Transmission Electron Microscopy

Multimodal large language models (MLLMs) are increasingly explored as interfaces for scientific image analysis, where a visual question-answering (VQA) response may be paired with a spatial output that guides a downstream stage. A supervisor reads the language answer, while a downstream workflow such as segmentation or region review consumes the point-set output. We call this transition from inspecting the answer to relying on its point action the language-to-action hand-off. A silent failure occurs when the answer is correct while the paired action misses annotated objects needed downstream, so answer-based oversight clears a region whose action is unreliable. We introduce Spatial Action Review, a visual analytics dashboard for auditing this failure mode in electron microscopy (EM) mitochondria analysis. It links paired answer-action records through an answer-action ledger, a task-by-dataset risk map, and an image-region audit view, connecting aggregate patterns to image evidence while an adjustable action-reliability gate supports re-audit. The review ends in a human-AI hand-off, where a supervisor records whether the action is accepted, escalated, held under a stricter gate, or flagged for model revision. Across 541 image regions from an EM-adapted Qwen3-VL case-study run, point actions fail the gate in 54.4% of records with a correct VQA response, and 27.4% of all records are silent failures. A correct answer is associated with only a 5.8-percentage-point higher probability of a reliable action, with a bootstrap interval spanning zero; the point-biserial correlation between answer correctness and object coverage is 0.061. This weak coupling persists across five model conditions on 753 matched image regions. Spatial Action Review makes answer-action mismatches visible and ties them to image evidence and a recorded decision before MLLM outputs enter autonomous scientific workflows.

High-quality pre-training data is a critical bottleneck for educational and STEM-specific language models targeting edge AI and on-device deployment where token budgets are tightly constrained. While major organizations train ever-larger models on private corpora, the open ecosystem lacks STEM-focused synthetic datasets that deliver high per-token learning value efficiently for small models. To address this gap, we introduce QVAC Genesis III, a 191.43B-token, STEM-focused multi-domain synthetic corpus covering 19 domains across several difficulty levels and different educational styles. QVAC Genesis III is built via a dual generation strategy that performs targeted teacher distillation using a weak edge-scale student model as signal: the student's failures are converted into corrective explanations, while its successes are expanded into contrastive option-level reasoning over all answer choices. We further introduce an LLM-as-a-parser evaluation protocol that extracts final answers from free-form outputs and tracks both accuracy and answer validity. To validate the effectiveness of our QVAC Genesis III data, we conduct controlled from-scratch ablations with 1.7B-parameter models, showing that models trained with QVAC Genesis III consistently outperform both models trained with the open-source synthetic corpus Cosmopedia-v2 and the publicly released Cosmo-1B model across ARC, GPQA Diamond, and MMLU STEM benchmarks, achieving up to +28.57% on ARC-E and +21.35% on ARC-C, while reaching a Valid Answer Rate of up to 99.45%.

Recorded lecture videos, often enhanced with search and summarization features, are a standard study resource. However, students cannot easily ask course specific questions or verify answers against an instructor's lecture. We report a semester-long deployment of VideoPoints platform with a retrieval-augmented chatbot that answers from course lecture materials and returns timestamped citations. The chatbot retrieves only from the active course, uses chapter summaries to guide transcript ranking, and returns clickable timestamped citations. Students used it for quick lookups and exam review. Across 833 messages, 70.5% included citations, none crossed a course boundary, and when no lecture evidence matched, the chatbot usually declined rather than answering. Among the users, citations were the most consistently useful feature, while practice-question generation was the strongest unmet request. We also evaluated the design on the real-world test split of EduVidQA, a public multimodal benchmark for lecture-video question answering. Our design improved correct-lecture retrieval by 6.3 percentage points over dense-only retrieval. Together, the results show that effective deployment depends on course isolation, supported citations, and alignment with students' study practices.

Hardware assurance relies on scanning electron microscopy (SEM) to verify nanoscale structures, but assembling the large, high-quality datasets required for automated analysis is impeded by time-intensive acquisition and strict intellectual property (IP) constraints on proprietary designs. We propose a privacy-preserving pipeline that secures IP by heavily distorting the functional design while generating a visually realistic synthetic dataset from a small set of initial examples. A StyleGAN first learns the distribution of hardware layout masks to generate novel, macroscopically varied structures. Subsequently, a conditional GAN (Pix2PixHD) translates these masks into realistic SEM images that preserve authentic textures and noise. The primary finding of this work is that a segmentation model trained exclusively on this synthetic data not only demonstrates a successful "sim-to-real" transfer to real images but also outperforms a baseline model trained on the limited real dataset. Because the underlying synthetic layouts are demonstrably novel and reproduce none of the specific proprietary routing of the original design, deploying the final segmentation model mitigates the risk of exposing sensitive IP to attacks like gradient inversion and membership inference, providing a highly secure, high-performance solution for hardware assurance.

