Runze Ma

Zhongmin Li, Runze Ma, Jiahao Tan et al.

Nucleotide sequence variation can induce significant shifts in functional fitness. Recent nucleotide foundation models promise to predict such fitness effects directly from sequence, yet heterogeneous datasets and inconsistent preprocessing make it difficult to compare methods fairly across DNA and RNA families. Here we introduce NABench, a large-scale, systematic benchmark for nucleic acid fitness prediction. NABench aggregates 162 high-throughput assays and curates 2.6 million mutated sequences spanning diverse DNA and RNA families, with standardized splits and rich metadata. We show that NABench surpasses prior nucleotide fitness benchmarks in scale, diversity, and data quality. Under a unified evaluation suite, we rigorously assess 29 representative foundation models across zero-shot, few-shot prediction, transfer learning, and supervised settings. The results quantify performance heterogeneity across tasks and nucleic-acid types, demonstrating clear strengths and failure modes for different modeling choices and establishing strong, reproducible baselines. We release NABench to advance nucleic acid modeling, supporting downstream applications in RNA/DNA design, synthetic biology, and biochemistry. Our code is available at https://github.com/mrzzmrzz/NABench.

Peihceng Wu, Runze Ma, Teoh Teik Toe

This paper proposes a CNN classification network based on Bagging and stacking ensemble learning methods for breast cancer classification. The model was trained and tested on the public dataset of DDSM. The model is capable of fast and accurate classification of input images. According to our research results, for binary classification (presence or absence of breast cancer), the accuracy reached 98.84%, and for five-class classification, the accuracy reached 98.34%. The model also achieved a micro-average recall rate of 94.80% and an F1 score of 94.19%. In comparative experiments, we compared the effects of different values of bagging_ratio and n_models on the model, as well as several methods for ensemble bagging models. Furthermore, under the same parameter settings, our BSECNN outperformed VGG16 and ResNet-50 in terms of accuracy by 8.22% and 6.33% respectively.

Peicheng Wu, Zhenyu Bu, Runze Ma et al.

Spike activity has been the dominant neural signal for behavior decoding due to its high spatial and temporal resolution. However, as brain-computer interfaces (BCIs) move toward high channel counts and wireless operation, the high sampling frequency of spike signals becomes a bottleneck due to high power and bandwidth requirements. Local field potentials (LFPs) represent a different spatial-temporal scale of brain activity compared to spikes, offering key advantages including improved long-term stability, reduced energy consumption, and lower bandwidth requirement. Despite these benefits, LFP-based decoding models typically show reduced accuracy and often rely on non-causal architectures that are unsuitable for real-time deployment. To address these challenges, we propose REALM: a retrospective distillation framework that enables causal LFP decoding. Inspired by offline-to-online distillation strategies in speech recognition, REALM transfers representational knowledge from a pretrained multi-session bidirectional LFP model to a causal version for real-time deployment. We first pretrain a bidirectional Mamba-2 teacher model using a masked autoencoding objective. We then distill this teacher model into a compact student model via a combined objective of representation alignment and task supervision. REALM consistently outperforms both causal and non-causal LFP-based SOTA methods for behavior decoding. Notably, our REALM improves decoding performance while achieving a $2\times$ reduction in parameter count and a $10\times$ reduction in training time. These results demonstrate that retrospective distillation effectively bridges the gap between offline and real-time neural decoding. REALM shows that LFP-only models can achieve competitive decoding performance without reliance on spike signals, offering a practical and scalable alternative for next-generation wireless implantable BCIs.

Runze Ma, Shunbo Jia, Haonan Lyu et al.

The reasoning gap between large and compact vision-language models (VLMs) limits the deployment of medical AI on portable clinical devices. Compact VLMs of 2--4B parameters can run on resource-constrained hardware but lack the multi-step reasoning capacity needed for interpretable clinical decision support. Existing knowledge distillation methods transfer answers without the reasoning process behind them. Medical visual question answering (VQA) serves as a testbed for this problem, as it requires models to integrate visual evidence with clinical knowledge through structured reasoning chains. We introduce LiteMedCoT-VL, a pipeline that transfers chain-of-thought reasoning from a 235B teacher model to 2B student models through LoRA-based fine-tuning on explanation-enriched training data. All inference is conducted without image captions by default, simulating the clinical scenario in which a physician interprets a medical image directly without an accompanying radiology report. On the PMC-VQA benchmark, LiteMedCoT-VL achieves 64.9% accuracy, exceeding the zero-shot Qwen3-VL-4B baseline of 53.9% by 11.0 percentage points and outperforming all published baselines. This result indicates that a 2B model with reasoning distillation can match or exceed models with twice the parameters. Visual grounding analysis shows that the model relies on image content rather than exploiting textual priors. Our code is publicly available at https://anonymous.4open.science/r/LiteMedCoT-VL.

