We present a systematic recipe for translating ReLU approximation results to softmax Transformers1. Given a constructive ReLU approximator for a target, we construct an explicit softmax transformer with the same accuracy. The recipe applies to many common approximation targets and yields quantitative resource bounds beyond universal approximation statements. This matters because broad Universal Approximation Properties (UAP) still dominate Transformer approximation theory. For softmax Transformer, many universality results provide explicit constructions and quantitative resource bounds (e.g., parameters, depth, width...etc) [Yun et al., 2020, Kajitsuka and Sato, 2023, Takakura and Suzuki, 2023, Jiang and Li, 2024, Hu et al., 2025,

Radiotherapy planning is a highly complex process that often varies significantly across institutions and individual planners. Most existing deep learning approaches for 3D dose prediction rely on reference plans as ground truth during training, which can inadvertently bias models toward specific planning styles or institutional preferences. In this study, we introduce a novel generative model that predicts 3D dose distributions based solely on user-defined preference flavors. These customizable preferences enable planners to prioritize specific trade-offs between organs-at-risk (OARs) and planning target volumes (PTVs), offering greater flexibility and personalization. Designed for seamless integration with clinical treatment planning systems, our approach assists users in generating high-quality plans efficiently. Comparative evaluations demonstrate that our method can surpasses the Varian RapidPlan model in both adaptability and plan quality in some scenarios.

Self-driving laboratories offer a promising path toward reducing the labor-intensive, time-consuming, and often irreproducible workflows in the biological sciences. Yet their stringent precision requirements demand highly robust models whose training relies on large amounts of annotated data. However, this kind of data is difficult to obtain in routine practice, especially negative samples. In this work, we focus on pipetting, the most critical and precision sensitive action in SDLs. To overcome the scarcity of training data, we build a hybrid pipeline that fuses real and virtual data generation. The real track adopts a human-in-the-loop scheme that couples automated acquisition with selective human verification to maximize accuracy with minimal effort. The virtual track augments the real data using reference-conditioned, prompt-guided image generation, which is further screened and validated for reliability. Together, these two tracks yield a class-balanced dataset that enables robust bubble detection training. On a held-out real test set, a model trained entirely on automatically acquired real images reaches 99.6% accuracy, and mixing real and generated data during training sustains 99.4% accuracy while reducing collection and review load. Our approach offers a scalable and cost-effective strategy for supplying visual feedback data to SDL workflows and provides a practical solution to data scarcity in rare event detection and broader vision tasks.

The increasing availability of large-scale datasets has fueled rapid progress across many scientific fields, creating unprecedented opportunities for research and discovery while posing significant analytical challenges. Recent advances in large language models (LLMs) and AI agents have opened new possibilities for human-AI collaboration, offering powerful tools to navigate this complex research landscape. In this paper, we introduce SciSciGPT, an open-source, prototype AI collaborator that uses the science of science as a testbed to explore the potential of LLM-powered research tools. SciSciGPT automates complex workflows, supports diverse analytical approaches, accelerates research prototyping and iteration, and facilitates reproducibility. Through case studies, we demonstrate its ability to streamline a wide range of empirical and analytical research tasks while highlighting its broader potential to advance research. We further propose an LLM Agent capability maturity model for human-AI collaboration, envisioning a roadmap to further improve and expand upon frameworks like SciSciGPT. As AI capabilities continue to evolve, frameworks like SciSciGPT may play increasingly pivotal roles in scientific research and discovery, unlocking further opportunities. At the same time, these new advances also raise critical challenges, from ensuring transparency and ethical use to balancing human and AI contributions. Addressing these issues may shape the future of scientific inquiry and inform how we train the next generation of scientists to thrive in an increasingly AI-integrated research ecosystem.

Whole-genome sequencing (WGS) has revealed numerous non-coding short variants whose functional impacts remain poorly understood. Despite recent advances in deep-learning genomic approaches, accurately predicting and prioritizing clinically relevant mutations in gene regulatory regions remains a major challenge. Here we introduce Deep VRegulome, a deep-learning method for prediction and interpretation of functionally disruptive variants in the human regulome, which combines 700 DNABERT fine-tuned models, trained on vast amounts of ENCODE gene regulatory regions, with variant scoring, motif analysis, attention-based visualization, and survival analysis. We showcase its application on TCGA glioblastoma WGS dataset in prioritizing survival-associated mutations and regulatory regions. The analysis identified 572 splice-disrupting and 9,837 transcription-factor binding site altering mutations occurring in greater than 10% of glioblastoma samples. Survival analysis linked 1352 mutations and 563 disrupted regulatory regions to patient outcomes, enabling stratification via non-coding mutation signatures. All the code, fine-tuned models, and an interactive data portal are publicly available.

