A Generalized Genetic Random Field Method for the Genetic Association Analysis of Sequencing Data

With the advance of high-throughput sequencing technologies, it has become feasible to investigate the influence of the entire spectrum of sequencing variations on complex human diseases. Although association studies utilizing the new sequencing technologies hold great promise to unravel novel genetic variants, especially rare genetic variants that contribute to human diseases, the statistical analysis of high-dimensional sequencing data remains a challenge. Advanced analytical methods are in great need to facilitate high-dimensional sequencing data analyses. In this article, we propose a generalized genetic random field (GGRF) method for association analyses of sequencing data. Like other similarity-based methods (e.g., SIMreg and SKAT), the new method has the advantages of avoiding the need to specify thresholds for rare variants and allowing for testing multiple variants acting in different directions and magnitude of effects. The method is built on the generalized estimating equation framework and thus accommodates a variety of disease phenotypes (e.g., quantitative and binary phenotypes). Moreover, it has a nice asymptotic property, and can be applied to small-scale sequencing data without need for small-sample adjustment. Through simulations, we demonstrate that the proposed GGRF attains an improved or comparable power over a commonly used method, SKAT, under various disease scenarios, especially when rare variants play a significant role in disease etiology. We further illustrate GGRF with an application to a real dataset from the Dallas Heart Study. By using GGRF, we were able to detect the association of two candidate genes, ANGPTL3 and ANGPTL4, with serum triglyceride.

On The Role of Pretrained Language Models in General-Purpose Text Embeddings: A Survey

Text embeddings have attracted growing interest due to their effectiveness across a wide range of natural language processing (NLP) tasks, such as retrieval, classification, clustering, bitext mining, and summarization. With the emergence of pretrained language models (PLMs), general-purpose text embeddings (GPTE) have gained significant traction for their ability to produce rich, transferable representations. The general architecture of GPTE typically leverages PLMs to derive dense text representations, which are then optimized through contrastive learning on large-scale pairwise datasets. In this survey, we provide a comprehensive overview of GPTE in the era of PLMs, focusing on the roles PLMs play in driving its development. We first examine the fundamental architecture and describe the basic roles of PLMs in GPTE, i.e., embedding extraction, expressivity enhancement, training strategies, learning objectives, and data construction. Then, we describe advanced roles enabled by PLMs, such as multilingual support, multimodal integration, code understanding, and scenario-specific adaptation. Finally, we highlight potential future research directions that move beyond traditional improvement goals, including ranking integration, safety considerations, bias mitigation, structural information incorporation, and the cognitive extension of embeddings. This survey aims to serve as a valuable reference for both newcomers and established researchers seeking to understand the current state and future potential of GPTE.

AQuilt: Weaving Logic and Self-Inspection into Low-Cost, High-Relevance Data Synthesis for Specialist LLMs

Despite the impressive performance of large language models (LLMs) in general domains, they often underperform in specialized domains. Existing approaches typically rely on data synthesis methods and yield promising results by using unlabeled data to capture domain-specific features. However, these methods either incur high computational costs or suffer from performance limitations, while also demonstrating insufficient generalization across different tasks. To address these challenges, we propose AQuilt, a framework for constructing instruction-tuning data for any specialized domains from corresponding unlabeled data, including Answer, Question, Unlabeled data, Inspection, Logic, and Task type. By incorporating logic and inspection, we encourage reasoning processes and self-inspection to enhance model performance. Moreover, customizable task instructions enable high-quality data generation for any task. As a result, we construct a dataset of 703k examples to train a powerful data synthesis model. Experiments show that AQuilt is comparable to DeepSeek-V3 while utilizing just 17% of the production cost. Further analysis demonstrates that our generated data exhibits higher relevance to downstream tasks. Source code, models, and scripts are available at https://github.com/Krueske/AQuilt.

