three key tasks: chemical structure recognition, bioactivity data extraction, and compound identifier association. Our analysis indicates that the chemical space covered by patents is largely complementary to that contained in established public database ChEMBL. Consequently, by enabling systematic patent mining, BioChemInsight provides access to chemical information underrepresented in ChEMBL. This capability expands the landscape of explorable compound-target interactions, enriches the data foundation for quantitative structure-activity relationship modeling and targeted screening, and reduces data preprocessing time from weeks to hours. BioChemInsight is available at https://github.com/dahuilangda/BioChemInsight.

q-bio.QM↗

arXiv2026

AI4CAREER: Responsible AI for STEM Career Development at Scale in K-16 Education

Rapid advances in artificial intelligence (AI) are reshaping how students imagine, explore, and prepare for STEM careers across K-16 education. As AI systems increasingly influence feedback, advising, and access to information about opportunities, they are becoming part of the developmental infrastructure that shapes career identity formation and readiness. Yet uncertainty remains about how AI-supported career exploration tools should be designed, governed, and evaluated at scale, particularly across developmental stages and institutional contexts. This half-day workshop convenes researchers, educators, practitioners, and policymakers to examine responsible AI for STEM career development. We focus on four themes: (1) how AI reshapes definitions and assessment of STEM career readiness; (2) appropriate roles and boundaries for AI in career decision-making; (3) developmental alignment of AI supports across the K-16 continuum; and (4) equity-related design considerations that prevent the reproduction of structural disparities. Through lightning talks, structured group activities, and cross-sector dialogue, participants will surface design tensions, articulate governance principles, and identify research gaps. The workshop aims to advance shared language and actionable frameworks for responsible, developmentally grounded AI use in STEM career learning at scale.

cs.CY↗

arXiv2026

Optimizing Mirror-Image Peptide Sequence Design for Data Storage via Peptide Bond Cleavage Prediction

Traditional non-biological storage media, such as hard drives, face limitations in both storage density and lifespan due to the rapid growth of data in the big data era. Mirror-image peptides composed of D-amino acids have emerged as a promising biological storage medium due to their high storage density, structural stability, and long lifespan. The sequencing of mirror-image peptides relies on \textit{de-novo} technology. However, its accuracy is limited by the scarcity of tandem mass spectrometry datasets and the challenges that current algorithms encounter when processing these peptides directly. This study is the first to propose improving sequencing accuracy indirectly by optimizing the design of mirror-image peptide sequences. In this work, we introduce DBond, a deep neural network based model that integrates sequence features, precursor ion properties, and mass spectrometry environmental factors for the prediction of mirror-image peptide bond cleavage. In this process, sequences with a high peptide bond cleavage ratio, which are easy to sequence, are selected. The main contributions of this study are as follows. First, we constructed MiPD513, a tandem mass spectrometry dataset containing 513 mirror-image peptides. Second, we developed the peptide bond cleavage labeling algorithm (PBCLA), which generated approximately 12.5 million labeled data based on MiPD513. Third, we proposed a dual prediction strategy that combines multi-label and single-label classification. On an independent test set, the single-label classification strategy outperformed other methods in both single and multiple peptide bond cleavage prediction tasks, offering a strong foundation for sequence optimization.

