Segmentation-before-Staining Improves Structural Fidelity in Virtual IHC-to-Multiplex IF Translation

Multiplex immunofluorescence (mIF) enables simultaneous single-cell quantification of multiple biomarkers within intact tissue architecture, yet its high reagent cost, multi-round staining protocols, and need for specialized imaging platforms limit routine clinical adoption. Virtual staining can synthesize mIF channels from widely available brightfield immunohistochemistry (IHC), but current translators optimize pixel-level fidelity without explicitly constraining nuclear morphology. In pathology, this gap is clinically consequential: subtle distortions in nuclei count, shape, or spatial arrangement propagate directly to quantification endpoints such as the Ki67 proliferation index, where errors of a few percent can shift treatment-relevant risk categories. This work introduces a supervision-free, architecture-agnostic conditioning strategy that injects a continuous cell probability map from a pretrained nuclei segmentation foundation model as an explicit input prior, together with a variance-preserving regularization term that matches local intensity statistics to maintain cell-level heterogeneity in synthesized fluorescence channels. The soft prior retains gradient-level boundary information lost by binary thresholding, providing a richer conditioning signal without task-specific tuning. Controlled experiments across Pix2Pix with U-Net and ResNet generators, deterministic regression U-Net, and conditional diffusion on two independent datasets demonstrate consistent improvements in nuclei count fidelity and perceptual quality, as the sole modifications. Code will be made publicly available upon acceptance.

SciZoom: A Large-scale Benchmark for Hierarchical Scientific Summarization across the LLM Era

The explosive growth of AI research has created unprecedented information overload, increasing the demand for scientific summarization at multiple levels of granularity beyond traditional abstracts. While LLMs are increasingly adopted for summarization, existing benchmarks remain limited in scale, target only a single granularity, and predate the LLM era. Moreover, since the release of ChatGPT in November 2022, researchers have rapidly adopted LLMs for drafting manuscripts themselves, fundamentally transforming scientific writing, yet no resource exists to analyze how this writing has evolved. To bridge these gaps, we introduce SciZoom, a benchmark comprising 44,946 papers from four top-tier ML venues (NeurIPS, ICLR, ICML, EMNLP) spanning 2020 to 2025, explicitly stratified into Pre-LLM and Post-LLM eras. SciZoom provides three hierarchical summarization targets (Abstract, Contributions, and TL;DR) achieving compression ratios up to 600:1, enabling both multi-granularity summarization research and temporal mining of scientific writing patterns. Our linguistic analysis reveals striking shifts in phrase patterns (up to 10x for formulaic expressions) and rhetorical style (23% decline in hedging), suggesting that LLM-assisted writing produces more confident yet homogenized prose. SciZoom serves as both a challenging benchmark and a unique resource for mining the evolution of scientific discourse in the generative AI era. Our code and dataset are publicly available on GitHub (https://github.com/janghana/SciZoom) and Hugging Face (https://huggingface.co/datasets/hanjang/SciZoom), respectively.

Evidential Perfusion Physics-Informed Neural Networks with Residual Uncertainty Quantification

Physics-informed neural networks (PINNs) have shown promise in addressing the ill-posed deconvolution problem in computed tomography perfusion (CTP) imaging for acute ischemic stroke assessment. However, existing PINN-based approaches remain deterministic and do not quantify uncertainty associated with violations of physics constraints, limiting reliability assessment. We propose Evidential Perfusion Physics-Informed Neural Networks (EPPINN), a framework that integrates evidential deep learning with physics-informed modeling to enable uncertainty-aware perfusion parameter estimation. EPPINN models arterial input, tissue concentration, and perfusion parameters using coordinate-based networks, and places a Normal--Inverse--Gamma distribution over the physics residual to characterize voxel-wise aleatoric and epistemic uncertainty in physics consistency without requiring Bayesian sampling or ensemble inference. The framework further incorporates physiologically constrained parameterization and stabilization strategies to promote robust per-case optimization. We evaluate EPPINN on digital phantom data, the ISLES 2018 benchmark, and a clinical cohort. On the evaluated datasets, EPPINN achieves lower normalized mean absolute error than classical deconvolution and PINN baselines, particularly under sparse temporal sampling and low signal-to-noise conditions, while providing conservative uncertainty estimates with high empirical coverage. On clinical data, EPPINN attains the highest voxel-level and case-level infarct-core detection sensitivity. These results suggest that evidential physics-informed learning can improve both accuracy and reliability of CTP analysis for time-critical stroke assessment.