KaLM-Embedding-V2: Superior Training Techniques and Data Inspire A Versatile Embedding Model

In this paper, we propose KaLM-Embedding-V2, a versatile and compact embedding model, which achieves impressive performance in general-purpose text embedding tasks by leveraging superior training techniques and data. Our key innovations include: (1) To better align the architecture with representation learning, we remove the causal attention mask and adopt a fully bidirectional transformer with simple yet effective mean-pooling to produce fixed-length embeddings; (2) We employ a multi-stage training pipeline: (i) pre-training on large-scale weakly supervised open-source corpora; (ii) fine-tuning on high-quality retrieval and non-retrieval datasets; and (iii) model-soup parameter averaging for robust generalization. Besides, we introduce a focal-style reweighting mechanism that concentrates learning on difficult samples and an online hard-negative mixing strategy to continuously enrich hard negatives without expensive offline mining; (3) We collect over 20 categories of data for pre-training and 100 categories of data for fine-tuning, to boost both the performance and generalization of the embedding model. Extensive evaluations on the Massive Text Embedding Benchmark (MTEB) Chinese and English show that our model significantly outperforms others of comparable size, and competes with 3x, 14x, 18x, and 26x larger embedding models, setting a new standard for a versatile and compact embedding model with less than 1B parameters.

Augmenting Multi-Agent Communication with State Delta Trajectory

Multi-agent techniques such as role playing or multi-turn debates have been shown to be effective in improving the performance of large language models (LLMs) in downstream tasks. Despite their differences in workflows, existing LLM-based multi-agent systems mostly use natural language for agent communication. While this is appealing for its simplicity and interpretability, it also introduces inevitable information loss as one model must down sample its continuous state vectors to concrete tokens before transferring them to the other model. Such losses are particularly significant when the information to transfer is not simple facts, but reasoning logics or abstractive thoughts. To tackle this problem, we propose a new communication protocol that transfers both natural language tokens and token-wise state transition trajectory from one agent to another. Particularly, compared to the actual state value, we find that the sequence of state changes in LLMs after generating each token can better reflect the information hidden behind the inference process, so we propose a State Delta Encoding (SDE) method to represent state transition trajectories. The experimental results show that multi-agent systems with SDE achieve SOTA performance compared to other communication protocols, particularly in tasks that involve complex reasoning. This shows the potential of communication augmentation for LLM-based multi-agent systems.

How Far Can LLMs Improve from Experience? Measuring Test-Time Learning Ability in LLMs with Human Comparison

As evaluation designs of large language models may shape our trajectory toward artificial general intelligence, comprehensive and forward-looking assessment is essential. Existing benchmarks primarily assess static knowledge, while intelligence also entails the ability to rapidly learn from experience. To this end, we advocate for the evaluation of Test-time Learning, the capacity to improve performance in experience-based, reasoning-intensive tasks during test time. In this work, we propose semantic games as effective testbeds for evaluating test-time learning, due to their resistance to saturation and inherent demand for strategic reasoning. We introduce an objective evaluation framework that compares model performance under both limited and cumulative experience settings, and contains four forms of experience representation. To provide a comparative baseline, we recruit eight human participants to complete the same task. Results show that LLMs exhibit measurable test-time learning capabilities; however, their improvements are less stable under cumulative experience and progress more slowly than those observed in humans. These findings underscore the potential of LLMs as general-purpose learning machines, while also revealing a substantial intellectual gap between models and humans, irrespective of how well LLMs perform on static benchmarks.

CALM: Consensus-Aware Localized Merging for Multi-Task Learning

Model merging aims to integrate the strengths of multiple fine-tuned models into a unified model while preserving task-specific capabilities. Existing methods, represented by task arithmetic, are typically classified into global- and local-aware methods. However, global-aware methods inevitably cause parameter interference, while local-aware methods struggle to maintain the effectiveness of task-specific details in the merged model. To address these limitations, we propose a Consensus-Aware Localized Merging (CALM) method which incorporates localized information aligned with global task consensus, ensuring its effectiveness post-merging. CALM consists of three key components: (1) class-balanced entropy minimization sampling, providing a more flexible and reliable way to leverage unsupervised data; (2) an efficient-aware framework, selecting a small set of tasks for sequential merging with high scalability; (3) a consensus-aware mask optimization, aligning localized binary masks with global task consensus and merging them conflict-free. Experiments demonstrate the superiority and robustness of our CALM, significantly outperforming existing methods and achieving performance close to traditional MTL.