q-bio.QM↗

arXiv2026

Building Scaffolding Dialogue Data with LLM-Simulated Novices

High-quality, multi-turn instructional dialogues between novices and experts are essential for developing AI systems that support teaching, learning, and decision-making. These dialogues often involve scaffolding -- the process by which an expert supports a novice's thinking through questions, feedback, and step-by-step guidance. However, such data are scarce due to privacy concerns in recording and the vulnerability inherent in help-seeking. We present SimInstruct, a scalable, expert-in-the-loop tool for collecting scaffolding dialogues. Using teaching development coaching as an example domain, SimInstruct simulates novice instructors via LLMs, varying their teaching challenges and LLM's persona traits, while human experts provide multi-turn feedback, reasoning, and instructional support. This design enables the creation of realistic, pedagogically rich dialogues without requiring real novice participants. Our results reveal that persona traits, such as extroversion and introversion, meaningfully influence how experts engage. Compared to real mentoring recordings, SimInstruct dialogues demonstrate comparable pedagogical relevance and cognitive depth. Experts also reported the process as engaging and reflective, improving both data quality and their own professional insight. We further fine-tuned a LLaMA model to be an expert model using the augmented dataset, which outperformed GPT-4o in instructional quality. Our analysis highlights GPT-4o's limitations in weak reflective questioning, overuse of generic praise, a condescending tone, and a tendency to overwhelm novices with excessive suggestions.

cs.AI↗

arXiv2026

Automated Benchmark Generation from Domain Guidelines Informed by Bloom's Taxonomy

Open-ended question answering (QA) evaluates a model's ability to perform contextualized reasoning beyond factual recall. This challenge is especially acute in practice-based domains, where knowledge is procedural and grounded in professional judgment, while most existing LLM benchmarks depend on pre-existing human exam datasets that are often unavailable in such settings. We introduce a framework for automated benchmark generation from expert-authored guidelines informed by Bloom's Taxonomy. It converts expert practices into implicit violation-based scenarios and expands them into auto-graded multiple-choice questions (MCQs) and multi-turn dialogues across four cognitive levels, enabling deterministic, reproducible, and scalable evaluation. Applied to three applied domains: teaching, dietetics, and caregiving, we find differences between model and human-like reasoning: LLMs sometimes perform relatively better on higher-order reasoning (Analyze) but fail more frequently on lower-level items (Remember). We produce large-scale, psychometrically informed benchmarks that surface these non-intuitive model behaviors and enable evaluation of contextualized reasoning in real-world settings.

cs.CL↗

arXiv2026

A Human-Centred AI System for Multi-Actor Planning and Collaboration in Family Learning

Family learning takes place in everyday routines where children and caregivers read, practice, and develop new skills together. Despite growing interest in AI tutors, most existing systems are designed for single learners or classroom settings and do not address the distributed planning, coordination, and execution demands of learning at home. This paper introduces ParPal, a human-centred, LLM-powered system that supports multi-actor family learning by decomposing learning goals into actionable subtasks, allocating them across caregivers under realistic availability and expertise constraints, and providing caregiver-in-the-loop tutoring support with visibility into individual and collective contributions. Through expert evaluation of generated weekly learning plans and a one-week field deployment with 11 families, we identify systematic failure modes in current LLM-based planning, including misalignment with role expertise, unnecessary or costly collaboration, missing pedagogical learning trajectories, and physically or temporally infeasible tasks. While ParPal improves coordination clarity and recognition of caregiving effort, these findings expose fundamental limitations in how current LLMs operationalize pedagogical knowledge, reason about collaboration, and account for real-world, embodied constraints. We discuss implications for human-centred AI design and AI methodology, positioning multi-actor family learning as a critical testbed for advancing planning, adaptation, and pedagogical structure in next-generation AI systems.

cs.HC↗

arXiv2026

AttoSHINE: Generation of continuous-wave terawatt-scale attosecond X-ray pulses at SHINE

Attosecond X-ray pulses are a critical tool for tracking ultrafast electron dynamics in condensed matter, molecular systems, and strongly correlated materials. Recent breakthroughs have pushed X-ray free electron lasers (XFELs) into the attosecond domain, significantly surpassing their previous femtosecond capabilities. Building on these advancements, this work investigates the potential of the Shanghai High Repetition Rate XFEL and Extreme Light Facility (SHINE), China's first continuous-wave (CW) XFEL, to generate intense attosecond X-ray pulses, thereby offering transformative capabilities for X-ray science. Through comprehensive start-to-end simulations, we show that SHINE is capable of producing hard X-ray pulses with peak powers reaching the terawatt-scale and average pulse durations of approximately 300 as. This is achieved using a self-chirping scheme within the existing machine configuration, requiring no additional hardware. Our findings demonstrate that CW XFELs can generate intense attosecond X-ray pulses at megahertz repetition rates, opening new opportunities for real-time studies of electronic dynamics in complex systems.