Runze Ma, Caizhi Liao

Although deep learning has advanced automated electrocardiogram (ECG) diagnosis, prevalent supervised methods typically treat recordings as undifferentiated one-dimensional (1D) signals or two-dimensional (2D) images. This formulation compels models to learn physiological structures implicitly, resulting in data inefficiency and opacity that diverge from medical reasoning. To address these limitations, we propose BEAT-Net, a Biomimetic ECG Analysis with Tokenization framework that reformulates the problem as a language modeling task. Utilizing a QRS tokenization strategy to transform continuous signals into biologically aligned heartbeat sequences, the architecture explicitly decomposes cardiac physiology through specialized encoders that extract local beat morphology while normalizing spatial lead perspectives and modeling temporal rhythm dependencies. Evaluations across three large-scale benchmarks demonstrate that BEAT-Net matches the diagnostic accuracy of dominant convolutional neural network (CNN) architectures while substantially improving robustness. The framework exhibits exceptional data efficiency, recovering fully supervised performance using only 30 to 35 percent of annotated data. Moreover, learned attention mechanisms provide inherent interpretability by spontaneously reproducing clinical heuristics, such as Lead II prioritization for rhythm analysis, without explicit supervision. These findings indicate that integrating biological priors offers a computationally efficient and interpretable alternative to data-intensive large-scale pre-training.

Zhongyue Zhang, Jiahua Rao, Jie Zhong et al.

Most human proteins remain undrugged, over 96% of human proteins remain unexploited by approved therapeutics. While structure-based virtual screening promises to expand the druggable proteome, existing methods lack atomic-level precision and fail to predict binding fitness, limiting translational impact. We present AuroBind, a scalable virtual screening framework that fine-tunes a custom atomic-level structural model on million-scale chemogenomic data. AuroBind integrates direct preference optimization, self-distillation from high-confidence complexes, and a teacher-student acceleration strategy to jointly predict ligand-bound structures and binding fitness. The proposed models outperform state-of-the-art models on structural and functional benchmarks while enabling 100,000-fold faster screening across ultra-large compound libraries. In a prospective screen across ten disease-relevant targets, AuroBind achieved experimental hit rates of 7-69%, with top compounds reaching sub-nanomolar to picomolar potency. For the orphan GPCRs GPR151 and GPR160, AuroBind identified both agonists and antagonists with success rates of 16-30%, and functional assays confirmed GPR160 modulation in liver and prostate cancer models. AuroBind offers a generalizable framework for structure-function learning and high-throughput molecular screening, bridging the gap between structure prediction and therapeutic discovery.

Munan Li, Xianshi Su, Runze Ma et al.

Dynamic graphs are extensively employed for detecting anomalous behavior in nodes within the Internet of Things (IoT). Graph generative models are often used to address the issue of imbalanced node categories in dynamic graphs. Nevertheless, the constraints it faces include the monotonicity of adjacency relationships, the difficulty in constructing multi-dimensional features for nodes, and the lack of a method for end-to-end generation of multiple categories of nodes. In this paper, we propose a novel graph generation model, called CGGM, specifically for generating samples belonging to the minority class. The framework consists two core module: a conditional graph generation module and a graph-based anomaly detection module. The generative module adapts to the sparsity of the matrix by downsampling a noise adjacency matrix, and incorporates a multi-dimensional feature encoder based on multi-head self-attention to capture latent dependencies among features. Additionally, a latent space constraint is combined with the distribution distance to approximate the latent distribution of real data. The graph-based anomaly detection module utilizes the generated balanced dataset to predict the node behaviors. Extensive experiments have shown that CGGM outperforms the state-of-the-art methods in terms of accuracy and divergence. The results also demonstrate CGGM can generated diverse data categories, that enhancing the performance of multi-category classification task.

Yue Tao, Zhiwei Jia, Runze Ma et al.

Scene text recognition (STR) is an important bridge between images and text, attracting abundant research attention. While convolutional neural networks (CNNS) have achieved remarkable progress in this task, most of the existing works need an extra module (context modeling module) to help CNN to capture global dependencies to solve the inductive bias and strengthen the relationship between text features. Recently, the transformer has been proposed as a promising network for global context modeling by self-attention mechanism, but one of the main shortcomings, when applied to recognition, is the efficiency. We propose a 1-D split to address the challenges of complexity and replace the CNN with the transformer encoder to reduce the need for a context modeling module. Furthermore, recent methods use a frozen initial embedding to guide the decoder to decode the features to text, leading to a loss of accuracy. We propose to use a learnable initial embedding learned from the transformer encoder to make it adaptive to different input images. Above all, we introduce a novel architecture for text recognition, named TRansformer-based text recognizer with Initial embedding Guidance (TRIG), composed of three stages (transformation, feature extraction, and prediction). Extensive experiments show that our approach can achieve state-of-the-art on text recognition benchmarks.