Contribution: This paper presents a six-phase AI-assisted instructional design architecture based on the Curriculum as Code paradigm, integrating Generative AI with LaTeX and Python to automate the creation of reproducible, visually consistent, and technically precise materials for STEM education. Background: Creating customized instructional materials for active learning imposes a heavy workload on faculty. Standard presentation tools lack robust support for technical content, while current AI applications often hallucinate and fail to formalize the instructional authoring process, limiting their utility for rigorous academic design. Intended Outcomes: The framework aims to reduce preparation time while ensuring mathematical accuracy, adherence to institutional visual identity, and preservation of the instructor's tacit pedagogical knowledge through explicit rules. Application Design: The solution comprises a six-phase pipeline that replaces ad-hoc prompt engineering with a systematic workflow, utilizing text-based interfaces and code-driven generation (LaTeX/Beamer for slides, Python for figures), governed by pedagogical constraints, contextual calibrations, and automated review cycles. Findings: Validated over one year across 8 modules and 28 project contexts in a Project-Based Learning environment, the architecture significantly reduced instructor workload. Generated assets underwent independent peer review and were deployed by six different faculty members, confirming scalability beyond a single author. Based on over 600 voluntary student evaluations, materials achieved high quality ratings from 8.5 to 9.9/10. Results indicate high reproducibility, minimized hallucinations, and sustained pedagogical and visual fidelity, suggesting viability for broad STEM educational applications.

Many open educational resources are lacking in accessibility, especially in-depth image descriptions. In subjects like Science and Mathematics, however, it can be particularly difficult to write image descriptions since there can be many complicated expressions and names depending upon the course level. To help fill that gap in a small way, we introduce Math Image Descriptions for Accessible Learning (MIDAL), a math image-description dataset of 2,020 mathematical images spanning multiple educational levels, to aid in training vision language models to create image descriptions following accessibility best practices. We hope MIDAL is a valuable resource in enhancing the conversation and innovation regarding accessibility of STEM content in higher education. This dataset is however not just limited in math description generation but can also be used to fine-tune language models that can have improved mathematical reasoning and answers.

Student engagement (SE) is a critical predictor of academic performance and retention in STEM education, yet existing measurement approaches are often intrusive, manually intensive, or unsuitable for real-time classroom use. This thesis proposes a novel $\textit{Biometric Sensor Network}$ (BSN) designed to enable real-time measurement and continuous tracking of individual student engagement in STEM classroom environments. The system enables capturing of behavioral, emotional, and cognitive indicators through camera-based sensing while preserving ethical and privacy constraints. To measure these indicators unobtrusively and ethically, we propose a BSN composed of $\textit{Student Processing Units}$ (SPUs) that function as distributed sensing nodes. The network is explicitly designed to satisfy five objectives: it must be $\textbf{non-intrusive}, \textbf{non-invasive}, \textbf{non-stigmatizing}, \textbf{real-time}$, and $\textbf{automatic}$, while ensuring rigorous protection of student data security and privacy. Each SPU supports two operational modes: (i) a $\textit{dataset-collection mode}$, in which raw student video is temporarily recorded to construct a private SE dataset for model training and validation, and (ii) an $\textit{analysis mode}$, in which the SPU performs real-time inference on 10-second video segments without storing or transmitting raw frames. In this analysis role, each SPU enables fully on-device processing---including face detection, gaze estimation, and affective analysis---ensuring that no identifiable video data leaves the device. A secure backend infrastructure manages device authentication, session orchestration, and encrypted data ingestion. The full system integrates hardware design, computer-vision pipelines, wireless networking, security protocols, and session-level data management.

Data augmentations define the invariances learned by self-supervised learning (SSL). Standard augmentation pipelines were designed for natural images, yet scientific imaging modalities are governed by physical measurement processes with distinct symmetry and acquisition constraints. Enforcing invariances that contradict these constraints can distort learned representations and limit downstream performance, but practitioners moving from machine learning into a new scientific modality currently have little guidance beyond transferring natural-image pipelines unexamined. We address this gap with a principled, reproducible procedure for augmentation design in scientific SSL: we formalise the physics-aligned augmentation set as a union of measurement-consistent symmetries and acquisition-driven perturbations, and we give a concrete, largely label-free workflow---enumerate candidates, label each by the measurement operator, validate with representation-geometry diagnostics, and confirm by single-factor ablation---for selecting them. We instantiate the procedure for real-space electron microscopy and reciprocal-space 4D-STEM diffraction, and evaluate it across five SSL paradigms (DINOv2, SimCLR, MAE, VICRegL, I-JEPA) on classification and crystal-orientation regression. Physics-aligned augmentations substantially improve downstream performance for objectives relying on cross-view consistency, reduce geodesic error and improve robustness under realistic acquisition variability (detector gain, resolution loss), and systematically reshape representation geometry. While our experiments use electron microscopy, the procedure is modality-agnostic and applies to other measurement-driven domains such as medical and remote-sensing imaging. These results position augmentation design as a primary, and controllable, source of inductive bias in scientific self-supervised learning.