physics.acc-ph↗

arXiv2025

Peregrine: One-Shot Fine-Tuning for FHE Inference of General Deep CNNs

We address two fundamental challenges in adapting general deep CNNs for FHE-based inference: approximating non-linear activations such as ReLU with low-degree polynomials while minimizing accuracy degradation, and overcoming the ciphertext capacity barrier that constrains high-resolution image processing on FHE inference. Our contributions are twofold: (1) a single-stage fine-tuning (SFT) strategy that directly converts pre-trained CNNs into FHE-friendly forms using low-degree polynomials, achieving competitive accuracy with minimal training overhead; and (2) a generalized interleaved packing (GIP) scheme that is compatible with feature maps of virtually arbitrary spatial resolutions, accompanied by a suite of carefully designed homomorphic operators that preserve the GIP-form encryption throughout computation. These advances enable efficient, end-to-end FHE inference across diverse CNN architectures. Experiments on CIFAR-10, ImageNet, and MS COCO demonstrate that the FHE-friendly CNNs obtained via our SFT strategy achieve accuracy comparable to baselines using ReLU or SiLU activations. Moreover, this work presents the first demonstration of FHE-based inference for YOLO architectures in object detection leveraging low-degree polynomial activations.

cs.CV↗

arXiv2025

Building AI Literacy at Home: How Families Navigate Children's Self-Directed Learning with AI

As generative AI becomes embedded in children's learning spaces, families face new challenges in guiding its use. Middle childhood (ages 7-13) is a critical stage where children seek autonomy even as parental influence remains strong. Using self-directed learning (SDL) as a lens, we examine how parents perceive and support children's developing AI literacy through focus groups with 13 parent-child pairs. Parents described evolving phases of engagement driven by screen time, self-motivation, and growing knowledge. While many framed AI primarily as a study tool, few considered its non-educational roles or risks, such as privacy and infrastructural embedding. Parents also noted gaps in their own AI understanding, often turning to joint exploration and engagement as a form of co-learning. Our findings reveal how families co-construct children's AI literacy, exposing tensions between practical expectations and critical literacies, and provide design implications that foster SDL while balancing autonomy and oversight.

cs.HC↗

arXiv2025

"Learning Together": AI-Mediated Support for Parental Involvement in Everyday Learning

Family learning takes place in everyday routines where children and caregivers read, practice, and develop new skills together. Although AI is increasingly present in learning environments, most systems remain child-centered and overlook the collaborative, distributed nature of family education. This paper investigates how AI can mediate family collaboration by addressing tensions of coordination, uneven workloads, and parental mediation. From a formative study with families using AI in daily learning, we identified challenges in responsibility sharing and recognition of contributions. Building on these insights, we designed FamLearn, an LLM-powered prototype that distributes tasks, visualizes contributions, and provides individualized support. A one-week field study with 11 families shows how this prototype can ease caregiving burdens, foster recognition, and enrich shared learning experiences. Our findings suggest that LLMs can move beyond the role of tutor to act as family mediators - balancing responsibilities, scaffolding intergenerational participation, and strengthening the relational fabric of family learning.

cs.HC↗

arXiv2025

Text2Schema: Filling the Gap in Designing Database Table Structures based on Natural Language

