We build a mechanism design framework where a platform designs GenAI models to screen users who obtain instrumental value from the generated conversation and privately differ in their preference for latency. We show that the revenue-optimal mechanism is simple: deploy a single aligned (user-optimal) model and use token cap as the only instrument to screen the user. The design decouples model training from pricing, is readily implemented with token metering, and mitigates misalignment pressures.

Autoregressive (AR) models, common in sequence generation, are limited in many biological tasks such as de novo peptide sequencing and protein modeling by their unidirectional nature, failing to capture crucial global bidirectional token dependencies. Non-Autoregressive (NAR) models offer holistic, bidirectional representations but face challenges with generative coherence and scalability. To transcend this, we propose a hybrid framework enhancing AR generation by dynamically integrating rich contextual information from non-autoregressive mechanisms. Our approach couples a shared input encoder with two decoders: a non-autoregressive one learning latent bidirectional biological features, and an AR decoder synthesizing the biological sequence by leveraging these bidirectional features. A novel cross-decoder attention module enables the AR decoder to iteratively query and integrate these bidirectional features, enriching its predictions. This synergy is cultivated via a tailored training strategy with importance annealing for balanced objectives and cross-decoder gradient blocking for stable, focused learning. Evaluations on a demanding nine-species benchmark of de novo peptide sequencing show that our model substantially surpasses AR and NAR baselines. It uniquely harmonizes AR stability with NAR contextual awareness, delivering robust, superior performance on diverse downstream data. This research advances biological sequence modeling techniques and contributes a novel architectural paradigm for augmenting AR models with enhanced bidirectional understanding for complex sequence generation. Code is available at https://github.com/BEAM-Labs/denovo.

Deep Research Agents (DRAs) can autonomously conduct complex investigations and generate comprehensive reports, demonstrating strong real-world potential. However, existing benchmarks primarily evaluate DRAs on generic quality metrics and overlook personalization, a critical dimension for individual users. However, existing evaluations mostly rely on close-ended benchmarks, while open-ended deep research benchmarks remain scarce and typically neglect personalized scenarios. To bridge this gap, we introduce Personalized Deep Research Bench (PDR-Bench), the first benchmark for evaluating personalization in DRAs. It pairs 50 diverse research tasks across 10 domains with 25 authentic user profiles that combine structured persona attributes with dynamic real-world contexts, yielding 250 realistic user-task queries. To assess system performance, we propose the PQR Evaluation Framework, which jointly measures Personalization Alignment, Content Quality, and Factual Reliability. Our experiments on a range of systems highlight current capabilities and limitations in handling personalized deep research. This work establishes a rigorous foundation for developing and evaluating the next generation of truly personalized AI research assistants.

The rise of Artificial Intelligence (AI) is reshaping how software systems are developed and maintained. However, AI-based systems give rise to new software issues that existing detection tools often miss. Among these, we focus on AI-specific code smells, recurring patterns in the code that may indicate deeper problems such as unreproducibility, silent failures, or poor model generalization. We introduce SpecDetect4AI, a tool-based approach for the specification and detection of these code smells at scale. This approach combines a high-level declarative Domain-Specific Language (DSL) for rule specification with an extensible static analysis tool that interprets and detects these rules for AI-based systems. We specified 22 AI-specific code smells and evaluated SpecDetect4AI on 826 AI-based systems (20M lines of code), achieving a precision of 88.66% and a recall of 88.89%, outperforming other existing detection tools. Our results show that SpecDetect4AI supports the specification and detection of AI-specific code smells through dedicated rules and can effectively analyze large AI-based systems, demonstrating both efficiency and extensibility (SUS 81.7/100).

Clinical diagnosis is a highly specialized discipline requiring both domain expertise and strict adherence to rigorous guidelines. While current AI-driven medical research predominantly focuses on knowledge graphs or natural text pretraining paradigms to incorporate medical knowledge, these approaches primarily rely on implicitly encoded knowledge within model parameters, neglecting task-specific knowledge required by diverse downstream tasks. To address this limitation, we propose Retrieval-Augmented Diagnosis (RAD), a novel framework that explicitly injects external knowledge into multimodal models directly on downstream tasks. Specifically, RAD operates through three key mechanisms: retrieval and refinement of disease-centered knowledge from multiple medical sources, a guideline-enhanced contrastive loss that constrains the latent distance between multi-modal features and guideline knowledge, and the dual transformer decoder that employs guidelines as queries to steer cross-modal fusion, aligning the models with clinical diagnostic workflows from guideline acquisition to feature extraction and decision-making. Moreover, recognizing the lack of quantitative evaluation of interpretability for multimodal diagnostic models, we introduce a set of criteria to assess the interpretability from both image and text perspectives. Extensive evaluations across four datasets with different anatomies demonstrate RAD's generalizability, achieving state-of-the-art performance. Furthermore, RAD enables the model to concentrate more precisely on abnormal regions and critical indicators, ensuring evidence-based, trustworthy diagnosis. Our code is available at https://github.com/tdlhl/RAD.

