Lina Zhang

Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou et al.

Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program package designed to leverage the power of ML to enhance typical computational chemistry simulations and to create complex workflows. This open-source package provides plenty of choice to the users who can run simulations with the command line options, input files, or with scripts using MLatom as a Python package, both on their computers and on the online XACS cloud computing at XACScloud.com. Computational chemists can calculate energies and thermochemical properties, optimize geometries, run molecular and quantum dynamics, and simulate (ro)vibrational, one-photon UV/vis absorption, and two-photon absorption spectra with ML, quantum mechanical, and combined models. The users can choose from an extensive library of methods containing pre-trained ML models and quantum mechanical approximations such as AIQM1 approaching coupled-cluster accuracy. The developers can build their own models using various ML algorithms. The great flexibility of MLatom is largely due to the extensive use of the interfaces to many state-of-the-art software packages and libraries.

Lina Zhang, Tonmoy Monsoor, Mehmet Efe Lorasdagi et al.

Multimodal Large Language Models (MLLMs) have demonstrated robust capabilities in recognizing everyday human activities, yet their potential for analyzing clinically significant involuntary movements in neurological disorders remains largely unexplored. This pilot study evaluates the capability of MLLMs for automated recognition of pathological movements in seizure videos. We assessed the zero-shot performance of state-of-the-art MLLMs on 20 ILAE-defined semiological features across 90 clinical seizure recordings. MLLMs outperformed fine-tuned Convolutional Neural Network (CNN) and Vision Transformer (ViT) baseline models on 13 of 18 features without task-specific training, demonstrating particular strength in recognizing salient postural and contextual features while struggling with subtle, high-frequency movements. Feature-targeted signal enhancement (facial cropping, pose estimation, audio denoising) improved performance on 10 of 20 features. Expert evaluation showed that 94.3 percent of MLLM-generated explanations for correctly predicted cases achieved at least 60 percent faithfulness scores, aligning with epileptologist reasoning. These findings demonstrate the potential of adapting general-purpose MLLMs for specialized clinical video analysis through targeted preprocessing strategies, offering a path toward interpretable, efficient diagnostic assistance. Our code is publicly available at https://github.com/LinaZhangUCLA/PathMotionMLLM.

Lina Zhang, Tonmoy Monsoor, Peizheng Li et al.

While Multimodal Large Language Models (MLLMs) have demonstrated remarkable proficiency in general video understanding, their capacity to interpret involuntary, and spatio-temporally evolving pathologic motor behaviors such as seizure semiology remains largely untested. To address this gap, we introduce Seizure-Semiology-Suite, a clinically grounded dataset and benchmark for fine-grained, structured seizure semiology understanding. The dataset includes 438 seizure videos annotated with over 35,000 dense labels covering 20 ILAE-defined semiological features. Building on this dataset, we propose a seven-task hierarchical benchmark that systematically evaluates MLLMs from low-level visual perception to temporal sequencing, narrative report generation, and seizure diagnosis. To enable clinically meaningful evaluation of generated reports, we further introduce the Report Quality Index for Seizure Semiology (Seizure-RQI). Extensive baselines across 11 open-weight MLLMs reveal systematic weaknesses in laterality reasoning, temporal localization, symptom sequencing, and clinically faithful reporting. We show that seizure-specific fine-tuning substantially improves performance across tasks, and that a two-stage neuro-symbolic framework achieves an F1 score of 0.96 on epileptic versus non-epileptic seizure classification. Seizure-Semiology-Suite establishes a rigorous benchmark for evaluating multimodal models in safety-critical medical video understanding and guides the development of clinically reliable, domain-adaptive multimodal intelligence.

Yi-Fan Hou, Lina Zhang, Quanhao Zhang et al.

Quantum chemical simulations can be greatly accelerated by constructing machine learning potentials, which is often done using active learning (AL). The usefulness of the constructed potentials is often limited by the high effort required and their insufficient robustness in the simulations. Here we introduce the end-to-end AL for constructing robust data-efficient potentials with affordable investment of time and resources and minimum human interference. Our AL protocol is based on the physics-informed sampling of training points, automatic selection of initial data, uncertainty quantification, and convergence monitoring. The versatility of this protocol is shown in our implementation of quasi-classical molecular dynamics for simulating vibrational spectra, conformer search of a key biochemical molecule, and time-resolved mechanism of the Diels-Alder reactions. These investigations took us days instead of weeks of pure quantum chemical calculations on a high-performance computing cluster. The code in MLatom and tutorials are available at https://github.com/dralgroup/mlatom.

Jakub Martinka, Lina Zhang, Yi-Fan Hou et al.

Nonadiabatic couplings (NACs) play a crucial role in modeling photochemical and photophysical processes with methods such as the widely used fewest-switches surface hopping (FSSH). There is therefore a strong incentive to machine learn NACs for accelerating simulations. However, this is challenging due to NACs' vectorial, double-valued character and the singularity near a conical intersection seam. For the first time, we design NAC-specific descriptors based on our domain expertise and show that they allow learning NACs with never-before-reported accuracy of $R^2$ exceeding 0.99. The key to success is also our new ML phase-correction procedure. We demonstrate the efficiency and robustness of our approach on a prototypical example of fully ML-driven FSSH simulations of fulvene targeting the SA-2-CASSCF(6,6) electronic structure level. This ML-FSSH dynamics leads to an accurate description of $S_1$ decay while reducing error bars by allowing the execution of a large ensemble of trajectories. Our implementations are available in open-source MLatom.

Qi Sun, Dingju Zhou, Lina Zhang

The analysis of character appearance frequency is essential for understanding narrative structure, character prominence, and story progression in anime. In this work, we introduce OregairuChar, a benchmark dataset designed for appearance frequency analysis in the anime series My Teen Romantic Comedy SNAFU. The dataset comprises 1600 manually selected frames from the third season, annotated with 2860 bounding boxes across 11 main characters. OregairuChar captures diverse visual challenges, including occlusion, pose variation, and inter-character similarity, providing a realistic basis for appearance-based studies. To enable quantitative research, we benchmark several object detection models on the dataset and leverage their predictions for fine-grained, episode-level analysis of character presence over time. This approach reveals patterns of character prominence and their evolution within the narrative. By emphasizing appearance frequency, OregairuChar serves as a valuable resource for exploring computational narrative dynamics and character-centric storytelling in stylized media.

Zejin Wang, Guodong Sun, Lina Zhang et al.

Recently, flow-based methods have achieved promising success in video frame interpolation. However, electron microscopic (EM) images suffer from unstable image quality, low PSNR, and disorderly deformation. Existing flow-based interpolation methods cannot precisely compute optical flow for EM images since only predicting each position's unique offset. To overcome these problems, we propose a novel interpolation framework for EM images that progressively synthesizes interpolated features in a coarse-to-fine manner. First, we extract missing intermediate features by the proposed temporal spatial-adaptive (TSA) interpolation module. The TSA interpolation module aggregates temporal contexts and then adaptively samples the spatial-related features with the proposed residual spatial adaptive block. Second, we introduce a stacked deformable refinement block (SDRB) further enhance the reconstruction quality, which is aware of the matching positions and relevant features from input frames with the feedback mechanism. Experimental results demonstrate the superior performance of our approach compared to previous works, both quantitatively and qualitatively.