Scientific figure comprehension and reasoning using multimodal AI requires integrating visual perception with domain-specific reasoning to extract meaningful knowledge, often not presented in the text of a research publication. The Sci-ImageMiner benchmark dataset, accompanied by a community-driven competition, raises the bar over prior scientific competitions by curating a comprehensive, expert-annotated dataset across four end-to-end complementary tasks. The competition attracted 68 active participants and 1,263 public/private submissions from 9th January 2026 to 8th April 2026. Our results show that state-of-the-art multimodal models perform well on classification and summarization tasks but struggle with data extraction and scientific reasoning, particularly in visual question-answering. These findings reveal key limitations and highlight challenges and opportunities for improving domain-aware multimodal AI systems. Overall, the Sci-ImageMiner benchmark and competition establish a rigorous platform for advancing research in scientific figure comprehension and reasoning and demonstrate the potential of state-of-the-art approaches for a challenging and complex research area.

This study systematically benchmarks different data augmentation setups across the baseline YOLO26 model size variants to determine the most effective setup for adenovirus detection in TEM images. The benchmarked setups include NAS, GAS, GMAS, and DAS, all evaluated under identical training conditions. A modified YOLO26 model leveraging P2, expanded STAL, increased topk, and MuSGD was also tested across the same benchmarked setups. The adenovirus dataset, selected from the published TEM virus dataset, was re-annotated by leveraging adenovirus particle positions to generate YOLO-compatible bounding box annotations. The modifications produced their largest performance gains under GAS and GMAS, with modified YOLO26x trained using GAS achieving a mAP@50 of 0.80, Precision of 0.81 and a Recall of 0.80

Organic mixed ionic electronic conductors (OMIECs) are a promising class of polymer materials for applications spanning neuromorphic computation to energy efficient electronics and bioelectronics. Despite being highly tunable, the relationship between structural features and key performance properties such as charge carrier mobility is poorly understood. Scanning nanodiffraction in the transmission electron microscope (TEM) is a powerful probe for elucidating this structure-property relationship, but produces large, noisy datasets that are difficult to interpret because polymer reflections exhibit several distinct morphologies. To address the complexity, we trained a machine learning (ML) model to detect these polymer diffraction peaks and their intensities from synthetic data. Compared to correlative peak detection algorithms, the conventional method for analyzing nanobeam 4D scanning transmission electron microscopy (4DSTEM) data, we show that the ML model is significantly faster and outperforms correlative algorithms in almost all cases, opening up the possibility of near-live visualization of 4DSTEM experiments.

Artificial intelligence (AI) is transforming electron microscopy by enabling quantitative analysis of increasingly large and complex datasets for nanoparticle characterization. Recent advances in machine learning (ML) and deep learning (DL) have expanded microscopy from a descriptive imaging technique into a data-driven platform for structural interpretation, dynamic analysis, and scientific inference. This review examines AI methodologies for nanoparticle electron microscopy, focusing on transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), scanning transmission electron microscopy (STEM), and in situ TEM. The discussion is organized around the principal challenges in nanoparticle characterization, including particle detection, segmentation, morphology quantification, atomic-resolution restoration, defect identification, two-dimensional-to-three-dimensional structural inference, and analysis of dynamic processes in situ. We review computational approaches from conventional ML and convolutional neural networks to transformer architectures, self-supervised learning, foundation models, multimodal AI, and physics-informed learning. We further discuss integrating microscopy data with simulations, metadata, and autonomous experimentation to relate nanoparticle structure, dynamics, synthesis conditions, and functional properties. The advantages, limitations, benchmarking, and data requirements of current methodologies are critically assessed. Finally, emerging opportunities for foundation models, AI-guided microscopy, closed-loop experimentation, and autonomous materials discovery are discussed. By integrating advances across computer vision, materials informatics, and electron microscopy, this review highlights the role of AI in next-generation nanoparticle characterization and accelerated materials discovery.

A central premise of autonomous scientific imaging is that smarter navigation, whether Bayesian, RL-based, or otherwise adaptive, is the principal lever for sample-efficient acquisition. We present evidence to the contrary in scanning transmission electron microscopy (STEM), an atomic-resolution imaging modality whose every measurement deposits damaging electron dose. We introduce STEMGym, an open-source Gymnasium benchmark of 15 physics-simulated STEM worlds spanning five materials, three difficulty levels, and four characterisation tasks, scored by the Dose-Efficiency Curve area (DEC-AUC), a single scalar capturing the information-vs-dose Pareto frontier. Across 33 agent configurations under realistic dose budgets, the dominant determinant of dose efficiency is the analyst (perception) pipeline, not the navigator: pairing a trained CNN analyst with naïve raster scanning raises DEC-AUC by 5.5x over a CNN-free raster baseline (0.287 vs.\ 0.052), while substituting Bayesian or adaptive finite-state-machine navigation for raster yields no statistically significant further gain. Production-tier vision-language models further underperform task-specific CNNs by {\sim}13x on crystallographic defect analysis. By decoupling perception, navigation, and planning under a unified dose budget, STEMGym reframes where ML effort should be invested in autonomous electron microscopy and provides the measurement infrastructure to test it.