MPIB: A Benchmark for Medical Prompt Injection Attacks and Clinical Safety in LLMs

Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) systems are increasingly integrated into clinical workflows; however, prompt injection attacks can steer these systems toward clinically unsafe or misleading outputs. We introduce the Medical Prompt Injection Benchmark (MPIB), a dataset-and-benchmark suite for evaluating clinical safety under both direct prompt injection and indirect, RAG-mediated injection across clinically grounded tasks. MPIB emphasizes outcome-level risk via the Clinical Harm Event Rate (CHER), which measures high-severity clinical harm events under a clinically grounded taxonomy, and reports CHER alongside Attack Success Rate (ASR) to disentangle instruction compliance from downstream patient risk. The benchmark comprises 9,697 curated instances constructed through multi-stage quality gates and clinical safety linting. Evaluating MPIB across a diverse set of baseline LLMs and defense configurations, we find that ASR and CHER can diverge substantially, and that robustness depends critically on whether adversarial instructions appear in the user query or in retrieved context. We release MPIB with evaluation code, adversarial baselines, and comprehensive documentation to support reproducible and systematic research on clinical prompt injection. Code and data are available at GitHub (code) and Hugging Face (data).

Motif-2-12.7B-Reasoning: A Practitioner's Guide to RL Training Recipes

We introduce Motif-2-12.7B-Reasoning, a 12.7B parameter language model designed to bridge the gap between open-weight systems and proprietary frontier models in complex reasoning and long-context understanding. Addressing the common challenges of model collapse and training instability in reasoning adaptation, we propose a comprehensive, reproducible training recipe spanning system, data, and algorithmic optimizations. Our approach combines memory-efficient infrastructure for 64K-token contexts using hybrid parallelism and kernel-level optimizations with a two-stage Supervised Fine-Tuning (SFT) curriculum that mitigates distribution mismatch through verified, aligned synthetic data. Furthermore, we detail a robust Reinforcement Learning Fine-Tuning (RLFT) pipeline that stabilizes training via difficulty-aware data filtering and mixed-policy trajectory reuse. Empirical results demonstrate that Motif-2-12.7B-Reasoning achieves performance comparable to models with significantly larger parameter counts across mathematics, coding, and agentic benchmarks, offering the community a competitive open model and a practical blueprint for scaling reasoning capabilities under realistic compute constraints.

Motif 2 12.7B technical report

We introduce Motif-2-12.7B, a new open-weight foundation model that pushes the efficiency frontier of large language models by combining architectural innovation with system-level optimization. Designed for scalable language understanding and robust instruction generalization under constrained compute budgets, Motif-2-12.7B builds upon Motif-2.6B with the integration of Grouped Differential Attention (GDA), which improves representational efficiency by disentangling signal and noise-control attention pathways. The model is pre-trained on 5.5 trillion tokens spanning diverse linguistic, mathematical, scientific, and programming domains using a curriculum-driven data scheduler that gradually changes the data composition ratio. The training system leverages the MuonClip optimizer alongside custom high-performance kernels, including fused PolyNorm activations and the Parallel Muon algorithm, yielding significant throughput and memory efficiency gains in large-scale distributed environments. Post-training employs a three-stage supervised fine-tuning pipeline that successively enhances general instruction adherence, compositional understanding, and linguistic precision. Motif-2-12.7B demonstrates competitive performance across diverse benchmarks, showing that thoughtful architectural scaling and optimized training design can rival the capabilities of much larger models.