People without a database background usually rely on file systems or tools such as Excel for data management, which often lead to redundancy and data inconsistency. Relational databases possess strong data management capabilities, but require a high level of professional expertise from users. Although there are already many works on Text2SQL to automate the translation of natural language into SQL queries for data manipulation, all of them presuppose that the database schema is pre-designed. In practice, schema design itself demands domain expertise, and research on directly generating schemas from textual requirements remains unexplored. In this paper, we systematically define a new problem, called Text2Schema, to convert a natural language text requirement into a relational database schema. With an effective Text2Schema technique, users can effortlessly create database table structures using natural language, and subsequently leverage existing Text2SQL techniques to perform data manipulations, which significantly narrows the gap between non-technical personnel and highly efficient, versatile relational database systems. We propose SchemaAgent, an LLM-based multi-agent framework for Text2Schema. We emulate the workflow of manual schema design by assigning specialized roles to agents and enabling effective collaboration to refine their respective subtasks. We also incorporate dedicated roles for reflection and inspection, along with an innovative error detection and correction mechanism to identify and rectify issues across various phases. Moreover, we build and open source a benchmark containing 381 pairs of requirement description and schema. Experimental results demonstrate the superiority of our approach over comparative work.

cs.DB↗

arXiv2025

AutoScale: Scale-Aware Data Mixing for Pre-Training LLMs

Domain reweighting is an emerging research area aimed at adjusting the relative weights of different data sources to improve the effectiveness and efficiency of LLM pre-training. We show that data mixtures that perform well at smaller scales may not retain their advantage at larger scales, challenging the existing practice of determining competitive mixtures in small-scale experiments and directly applying them at much larger scales. To address this, we propose AutoScale, a two-stage, scale-aware data composition framework. First, AutoScale fits a parametric model that predicts the model's loss under different data compositions, then uses it to find an approximate best allocation at smaller, more manageable budgets. Next, leveraging a novel theoretical analysis of how optimal compositions evolve with scale, AutoScale extrapolates that composition to larger budgets without further retraining. Empirically, AutoScale accelerates convergence and improves downstream performance. For instance, when pre-training GPT-2 Large, it achieves a 28% faster perplexity reduction than baselines and up to a 38% speed-up over unweighted training, while yielding best-average results on various downstream tasks. Overall, our findings illustrate how domain importance shifts with training scale, underscoring the need for scale-dependent data curation in LLM training. Our code is open-sourced.

cs.LG↗

arXiv2025

Accurate Cobb Angle Estimation via SVD-Based Curve Detection and Vertebral Wedging Quantification

Adolescent idiopathic scoliosis (AIS) is a common spinal deformity affecting approximately 2.2% of boys and 4.8% of girls worldwide. The Cobb angle serves as the gold standard for AIS severity assessment, yet traditional manual measurements suffer from significant observer variability, compromising diagnostic accuracy. Despite prior automation attempts, existing methods use simplified spinal models and predetermined curve patterns that fail to address clinical complexity. We present a novel deep learning framework for AIS assessment that simultaneously predicts both superior and inferior endplate angles with corresponding midpoint coordinates for each vertebra, preserving the anatomical reality of vertebral wedging in progressive AIS. Our approach combines an HRNet backbone with Swin-Transformer modules and biomechanically informed constraints for enhanced feature extraction. We employ Singular Value Decomposition (SVD) to analyze angle predictions directly from vertebral morphology, enabling flexible detection of diverse scoliosis patterns without predefined curve assumptions. Using 630 full-spine anteroposterior radiographs from patients aged 10-18 years with rigorous dual-rater annotation, our method achieved 83.45% diagnostic accuracy and 2.55° mean absolute error. The framework demonstrates exceptional generalization capability on out-of-distribution cases. Additionally, we introduce the Vertebral Wedging Index (VWI), a novel metric quantifying vertebral deformation. Longitudinal analysis revealed VWI's significant prognostic correlation with curve progression while traditional Cobb angles showed no correlation, providing robust support for early AIS detection, personalized treatment planning, and progression monitoring.

cs.CV↗

arXiv2025

LLM-Powered AI Tutors with Personas for d/Deaf and Hard-of-Hearing Online Learners