FlexRAG: A Flexible and Comprehensive Framework for Retrieval-Augmented Generation

Retrieval-Augmented Generation (RAG) plays a pivotal role in modern large language model applications, with numerous existing frameworks offering a wide range of functionalities to facilitate the development of RAG systems. However, we have identified several persistent challenges in these frameworks, including difficulties in algorithm reproduction and sharing, lack of new techniques, and high system overhead. To address these limitations, we introduce \textbf{FlexRAG}, an open-source framework specifically designed for research and prototyping. FlexRAG supports text-based, multimodal, and network-based RAG, providing comprehensive lifecycle support alongside efficient asynchronous processing and persistent caching capabilities. By offering a robust and flexible solution, FlexRAG enables researchers to rapidly develop, deploy, and share advanced RAG systems. Our toolkit and resources are available at \href{https://github.com/ictnlp/FlexRAG}{https://github.com/ictnlp/FlexRAG}.

AniMaker: Automated Multi-Agent Animated Storytelling with MCTS-Driven Clip Generation

Despite rapid advancements in video generation models, generating coherent storytelling videos that span multiple scenes and characters remains challenging. Current methods often rigidly convert pre-generated keyframes into fixed-length clips, resulting in disjointed narratives and pacing issues. Furthermore, the inherent instability of video generation models means that even a single low-quality clip can significantly degrade the entire output animation's logical coherence and visual continuity. To overcome these obstacles, we introduce AniMaker, a multi-agent framework enabling efficient multi-candidate clip generation and storytelling-aware clip selection, thus creating globally consistent and story-coherent animation solely from text input. The framework is structured around specialized agents, including the Director Agent for storyboard generation, the Photography Agent for video clip generation, the Reviewer Agent for evaluation, and the Post-Production Agent for editing and voiceover. Central to AniMaker's approach are two key technical components: MCTS-Gen in Photography Agent, an efficient Monte Carlo Tree Search (MCTS)-inspired strategy that intelligently navigates the candidate space to generate high-potential clips while optimizing resource usage; and AniEval in Reviewer Agent, the first framework specifically designed for multi-shot animation evaluation, which assesses critical aspects such as story-level consistency, action completion, and animation-specific features by considering each clip in the context of its preceding and succeeding clips. Experiments demonstrate that AniMaker achieves superior quality as measured by popular metrics including VBench and our proposed AniEval framework, while significantly improving the efficiency of multi-candidate generation, pushing AI-generated storytelling animation closer to production standards.

ComfyUI-R1: Exploring Reasoning Models for Workflow Generation

AI-generated content has evolved from monolithic models to modular workflows, particularly on platforms like ComfyUI, enabling customization in creative pipelines. However, crafting effective workflows requires great expertise to orchestrate numerous specialized components, presenting a steep learning curve for users. To address this challenge, we introduce ComfyUI-R1, the first large reasoning model for automated workflow generation. Starting with our curated dataset of 4K workflows, we construct long chain-of-thought (CoT) reasoning data, including node selection, workflow planning, and code-level workflow representation. ComfyUI-R1 is trained through a two-stage framework: (1) CoT fine-tuning for cold start, adapting models to the ComfyUI domain; (2) reinforcement learning for incentivizing reasoning capability, guided by a fine-grained rule-metric hybrid reward, ensuring format validity, structural integrity, and node-level fidelity. Experiments show that our 7B-parameter model achieves a 97\% format validity rate, along with high pass rate, node-level and graph-level F1 scores, significantly surpassing prior state-of-the-art methods that employ leading closed-source models such as GPT-4o and Claude series. Further analysis highlights the critical role of the reasoning process and the advantage of transforming workflows into code. Qualitative comparison reveals our strength in synthesizing intricate workflows with diverse nodes, underscoring the potential of long CoT reasoning in AI art creation.