Grouped Differential Attention

The self-attention mechanism, while foundational to modern Transformer architectures, suffers from a critical inefficiency: it frequently allocates substantial attention to redundant or noisy context. Differential Attention addressed this by using subtractive attention maps for signal and noise, but its required balanced head allocation imposes rigid constraints on representational flexibility and scalability. To overcome this, we propose Grouped Differential Attention (GDA), a novel approach that introduces unbalanced head allocation between signal-preserving and noise-control groups. GDA significantly enhances signal focus by strategically assigning more heads to signal extraction and fewer to noise-control, stabilizing the latter through controlled repetition (akin to GQA). This design achieves stronger signal fidelity with minimal computational overhead. We further extend this principle to group-differentiated growth, a scalable strategy that selectively replicates only the signal-focused heads, thereby ensuring efficient capacity expansion. Through large-scale pretraining and continual training experiments, we demonstrate that moderate imbalance ratios in GDA yield substantial improvements in generalization and stability compared to symmetric baselines. Our results collectively establish that ratio-aware head allocation and selective expansion offer an effective and practical path toward designing scalable, computation-efficient Transformer architectures.

Expanding Foundational Language Capabilities in Open-Source LLMs through a Korean Case Study

We introduce Llama-3-Motif, a language model consisting of 102 billion parameters, specifically designed to enhance Korean capabilities while retaining strong performance in English. Developed on the Llama 3 architecture, Llama-3-Motif employs advanced training techniques, including LlamaPro and Masked Structure Growth, to effectively scale the model without altering its core Transformer architecture. Using the MoAI platform for efficient training across hyperscale GPU clusters, we optimized Llama-3-Motif using a carefully curated dataset that maintains a balanced ratio of Korean and English data. Llama-3-Motif shows decent performance on Korean-specific benchmarks, outperforming existing models and achieving results comparable to GPT-4.

Improving Factuality of 3D Brain MRI Report Generation with Paired Image-domain Retrieval and Text-domain Augmentation

Acute ischemic stroke (AIS) requires time-critical management, with hours of delayed intervention leading to an irreversible disability of the patient. Since diffusion weighted imaging (DWI) using the magnetic resonance image (MRI) plays a crucial role in the detection of AIS, automated prediction of AIS from DWI has been a research topic of clinical importance. While text radiology reports contain the most relevant clinical information from the image findings, the difficulty of mapping across different modalities has limited the factuality of conventional direct DWI-to-report generation methods. Here, we propose paired image-domain retrieval and text-domain augmentation (PIRTA), a cross-modal retrieval-augmented generation (RAG) framework for providing clinician-interpretative AIS radiology reports with improved factuality. PIRTA mitigates the need for learning cross-modal mapping, which poses difficulty in image-to-text generation, by casting the cross-modal mapping problem as an in-domain retrieval of similar DWI images that have paired ground-truth text radiology reports. By exploiting the retrieved radiology reports to augment the report generation process of the query image, we show by experiments with extensive in-house and public datasets that PIRTA can accurately retrieve relevant reports from 3D DWI images. This approach enables the generation of radiology reports with significantly higher accuracy compared to direct image-to-text generation using state-of-the-art multimodal language models.

Super Monotonic Alignment Search

Monotonic alignment search (MAS), introduced by Glow-TTS, is one of the most popular algorithm in TTS to estimate unknown alignments between text and speech. Since this algorithm needs to search for the most probable alignment with dynamic programming by caching all paths, the time complexity of the algorithm is $O(T \times S)$. The authors of Glow-TTS run this algorithm on CPU, and while they mentioned it is difficult to parallelize, we found that MAS can be parallelized in text-length dimension and CPU execution consumes an inordinate amount of time for inter-device copy. Therefore, we implemented a Triton kernel and PyTorch JIT script to accelerate MAS on GPU without inter-device copy. As a result, Super-MAS Triton kernel is up to 72 times faster in the extreme-length case. The code is available at \url{https://github.com/supertone-inc/super-monotonic-align}.