Intelligent tutoring systems (ITS) using artificial intelligence (AI) technology have shown promise in supporting learners with diverse abilities. Large language models (LLMs) provide new opportunities to incorporate personas to AI-based tutors and support dynamic interactive dialogue. This paper explores how DHH learners interact with LLM-powered AI tutors with different experiences in DHH education as personas to identify their accessibility preferences. A user study with 16 DHH participants showed that they asked DHH-related questions based on background information and evaluated the AI tutors' cultural knowledge of the DHH communities in their responses. Participants suggested providing more transparency in each AI tutor's position within the DHH community. Participants also pointed out the lack of support in the multimodality of sign language in current LLMs. We discuss design implications to support the diverse needs in interaction between DHH users and the LLMs, such as offering supports in tuning language styles of LLMs.

cs.HC↗

arXiv2025

AI Academy: Building Generative AI Literacy in Higher Ed Instructors

Generative AI is reshaping higher education, yet research has focused largely on students, while instructors remain understudied despite their central role in mediating adoption and modeling responsible use. We present the \textit{AI Academy}, a faculty development program that combined AI exploration with pedagogical reflection and peer learning. Rather than a course evaluated for outcomes, the Academy provided a setting to study how instructors build AI literacies in relation to tools, policies, peer practices, and institutional supports. We studied 25 instructors through pre/post surveys, learning logs, and facilitator interviews. Findings show AI literacy gains alongside new insights. We position instructors as designers of responsible AI practices and contribute a replicable program model, a co-constructed survey instrument, and design insights for professional development that adapts to evolving tools and fosters ethical discussion.

cs.HC↗

arXiv2025

Exploring Conversational Design Choices in LLMs for Pedagogical Purposes: Socratic and Narrative Approaches for Improving Instructor's Teaching Practice

Large language models (LLMs) typically generate direct answers, yet they are increasingly used as learning tools. Studying instructors' usage is critical, given their role in teaching and guiding AI adoption in education. We designed and evaluated TeaPT, an LLM for pedagogical purposes that supports instructors' professional development through two conversational approaches: a Socratic approach that uses guided questioning to foster reflection, and a Narrative approach that offers elaborated suggestions to extend externalized cognition. In a mixed-method study with 41 higher-education instructors, the Socratic version elicited greater engagement, while the Narrative version was preferred for actionable guidance. Subgroup analyses further revealed that less-experienced, AI-optimistic instructors favored the Socratic version, whereas more-experienced, AI-cautious instructors preferred the Narrative version. We contribute design implications for LLMs for pedagogical purposes, showing how adaptive conversational approaches can support instructors with varied profiles while highlighting how AI attitudes and experience shape interaction and learning.

cs.HC↗

arXiv2025

Aligning LLMs for the Classroom with Knowledge-Based Retrieval -- A Comparative RAG Study

Large language models like ChatGPT are increasingly used in classrooms, but they often provide outdated or fabricated information that can mislead students. Retrieval Augmented Generation (RAG) improves reliability of LLMs by grounding responses in external resources. We investigate two accessible RAG paradigms, vector-based retrieval and graph-based retrieval to identify best practices for classroom question answering (QA). Existing comparative studies fail to account for pedagogical factors such as educational disciplines, question types, and practical deployment costs. Using a novel dataset, EduScopeQA, of 3,176 questions across academic subjects, we measure performance on various educational query types, from specific facts to broad thematic discussions. We also evaluate system alignment with a dataset of systematically altered textbooks that contradict the LLM's latent knowledge. We find that OpenAI Vector Search RAG (representing vector-based RAG) performs well as a low-cost generalist, especially for quick fact retrieval. On the other hand, GraphRAG Global excels at providing pedagogically rich answers to thematic queries, and GraphRAG Local achieves the highest accuracy with the dense, altered textbooks when corpus integrity is critical. Accounting for the 10-20x higher resource usage of GraphRAG (representing graph-based RAG), we show that a dynamic branching framework that routes queries to the optimal retrieval method boosts fidelity and efficiency. These insights provide actionable guidelines for educators and system designers to integrate RAG-augmented LLMs into learning environments effectively.

cs.AI↗