We derive a deterministic, non-asymptotic upper bound on the Kullback-Leibler (KL) divergence of the flow-matching distribution approximation. In particular, if the $L_2$ flow-matching loss is bounded by $ε^2 > 0$, then the KL divergence between the true data distribution and the estimated distribution is bounded by $A_1 ε+ A_2 ε^2$. Here, the constants $A_1$ and $A_2$ depend only on the regularities of the data and velocity fields. Consequently, this bound implies statistical convergence rates of Flow Matching Transformers under the Total Variation (TV) distance. We show that, flow matching achieves nearly minimax-optimal efficiency in estimating smooth distributions. Our results make the statistical efficiency of flow matching comparable to that of diffusion models under the TV distance. Numerical studies on synthetic and learned velocities corroborate our theory.

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.

We introduce xLLM, an intelligent and efficient Large Language Model (LLM) inference framework designed for high-performance, large-scale enterprise-grade serving, with deep optimizations for diverse AI accelerators. To address these challenges, xLLM builds a novel decoupled service-engine architecture. At the service layer, xLLM-Service features an intelligent scheduling module that efficiently processes multimodal requests and co-locates online and offline tasks through unified elastic scheduling to maximize cluster utilization. This module also relies on a workload-adaptive dynamic Prefill-Decode (PD) disaggregation policy and a novel Encode-Prefill-Decode (EPD) disaggregation policy designed for multimodal inputs. Furthermore, it incorporates a distributed architecture to provide global KV Cache management and robust fault-tolerant capabilities for high availability. At the engine layer, xLLM-Engine co-optimizes system and algorithm designs to fully saturate computing resources. This is achieved through comprehensive multi-layer execution pipeline optimizations, an adaptive graph mode and an xTensor memory management. xLLM-Engine also further integrates algorithmic enhancements such as optimized speculative decoding and dynamic EPLB, collectively serving to substantially boost throughput and inference efficiency. Extensive evaluations demonstrate that xLLM delivers significantly superior performance and resource efficiency. Under identical TPOT constraints, xLLM achieves throughput up to 1.7x that of MindIE and 2.2x that of vLLM-Ascend with Qwen-series models, while maintaining an average throughput of 1.7x that of MindIE with Deepseek-series models. xLLM framework is publicly available at https://github.com/jd-opensource/xllm and https://github.com/jd-opensource/xllm-service.

We propose the first unified adversarial attack benchmark for Genomic Foundation Models (GFMs), named GenoArmory. Unlike existing GFM benchmarks, GenoArmory offers the first comprehensive evaluation framework to systematically assess the vulnerability of GFMs to adversarial attacks. Methodologically, we evaluate the adversarial robustness of five state-of-the-art GFMs using four widely adopted attack algorithms and three defense strategies. Importantly, our benchmark provides an accessible and comprehensive framework to analyze GFM vulnerabilities with respect to model architecture, quantization schemes, and training datasets. Additionally, we introduce GenoAdv, a new adversarial sample dataset designed to improve GFM safety. Empirically, classification models exhibit greater robustness to adversarial perturbations compared to generative models, highlighting the impact of task type on model vulnerability. Moreover, adversarial attacks frequently target biologically significant genomic regions, suggesting that these models effectively capture meaningful sequence features.

Structured State-Space Duality (SSD) [Dao & Gu, ICML 2024] is an equivalence between a simple Structured State-Space Model (SSM) and a masked attention mechanism. In particular, a state-space model with a scalar-times-identity state matrix is equivalent to a masked self-attention with a $1$-semiseparable causal mask. Consequently, the same sequence transformation (model) has two algorithmic realizations: as a linear-time $O(T)$ recurrence or as a quadratic-time $O(T^2)$ attention. In this note, we formalize and generalize this duality: (i) we extend SSD from the scalar-identity case to general diagonal SSMs (diagonal state matrices); (ii) we show that these diagonal SSMs match the scalar case's training complexity lower bounds while supporting richer dynamics; (iii) we establish a necessary and sufficient condition under which an SSM is equivalent to $1$-semiseparable masked attention; and (iv) we show that such duality fails to extend to standard softmax attention due to rank explosion. Together, these results tighten bridge between recurrent SSMs and Transformers, and widen the design space for expressive yet efficient sequence models.