Text-to-image diffusion models often exhibit degraded performance when generating images beyond their training resolution. Recent training-free methods can mitigate this limitation, but they often require substantial computation or are incompatible with recent Diffusion Transformer models. In this paper, we propose ScaleDiff, a model-agnostic and highly efficient framework for extending the resolution of pretrained diffusion models without any additional training. A core component of our framework is Neighborhood Patch Attention (NPA), an efficient mechanism that reduces computational redundancy in the self-attention layer with non-overlapping patches. We integrate NPA into an SDEdit pipeline and introduce Latent Frequency Mixing (LFM) to better generate fine details. Furthermore, we apply Structure Guidance to enhance global structure during the denoising process. Experimental results demonstrate that ScaleDiff achieves state-of-the-art performance among training-free methods in terms of both image quality and inference speed on both U-Net and Diffusion Transformer architectures.

Electronic Health Records (EHR) store clinical documentation as base64 encoded attachments in FHIR DocumentReference resources, which makes semantic question answering difficult. Traditional vector database methods often miss nuanced clinical relationships. The Clinical Entity Augmented Retrieval (CLEAR) method, introduced by Lopez et al. 2025, uses entity aware retrieval and achieved improved performance with an F1 score of 0.90 versus 0.86 for embedding based retrieval, while using over 70 percent fewer tokens. We developed a Clinical Notes QA Evaluation Platform to validate CLEAR against zero shot large context inference and traditional chunk based retrieval augmented generation. The platform was tested on 12 clinical notes ranging from 10,000 to 65,000 tokens representing realistic EHR content. CLEAR achieved a 58.3 percent win rate, an average semantic similarity of 0.878, and used 78 percent fewer tokens than wide context processing. The largest performance gains occurred on long notes, with a 75 percent win rate for documents exceeding 65,000 tokens. These findings confirm that entity aware retrieval improves both efficiency and accuracy in clinical natural language processing. The evaluation framework provides a reusable and transparent benchmark for assessing clinical question answering systems where semantic precision and computational efficiency are critical.

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.

Large language models (LLMs) have achieved remarkable success across diverse domains, due to their strong instruction-following capabilities. This has led to increasing interest in optimizing instructions for black-box LLMs, whose internal parameters are inaccessible but widely used due to their strong performance. To optimize instructions for black-box LLMs, recent methods employ white-box LLMs to generate candidate instructions from optimized soft prompts. However, white-box LLMs often map different soft prompts to the same instruction, leading to redundant queries. While previous studies regarded this many-to-one mapping as a structure that hinders optimization efficiency, we reinterpret it as a useful prior knowledge that can accelerate the optimization. To this end, we introduce PREimage-informed inSTruction Optimization (PRESTO), a novel framework that leverages the preimage structure of soft prompts for efficient optimization. PRESTO consists of three key components: (1) score sharing, which shares the evaluation score with all soft prompts in a preimage; (2) preimage-based initialization, which selects initial data points that maximize search space coverage using preimage information; and (3) score consistency regularization, which enforces prediction consistency within each preimage. By leveraging preimages, PRESTO achieves the effect of effectively obtaining 14 times more scored data under the same query budget, resulting in more efficient optimization. Experimental results on 33 instruction optimization tasks demonstrate the superior performance of PRESTO. Code is available at https://github.com/mlvlab/PRESTO

Single-cell RNA-seq foundation models achieve strong performance on downstream tasks but remain black boxes, limiting their utility for biological discovery. Recent work has shown that sparse dictionary learning can extract concepts from deep learning models, with promising applications in biomedical imaging and protein models. However, interpreting biological concepts remains challenging, as biological sequences are not inherently human-interpretable. We introduce a novel concept-based interpretability framework for single-cell RNA-seq models with a focus on concept interpretation and evaluation. We propose an attribution method with counterfactual perturbations that identifies genes that influence concept activation, moving beyond correlational approaches like differential expression analysis. We then provide two complementary interpretation approaches: an expert-driven analysis facilitated by an interactive interface and an ontology-driven method with attribution-based biological pathway enrichment. Applying our framework to two well-known single-cell RNA-seq models from the literature, we interpret concepts extracted by Top-K Sparse Auto-Encoders trained on two immune cell datasets. With a domain expert in immunology, we show that concepts improve interpretability compared to individual neurons while preserving the richness and informativeness of the latent representations. This work provides a principled framework for interpreting what biological knowledge foundation models have encoded, paving the way for their use for hypothesis generation and discovery.