The remarkable performance of Large Language Models (LLMs) can be enhanced with test-time computation, which relies on external tools and even other deep learning models. However, existing approaches for integrating non-text modality representations into LLMs typically require additional costly supervised training, restricting on-the-fly adaptation to new domains and modalities. In this work, we explore the feasibility of integrating representations from non-text foundational models (FMs) into text-based LLMs in a training-free manner. We propose In-Context Representation Learning (ICRL) as a proof-of-concept to allow LLMs to adaptively utilize non-text modality representations with few-shot learning. Unlike traditional in-context learning, which incorporates text-label pairs, ICRL replaces text inputs with FM representations, enabling the LLM to perform multi-modal inference without fine-tuning. We evaluate ICRL on a suite of tasks in the molecular domain, investigating three core research questions: (i) how to map FM representations into LLMs in a training-free manner, (ii) what factors influence ICRL performance, and (iii) what mechanisms underlie the effectiveness of ICRL. To the best of our knowledge, ICRL is the first training-free framework for integrating non-text modality representations into text-based LLMs, presenting a promising direction for adaptable, multi-modal generalization.

In the era of foundation models, fine-tuning pre-trained models for specific downstream tasks has become crucial. This drives the need for robust fine-tuning methods to address challenges such as model overfitting and sparse labeling. Molecular graph foundation models (MGFMs) face unique difficulties that complicate fine-tuning. These models are limited by smaller pre-training datasets and more severe data scarcity for downstream tasks, both of which require enhanced model generalization. Moreover, MGFMs must accommodate diverse objectives, including both regression and classification tasks. To better understand and improve fine-tuning techniques under these conditions, we classify eight fine-tuning methods into three mechanisms: weight-based, representation-based, and partial fine-tuning. We benchmark these methods on downstream regression and classification tasks across supervised and self-supervised pre-trained models in diverse labeling settings. This extensive evaluation provides valuable insights and informs the design of a refined robust fine-tuning method, ROFT-MOL. This approach combines the strengths of simple post-hoc weight interpolation with more complex weight ensemble fine-tuning methods, delivering improved performance across both task types while maintaining the ease of use inherent in post-hoc weight interpolation.

Reflection, the ability of large language models (LLMs) to evaluate and revise their own reasoning, has been widely used to improve performance on complex reasoning tasks. Yet, most prior works emphasizes designing reflective prompting strategies or reinforcement learning objectives, leaving the inner mechanisms of reflection underexplored. In this paper, we investigate reflection through the lens of latent directions in model activations. We propose a methodology based on activation steering to characterize how instructions with different reflective intentions: no reflection, intrinsic reflection, and triggered reflection. By constructing steering vectors between these reflection levels, we demonstrate that (1) new reflection-inducing instructions can be systematically identified, (2) reflective behavior can be directly enhanced or suppressed through activation interventions, and (3) suppressing reflection is considerably easier than stimulating it. Experiments on GSM8k-adv and Cruxeval-o-adv with Qwen2.5-3B and Gemma3-4B-IT reveal clear stratification across reflection levels, and steering interventions confirm the controllability of reflection. Our findings highlight both opportunities (e.g., reflection-enhancing defenses) and risks (e.g., adversarial inhibition of reflection in jailbreak attacks). This work opens a path toward mechanistic understanding of reflective reasoning in LLMs.

The advancement of large language models (LLMs) is critically dependent on the availability of high-quality datasets for Supervised Fine-Tuning (SFT), alignment tasks like Direct Preference Optimization (DPO), etc. In this work, we present a comprehensive synthetic data generation framework that facilitates scalable, configurable, and high-fidelity generation of synthetic data tailored for these training paradigms. Our approach employs a modular and configuration-based pipeline capable of modeling complex dialogue flows with minimal manual intervention. This framework uses a dual-stage quality tagging mechanism, combining heuristic rules and LLM-based evaluations, to automatically filter and score data extracted from OASST-formatted conversations, ensuring the curation of high-quality dialogue samples. The resulting datasets are structured under a flexible schema supporting both SFT and DPO use cases, enabling seamless integration into diverse training workflows. Together, these innovations offer a robust solution for generating and managing synthetic conversational data at scale, significantly reducing the overhead of data preparation in LLM training pipelines.

Accurately grounding regions of interest (ROIs) is critical for diagnosis and treatment planning in medical imaging. While multimodal large language models (MLLMs) combine visual perception with natural language, current medical-grounding pipelines still rely on supervised fine-tuning with explicit spatial hints, making them ill-equipped to handle the implicit queries common in clinical practice. This work makes three core contributions. We first define Unified Medical Reasoning Grounding (UMRG), a novel vision-language task that demands clinical reasoning and pixel-level grounding. Second, we release U-MRG-14K, a dataset of 14K samples featuring pixel-level masks alongside implicit clinical queries and reasoning traces, spanning 10 modalities, 15 super-categories, and 108 specific categories. Finally, we introduce MedReasoner, a modular framework that distinctly separates reasoning from segmentation: an MLLM reasoner is optimized with reinforcement learning, while a frozen segmentation expert converts spatial prompts into masks, with alignment achieved through format and accuracy rewards. MedReasoner achieves state-of-the-art performance on U-MRG-14K and demonstrates strong generalization to unseen clinical queries, underscoring the significant promise of reinforcement learning for interpretable medical grounding.