Advanced semiconductor nodes drastically increased demand for Transmission Electron Microscopy (TEM), yet destructive sample preparation, slow imaging and high costs severely limit the availability of diverse datasets needed for downstream machine learning (ML). Synthetic data generation is becoming essential, but current generative models often miss TEM-specific noise, structural detail, and stochastic variability crucial for evaluation. We present a Denoising Diffusion Probabilistic Model (DDPM) framework for synthetic TEM image generation under extreme data scarcity. A progressive patch-based training strategy scales from low-resolution patches to full images, enabling from-scratch training with only 15 samples. We integrate a custom TrivialAugment adaptation, cross-process domain transfer, classifier guidance, and RePaint-style inpainting, culminating in full-image generation that preserves global structural and spatial relationships in compliance with FAB metrology requirements. Beyond synthesis, we repurpose DDPM feature representations for segmentation, partitioning encoder feature maps to obtain coherent region masks. Our synthetic images achieve up to MS-SSIM > 0.98 and qualitative expert assessment consistent with structural similarity results, facilitating downstream ML training for defect detection, segmentation, and metrology while preserving statistical and physical realism.

Vision foundation models have substantially advanced computer vision, enabling state-of-the-art performance in zero- and few-shot settings. They have been successfully applied to biomedical imaging tasks ranging from organ segmentation in computed tomography to cell segmentation in light microscopy. Electron microscopy (EM) is a central modality for analyzing cellular ultrastructure due to its nanometer-scale resolution. However, the application of foundation models in EM has so far been limited to specific organelles, such as mitochondria, largely due to the diversity of segmentation tasks and the scarcity of comprehensively annotated data. As a result, EM segmentation still predominantly relies on supervised learning, requiring extensive manual annotation and limiting ultrastructural analysis. To address this gap, we propose $μ$Match, a framework for semi-supervised learning and domain adaptation that leverages foundation models. We implement state-of-the-art student-teacher-based methods and evaluate multiple foundation models (SAM, SAM2, $μ$SAM, DINOv2/v3) on challenging EM tasks, including mitochondrion, nucleus, and neurite segmentation. Our results demonstrate consistent improvements over strong baselines and highlight a path toward substantially reducing the annotation effort in EM.

Anisotropic volumetric acquisitions are common in clinical MRI and volume electron microscopy (vEM), where sparse through-plane sampling creates thick slices or sections that degrade orthogonal reformats and downstream analysis. We present CRIS, a cross-plane self-supervised framework for isotropic restoration without paired isotropic ground truth. CRIS casts 3D restoration as 2D stripe completion on orthogonal reformats of an isotropic grid: high-resolution in-plane slices are synthetically degraded and periodically masked for training, while at inference blank slices define the isotropic grid, two orthogonal reformats are restored, and predictions are fused by multi-view averaging. We evaluate CRIS on two MRI cohorts and two microscopy benchmarks up to 8x anisotropy. On brain MRI, CRIS achieves 32.921 +/- 0.436 dB PSNR and 0.963 +/- 0.003 SSIM, outperforming interpolation, ECLARE, SMORE4, SIMPLE, SA-INR, and ATME, and gives the best segmentation consistency (Dice 0.940 +/- 0.004, ASSD 0.245 +/- 0.014 mm, HD99 1.275 +/- 0.061 mm). On reference-free abdominal MRI, CRIS reduces FID/KID to 48.71/0.023, outperforming interpolation, ECLARE, SMORE4, and SIMPLE. On vEM, CRIS achieves 29.100 dB/0.830 3D PSNR/SSIM at 4x and 26.874 dB/0.722 at 8x on EPFL, and 21.935 +/- 0.437 dB/0.696 +/- 0.024 on noisy hemibrain data. In a dedicated robustness experiment, one variable-gap CRIS model evaluated across gap factors 3-7 and coronal, axial, and sagittal degradations maintained higher PSNR/SSIM than interpolation (36.36-31.14 dB and 0.977-0.932 vs. 33.07-27.85 dB and 0.951-0.853). These results support CRIS as a modality-flexible route to isotropic restoration without paired isotropic targets or configuration-specific retraining. Code is available at https://github.com/adi-hatav/CRIS.

STEM education faces challenges in personalization and interdisciplinary integration. AI technology has brought new possibilities, but the mechanisms by which AI reshapes the STEM education ecosystem require systematic investigation. This study employs bibliometric methods to analyze 242 publications from 2015-2025, constructing knowledge maps to reveal the evolutionary trajectory. The findings show that the field has transformed from intelligent tutoring systems to inquiry-based learning and computational thinking cultivation driven by LLMs. AI's key contribution lies in providing intelligent scaffolding that lowers the threshold for understanding knowledge. In this sense, AI is a core driving force promoting its shift from knowledge transmission to capability development.