Large language models (LLMs) are increasingly used in content moderation systems, where ensuring fairness and neutrality is essential. In this study, we examine how persona adoption influences the consistency and fairness of harmful content classification across different LLM architectures, model sizes, and content modalities (language vs. vision). At first glance, headline performance metrics suggest that personas have little impact on overall classification accuracy. However, a closer analysis reveals important behavioral shifts. Personas with different ideological leanings display distinct propensities to label content as harmful, showing that the lens through which a model "views" input can subtly shape its judgments. Further agreement analyses highlight that models, particularly larger ones, tend to align more closely with personas from the same political ideology, strengthening within-ideology consistency while widening divergence across ideological groups. To show this effect more directly, we conducted an additional study on a politically targeted task, which confirmed that personas not only behave more coherently within their own ideology but also exhibit a tendency to defend their perspective while downplaying harmfulness in opposing views. Together, these findings highlight how persona conditioning can introduce subtle ideological biases into LLM outputs, raising concerns about the use of AI systems that may reinforce partisan perspectives under the guise of neutrality.

Long-context language models unlock advanced capabilities in reasoning, code generation, and document summarization by leveraging dependencies across extended spans of text. However, a significant portion of readily available long-text data lacks meaningful long-distance dependencies; most spans can be predicted using only local context. Training on such data is inefficient, making careful data selection crucial. Therefore, we introduce LongFilter, a framework for curating training data tailored to long-context pretraining. LongFilter measures the information gain provided by extended context by contrasting model predictions under long-context versus short-context settings, thereby identifying samples where long-range dependencies are essential. Experiments with LLaMA-3-8B, extending its context length from 8K to 64K, show that LongFilter efficiently selects high-quality data and yields substantial improvements on benchmarks such as HELMET, LongBench, and RULER.

In this paper, we propose a novel hybrid deep learning architecture that synergistically combines Graph Neural Networks (GNNs), Recurrent Neural Networks (RNNs), and multi-head attention mechanisms to significantly enhance cybersecurity intrusion detection capabilities. By leveraging the comprehensive UNSW-NB15 dataset containing diverse network traffic patterns, our approach effectively captures both spatial dependencies through graph structural relationships and temporal dynamics through sequential analysis of network events. The integrated attention mechanism provides dual benefits of improved model interpretability and enhanced feature selection, enabling cybersecurity analysts to focus computational resources on high-impact security events -- a critical requirement in modern real-time intrusion detection systems. Our extensive experimental evaluation demonstrates that the proposed hybrid model achieves superior performance compared to traditional machine learning approaches and standalone deep learning models across multiple evaluation metrics, including accuracy, precision, recall, and F1-score. The model achieves particularly strong performance in detecting sophisticated attack patterns such as Advanced Persistent Threats (APTs), Distributed Denial of Service (DDoS) attacks, and zero-day exploits, making it a promising solution for next-generation cybersecurity applications in complex network environments.

The inherent autocorrelation of time series data presents an ongoing challenge to multivariate time series prediction. Recently, a widely adopted approach has been the incorporation of frequency domain information to assist in long-term prediction tasks. Many researchers have independently observed the spectral bias phenomenon in neural networks, where models tend to fit low-frequency signals before high-frequency ones. However, these observations have often been attributed to the specific architectures designed by the researchers, rather than recognizing the phenomenon as a universal characteristic across models. To unify the understanding of the spectral bias phenomenon in long-term time series prediction, we conducted extensive empirical experiments to measure spectral bias in existing mainstream models. Our findings reveal that virtually all models exhibit this phenomenon. To mitigate the impact of spectral bias, we propose the FreLE (Frequency Loss Enhancement) algorithm, which enhances model generalization through both explicit and implicit frequency regularization. This is a plug-and-play model loss function unit. A large number of experiments have proven the superior performance of FreLE. Code is available at https://github.com/Chenxing-Xuan/FreLE.

Human experts often struggle to select the best option from a large set of items with multiple competing objectives, a process bot-tlenecked by the difficulty of formalizing complex, implicit preferences. To address this, we introduce LISTEN (LLM-based Iterative Selection with Trade-off Evaluation from Natural-language), a framework that leverages a Large Language Model (LLM) as a zero-shot preference oracle, guided only by an expert's high-level priorities in natural language. To operate within LLM constraints like context windows and inference costs, we propose two iterative algorithms: LISTEN-U, which uses the LLM to refine a parametric utility function, and LISTEN-T, a non-parametric method that performs tournament-style selections over small batches of solutions. Evaluated on diverse tasks including flight booking, shopping, and exam scheduling, our results show LISTEN-U excels when preferences are para-metrically aligned (a property we measure with a novel concordance metric), while LISTEN-T offers more robust performance. This work explores a promising direction for steering complex multi-objective decisions directly with natural language, reducing the cognitive burden of traditional preference elicitation.