Energy Dispersive X-ray (EDX) tomography in Scanning Transmission Electron Microscopy (STEM) enables 3D compositional and elemental mapping at the nanoscale, but its use is limited by restricted tilt ranges and low-dose conditions required to avoid beam damage. Limited-angle acquisition introduces missing-wedge artefacts such as elongation and anisotropic resolution, while noisy low-dose data further degrade reconstruction quality and quantitative reliability. Here, we introduce an unsupervised deep learning framework based on Deep Image Prior with total variation regularization (DIP-TV) for limited-angle STEM-EDX tomography. We extend it to a multi-channel formulation (DIPm-TV) that jointly reconstructs multiple elemental maps by exploiting spatial correlations. Using a synthetic 3-channel phantom, we show that the method compensates for severe missing-wedge artefacts corresponding to approximately $100^\circ$ of missing angular range under moderate noise, outperforming simultaneous iterative reconstruction technique and compressed sensing approaches. We apply the method to 3D chemical analysis of Ge-Sb-Te (GST) memory devices in virgin (as-fabricated) and SET (crystalline) operational states. Samples were prepared as cross-sectional focused ion beam lamellae and acquired under a limited-angle tilt range from $-40^\circ$ to $+40^\circ$ with $5^\circ$ steps and a dose of $2.0\times10^5$ $e^-/Ang^2$. The multi-channel approach enables voxel-by-voxel elemental reconstruction using only EDX signals without external structural priors such as high-angle annular dark-field imaging. The reconstructed volumes show near-isotropic spatial resolution and reveal compositional heterogeneities associated with device operation. This approach enables 3D chemical characterization in experimentally accessible sample geometries where conventional methods fail due to severe angular limitations.

Artificial intelligence is rapidly advancing materials characterization, yet most applications in electron microscopy rely solely on image contrast, overlooking the chemical and experimental context that shapes image formation. This limitation makes defect classification inherently ambiguous, as similar contrasts can arise from different materials or imaging conditions. Here we develop a context-aware learning framework that integrates image-derived contrast with metadata describing composition, beam energy, and detector geometry. Using a systematically constructed dataset of ~55 million simulated patches spanning 576 cases across 96 doped monolayer transition-metal dichalcogenides, we show that conditioning on contextual variables transforms defect classification from an ill-posed image-only task into a well-posed, physically grounded problem. The framework achieves over 98% accuracy on simulations and near-human agreement on experimental data, with a 94% reduction in posterior entropy. By emphasizing contextual grounding over architectural complexity, this approach links experimental image contrast to the underlying chemical and imaging conditions, supporting physically grounded defect assignments and a general pathway toward multimodal AI models for autonomous materials characterization.

Symbolic benchmarks have emerged as a key approach to assess model robustness under minor modifications to STEM-related questions. However, existing symbolic benchmarks mostly remain limited to mathematical reasoning, lack visual grounding, and are predominantly in English. In this work, we introduce Sci-Rho (Science Rhobustness), a dynamic benchmark for visually-grounded STEM problems spanning five subjects and seven languages, comprising 4,242 problem templates (606 per language) crafted by domain experts, including Olympiad medalists. Each template is implemented as executable Python code that generates diverse but equivalent problem instances by varying numerical values, visual patterns, geometric shapes, color schemes, and function types, resulting in 42,420 instances in total, each paired with reasoning steps and ground-truth solutions. We evaluated 17 state-of-the-art VLMs and discovered a noticeable gap between worst-case accuracy (defined as the proportion of problem templates that a model answers correctly across every generated variation) and average accuracy. We also discovered that smaller models show noticeable performance degradation across languages, whereas proprietary and larger models remain robust. Step-level evaluation reflects this same trend, revealing a significant gap between average F1 and worst-case F1 scores. Finally, our inspection of attention heads of a VLM reveals substantial cross-lingual variation in the relative attention allocated to image tokens compared to text tokens. Our work highlights the importance of evaluation beyond static benchmarks as a metric to measure the quality of VLMs.

Analyzing microstructural defects in transmission electron microscopy (TEM) images, particularly in irradiated metal alloys, is often limited by the availability of high-quality, labeled data. To address this, we introduce a generative data augmentation approach using a mask-conditioned latent diffusion model (LDM) for synthesizing realistic TEM images with controllable, automatically labeled multi-class defect masks. Without requiring manual annotations for generation, our method enables the creation of synthetic image-mask pairs by sampling distributions learned from experimental masks. These generated data were used to augment small experimental datasets of varying sizes (10, 50, and 100 labeled experimental images) to train a Mask Regional Convolutional Neural Network (R-CNN) model for defect detection and classification. Our results show that generative augmentation yields small overall model performance improvements, with up to a 0.02 gain in the harmonic mean of detection and classification F1 scores. However, we also find that the relative contributions to detection and classification improvement depend on the specific train/test data split. These findings highlight the potential of targeted generative models to enhance deep learning performance in data-scarce microscopy-based image quantification tasks.

Reliable identification of fracture origins in alumina matrix composite hip and knee implants is critical for quality assurance and patient safety, yet current fractographic workflows are time-consuming, partly subjective, and reliant on high-magnification scanning electron microscopy (SEM). We present an interpretable vision-transformer (ViT) workflow for automated classification of fracture causes in an alumina matrix composite (BIOLOX delta, CeramTec GmbH) widely used in total joint replacements. A dataset of 8,493 SEM images (50x-10,000x) was curated from five years of in-production burst and proof tests and annotated into three defect categories defined along the manufacturing chain: green body, hard machining, and material defects. Under severe class imbalance, the fine-tuned ViT reached an accuracy of 0.907 and a macro-F1 of 0.888 in stratified five-fold cross-validation, with a two-stage perceptual-hash/SSIM leakage audit confirming negligible specimen overlap. Notably, performance at low magnification (50x) was comparable to that at high magnification (1k-10kx), indicating that macro-scale features - mirror geometry and hackle line fields - already encode sufficient diagnostic signal. Grad-CAM attributions consistently localised on canonical fractographic cues (mirrors, hackles, pores, machining marks), aligning with established fractographic criteria. Together, these results position interpretable ViTs as a complementary tool for ceramic-implant quality assurance, enabling low-magnification pre-screening and reducing reliance on time-intensive high-magnification inspection.

As Artificial Intelligence (AI) literacy initiatives expand in K-12 settings, understanding how gender shapes student baseline perceptions, tool-use, and responsiveness to interventions is essential for equitable curriculum design. This study examines gender differences in AI literacy, safety awareness, and STEM career aspirations among Australian secondary students (Years 7, 8, and 10; N(pre) = 199, n(post) = 136) from two co-educational government schools who participated in a one-day AI literacy workshop. Using statistical regression methods controlling for year level and school, we found that pre-workshop, male students reported significantly higher STEM career interest across all three domains (AI, computer science, and engineering), while female students were significantly more likely to use AI for schoolwork and to seek advice from AI tools. Gender-differentiated patterns also emerged in deepfake behaviours: males were significantly more likely to have created or shared deepfake content. Both genders improved in AI knowledge post-intervention, yet females showed a richer profile of gains: wider conceptual understanding, greater confidence, and meaningful increases in AI and CS career interest that partially narrowed the gender STEM gap. These findings highlight the need for gender-responsive AI curricula, particularly deepfake safety education for male students, and demonstrate that even single-day workshops can narrow gender gaps in STEM aspirations and AI confidence.

Long-horizon video generation has advanced in visual quality, yet existing methods still struggle to maintain knowledge consistency and coherent pedagogical narratives across multi-shot instructional videos, especially in STEM domains. To address these challenges, we propose EduStory, a unified framework for reliable instructional video generation. EduStory integrates pedagogical state modeling to track persistent knowledge states, script-guided structured control to organize multi-shot narratives, and learning-oriented evaluation metrics to assess knowledge fidelity and constraint satisfaction. To support rigorous evaluation, we further introduce EduVideoBench, a diagnostic benchmark with multi-granularity annotations, including pedagogical storyboards, shot-level semantics, and knowledge state transitions, together with baseline tasks for controllable instructional video generation. Extensive experiments demonstrate that domain-aware state modeling and structured control substantially reduce narrative breakdown and improve alignment with instructional intent. These results highlight the significance of domain-specific structural constraints and tailored benchmarks for advancing reliable, controllable, and also trustworthy long-horizon video generation.

Large Language Models (LLMs) are democratizing access to personalized tutoring; however, their effectiveness is hindered by challenges in processing multimodal content, which limits AI's potential to provide equitable, high-quality STEM support. This study evaluates LLM performance on multimodal physics problems, identifies specific failure modes through an empirical error taxonomy, and tests practical interventions designed to overcome multimodal processing limitations. We assessed three publicly available LLMs (Claude, Gemini, and ChatGPT) on multimodal physics problems from the OpenStax database and compared the results with text-only performance. An empirically derived error taxonomy was developed through pilot testing, followed by evaluation of a structured multimodal dialogue intervention. All three models achieved near-ceiling accuracy (96%) on text-only physics problems. Performance declined substantially on multimodal problems, consistent with what we term the Multimodal Interference Effect. Error analysis identified four failure modes: visual processing errors, context misinterpretation, mathematical computational errors, and hybrid errors, with visual processing errors being the most prevalent. The structured dialogue intervention corrected 82% of errors overall; visual processing errors were corrected at 100% across all models. Educators and students can implement these interventions immediately, requiring no model retraining, to improve AI tutoring reliability on image-rich STEM content, advancing equitable access to high-quality learning support.

Creating interactive STEM courseware traditionally requires HTML/CSS/JavaScript expertise, leaving barriers for educators. While generative AI can produce HTML codes, existing tools generate static presentations rather than interactive simulations, struggle with long documents, and lack pedagogical accuracy mechanisms. Furthermore, full regeneration for modifications requires 200--600 seconds, disrupting creative flow. We present MAIC-UI, a zero-code authoring system that enables educators to create and rapidly edit interactive courseware from textbooks, PPTs, and PDFs. MAIC-UI employs: (1) structured knowledge analysis with multi-modal understanding to ensure pedagogical rigor; (2) a two-stage generate-verify-optimize pipeline separating content alignment from visual refinement; and (3) Click-to-Locate editing with Unified Diff-based incremental generation achieving sub-10-second iteration cycles. A controlled lab study with 40 participants shows MAIC-UI reduces editing iterations (4.9 vs. 7.0) and significantly improves learnability and controllability compared to direct Text-to-HTML generation. A three-month classroom deployment with 53 high school students demonstrates that MAIC-UI fosters learning agency and reduces outcome disparities -- the pilot class achieved 9.21-point gains in STEM subjects compared to -2.32 points in control classes. Our code is available at https://github.com/THU-MAIC/MAIC-UI.

Kohn-Sham (KS) eigenvalues are routinely compared with angle-resolved photoemission (ARPES) and used as input for many-body methods, yet density functional theory (DFT) assigns them no physical meaning. For alkali and alkaline-earth metals, KS bandwidths overestimate ARPES measurements by 20-35%, a discrepancy that persists across all exchange-correlation functionals. We construct an effective field theory (EFT) of the inhomogeneous electron gas and show that two conditions imply KS bands are the quasiparticle bands, up to a frozen-core renormalization factor zcore: a scale separation between core excitation energies and the valence Fermi energy, and an approximate Galilean invariance of the uniform electron gas confirmed by diagrammatic Monte Carlo. This factor reflects dynamical core excitations that conventional pseudopotentials freeze out and no static potential can capture. The correction 1-zcore reaches 20-35% for alkali metals but falls below 5% for Al and Si, explaining both the failure and success of KS band theory. We derive a closed-form post-SCF formula and validate it for Li, Na, K, Ca, Mg, Al, and Si; the predicted quasiparticle bands resolve the long-standing ARPES bandwidth discrepancy, matching embedded dynamical mean-field theory at negligible cost. This work also exemplifies first-principles agentic science, a direction particularly suited to the AGI-for-Science paradigm: an LLM-co-developed derivation with controlled approximations, verified symbolically and against a few experiments, becomes a deterministic harness for agentic scale-out, resolving simultaneously the LLM audit bottleneck and the non-falsifiability of fit-based AI-for-science.

The transmission electron microscope facilitates the highest-resolution imaging of any instrument ever created, and its limiting factor is no longer spatial resolution but dose efficiency. Low electron doses avoid sample damage but produce noisy images for which, unlike in classical computer vision, there is no ground truth. Autonomous materials experimentation poses a related problem, since closed-loop instruments need representations grounded in the microscope state at acquisition. Both demand representations grounded in how an image was acquired. We release 7,330 paired high-angle annular dark-field scanning-TEM (HAADF-STEM) images and their seven-dimensional acquisition metadata, and propose Contrastive Image-Metadata Pre-training (CIMP), a CLIP-style encoder that aligns the two modalities and reaches 84.4% Top-1 cross-modal retrieval on a held-out split. All seven parameters are individually recoverable from the frozen visual embedding through a linear probe, and we use the embedding to condition a metadata-conditioned style-transfer model that re-renders experimental images under different acquisition parameters. Virtually scaling dwell time and beam current of low-dose images turns this model into a physics-informed denoiser; in a blind user study, experimental microscopists prefer it over the current state-of-the-art denoiser for STEM imagery on 70.2% of trials.

Argumentation is a core practice in STEM education, but its productivity depends on who participates and how they interact. Higher-achieving students often dominate the talk and decision-making, while lower-achieving peers may disengage, defer, or comply without contributing substantive reasoning. Forming groups strategically based on students' stances and argumentation skills could help foster inclusive, evidence-based discourse. In practice, however, teachers are constrained in implementing this grouping strategy because it requires real-time insight into students' positions and the quality of their argumentation, information that is difficult to assess reliably and at scale during instruction. We present a generative AI-powered system, ArguAgent, that creates groups optimizing for stance heterogeneity while constraining argumentation quality differences to +/-1 level on a validated learning progression. ArguAgent uses a two-component assessment pipeline: first scoring student arguments on a 0-4 rubric, then clustering positions via semantic analysis. We validated the scoring component against human expert consensus (Krippendorff's ααα = 0.817) using 200 expert-generated scores. Testing three OpenAI models (GPT-4o-mini, GPT-5.1, GPT-5.2) with identical calibrated prompts, we found that systematic prompt engineering informed by human disagreement analysis contributed 89% of scoring improvement (QWK: 0.531 to 0.686), while model upgrades contributed an additional 11% (QWK: 0.686 to 0.708). Simulation testing across 100 classes demonstrated that the grouping algorithm achieves 95.4% of groups that meet both design criteria, a 3.2x improvement over random assignment. These results suggest ArguAgent can enable real-time, theoretically grounded grouping that promotes productive STEM argumentation in classrooms.

STEM education researchers are often interested in identifying moments of students' mechanistic reasoning for deeper analysis, but have limited capacity to search through many team conversation transcripts to find segments with a high concentration of such reasoning. We offer a solution in the form of an interpretable machine learning model that outputs time-varying probabilities that individual students are engaging in acts of mechanistic reasoning, leveraging evidence from their own utterances as well as contributions from the rest of the group. Using the toolkit of intentionally-designed probabilistic models, we introduce a specific inductive bias that steers the probabilistic dynamics toward desired, domain-aligned behavior. Experiments compare trained models with and without the inductive bias components, investigating whether their presence improves the desired model behavior on transcripts involving never-before-seen students and a novel discussion context. Our results show that the inductive bias improves generalization -- supporting the claim that interpretability is built into the model for this task rather than imposed post hoc. We conclude with practical recommendations for STEM education researchers seeking to adopt the tool and for ML researchers aiming to extend the model's design. Overall, we hope this work encourages the development of mechanistically interpretable models that are understandable and controllable for both end users and model designers in STEM education research.

Multimodal large language models (MLLMs) have shown promising reasoning abilities, yet evaluating their performance in specialized domains remains challenging. STEM reasoning is a particularly valuable testbed because it provides highly verifiable feedback, but existing benchmarks often permit unimodal shortcuts due to modality redundancy and focus mainly on final-answer accuracy, overlooking the reasoning process itself. To address this challenge, we introduce StepSTEM: a graduate-level benchmark of 283 problems across mathematics, physics, chemistry, biology, and engineering for fine-grained evaluation of cross-modal reasoning in MLLMs. StepSTEM is constructed through a rigorous curation pipeline that enforces strict complementarity between textual and visual inputs. We further propose a general step-level evaluation framework for both text-only chain-of-thought and interleaved image-text reasoning, using dynamic programming to align predicted reasoning steps with multiple reference solutions. Experiments across a wide range of models show that current MLLMs still rely heavily on textual reasoning, with even Gemini 3.1 Pro and Claude Opus 4.6 achieving only 38.29% accuracy. These results highlight substantial headroom for genuine cross-modal STEM reasoning and position StepSTEM as a benchmark for fine-grained evaluation of multimodal reasoning. Source code is available at https://github.com/lll-hhh/STEPSTEM.

This dissertation explores how deep generative models can advance the analysis of challenging biological problems by integrating domain knowledge with deep learning. It focuses on two areas: DNA reaction kinetics and cryogenic electron microscopy (cryo-EM). In the first part, we present ViDa, a biophysics-informed framework leveraging variational autoencoders (VAEs) and geometric scattering transforms to generate biophysically-plausible embeddings of DNA reaction kinetics simulations. These embeddings are reduced to a two-dimensional space to visualize DNA hybridization and toehold-mediated strand displacement reactions. ViDa preserves structure and clusters trajectory ensembles into reaction pathways, making simulation results more interpretable and revealing new mechanistic insights. In the second part, we address key challenges in cryo-EM density map interpretation and protein structure modeling. We provide a comprehensive review and benchmarking of deep learning methods for atomic model building, with improved evaluation metrics and practical guidance. We then present Struc2mapGAN, a generative adversarial network that synthesizes high-fidelity experimental-like cryo-EM density maps from protein structures. Finally, we present CryoSAMU, a structure-aware multimodal U-Net that enhances intermediate-resolution cryo-EM maps by integrating density features with structural embeddings from protein language models via cross-attention. Overall, these contributions demonstrate the potential of deep generative models to interpret DNA reaction mechanisms and advance cryo-EM density map analysis and protein structure modeling.

Quantitative microstructural characterization is fundamental to materials science, and electron micrographs (EMs) provide indispensable high-resolution insights. However, progress in deep learning-based analysis of EMs has been hampered by the scarcity of large-scale, expert-annotated public datasets. To address this issue, we introduce EM3M, a large-scale and multimodal dataset for instance-level understanding of EMs. EM3M comprises 5,091 high-quality EMs, approximately 3 million instance segmentation annotations, and image-level textual descriptions with disentangled attributes. The dataset is constructed through a rigorous multi-stage curation and validation pipeline, with comprehensive statistical analyses to ensure reliability and reproducibility. Building upon these curated image-text pairs, we further provide a text-to-image diffusion model that serves as a controllable data augmentation engine, demonstrating that synthetic augmentation consistently improves downstream segmentation performance. To establish a systematic benchmark, we evaluate representative instance segmentation methods on EM3M. Our results reveal that conventional detection-based and query-based methods struggle with the extreme instance densities and textural complexities inherent in EMs. We additionally provide an optimized flow-based baseline to facilitate fair comparison and future research. EM3M {Dataset: https://huggingface.co/datasets/UniParser/EM3M}, the generative engine {Generation: https://huggingface.co/UniParser/EM3M-Gen}, and an online demo {Segmentation demo: https://www.bohrium.com/apps/uni-aims} are publicly available to support future research in automated materials analysis.