CellForge: Agentic Design of Virtual Cell Models

🤗 Upvotes: 91 | cs.CV Authors: Chenfei Wu, Jiahao Li, Jingren Zhou, Junyang Lin, Kaiyuan Gao, Kun Yan, Sheng-ming Yin, Shuai Bai, Xiao Xu, Yilei Chen, Yuxiang Chen, Zecheng Tang, Zekai Zhang, Zhengyi Wang, An Yang, Bowen Yu, Chen Cheng, Dayiheng Liu, Deqing Li, Hang Zhang, Hao Meng, Hu Wei, Jingyuan Ni, Kai Chen, Kuan Cao, Liang Peng, Lin Qu, Minggang Wu, Peng Wang, Shuting Yu, Tingkun Wen, Wensen Feng, Xiaoxiao Xu, Yi Wang, Yichang Zhang, Yongqiang Zhu, Yujia Wu, Yuxuan Cai, Zenan Liu Title: Qwen-Image Technical Report Arxiv: http://arxiv.org/abs/2508.02324v1 Abstract: We present Qwen-Image, an image generation foundation model in the Qwen series that achieves significant advances in complex text rendering and precise image editing. To address the challenges of complex text rendering, we design a comprehensive data pipeline that includes large-scale data collection, filtering, annotation, synthesis, and balancing. Moreover, we adopt a progressive training strategy that starts with non-text-to-text rendering, evolves from simple to complex textual inputs, and gradually scales up to paragraph-level descriptions. This curriculum learning approach substantially enhances the model's native text rendering capabilities. As a result, Qwen-Image not only performs exceptionally well in alphabetic languages such as English, but also achieves remarkable progress on more challenging logographic languages like Chinese. To enhance image editing consistency, we introduce an improved multi-task training paradigm that incorporates not only traditional text-to-image (T2I) and text-image-to-image (TI2I) tasks but also image-to-image (I2I) reconstruction, effectively aligning the latent representations between Qwen2.5-VL and MMDiT. Furthermore, we separately feed the original image into Qwen2.5-VL and the VAE encoder to obtain semantic and reconstructive representations, respectively. This dual-encoding mechanism enables the editing module to strike a balance between preserving semantic consistency and maintaining visual fidelity. Qwen-Image achieves state-of-the-art performance, demonstrating its strong capabilities in both image generation and editing across multiple benchmarks.

🤗 Upvotes: 39 | cs.CL Authors: Junjie Wu, Jiangnan Li, Yuqing Li, Lemao Liu, Liyan Xu, Jiwei Li, Dit-Yan Yeung, Jie Zhou, Mo Yu Title: SitEmb-v1.5: Improved Context-Aware Dense Retrieval for Semantic Association and Long Story Comprehension Arxiv: http://arxiv.org/abs/2508.01959v1 Abstract: Retrieval-augmented generation (RAG) over long documents typically involves splitting the text into smaller chunks, which serve as the basic units for retrieval. However, due to dependencies across the original document, contextual information is often essential for accurately interpreting each chunk. To address this, prior work has explored encoding longer context windows to produce embeddings for longer chunks. Despite these efforts, gains in retrieval and downstream tasks remain limited. This is because (1) longer chunks strain the capacity of embedding models due to the increased amount of information they must encode, and (2) many real-world applications still require returning localized evidence due to constraints on model or human bandwidth. We propose an alternative approach to this challenge by representing short chunks in a way that is conditioned on a broader context window to enhance retrieval performance -- i.e., situating a chunk's meaning within its context. We further show that existing embedding models are not well-equipped to encode such situated context effectively, and thus introduce a new training paradigm and develop the situated embedding models (SitEmb). To evaluate our method, we curate a book-plot retrieval dataset specifically designed to assess situated retrieval capabilities. On this benchmark, our SitEmb-v1 model based on BGE-M3 substantially outperforms state-of-the-art embedding models, including several with up to 7-8B parameters, with only 1B parameters. Our 8B SitEmb-v1.5 model further improves performance by over 10% and shows strong results across different languages and several downstream applications.

🤗 Upvotes: 30 | cs.LG, cs.AI, cs.CL, q-bio.QM Authors: Xiangru Tang, Zhuoyun Yu, Jiapeng Chen, Yan Cui, Daniel Shao, Weixu Wang, Fang Wu, Yuchen Zhuang, Wenqi Shi, Zhi Huang, Arman Cohan, Xihong Lin, Fabian Theis, Smita Krishnaswamy, Mark Gerstein Title: CellForge: Agentic Design of Virtual Cell Models Arxiv: http://arxiv.org/abs/2508.02276v1 Abstract: Virtual cell modeling represents an emerging frontier at the intersection of artificial intelligence and biology, aiming to predict quantities such as responses to diverse perturbations quantitatively. However, autonomously building computational models for virtual cells is challenging due to the complexity of biological systems, the heterogeneity of data modalities, and the need for domain-specific expertise across multiple disciplines. Here, we introduce CellForge, an agentic system that leverages a multi-agent framework that transforms presented biological datasets and research objectives directly into optimized computational models for virtual cells. More specifically, given only raw single-cell multi-omics data and task descriptions as input, CellForge outputs both an optimized model architecture and executable code for training virtual cell models and inference. The framework integrates three core modules: Task Analysis for presented dataset characterization and relevant literature retrieval, Method Design, where specialized agents collaboratively develop optimized modeling strategies, and Experiment Execution for automated generation of code. The agents in the Design module are separated into experts with differing perspectives and a central moderator, and have to collaboratively exchange solutions until they achieve a reasonable consensus. We demonstrate CellForge's capabilities in single-cell perturbation prediction, using six diverse datasets that encompass gene knockouts, drug treatments, and cytokine stimulations across multiple modalities. CellForge consistently outperforms task-specific state-of-the-art methods. Overall, CellForge demonstrates how iterative interaction between LLM agents with differing perspectives provides better solutions than directly addressing a modeling challenge. Our code is publicly available at https://github.com/gersteinlab/CellForge.

🤗 Upvotes: 25 | cs.AI Authors: Qingyu Ren, Qianyu He, Bowei Zhang, Jie Zeng, Jiaqing Liang, Yanghua Xiao, Weikang Zhou, Zeye Sun, Fei Yu Title: Beyond the Trade-off: Self-Supervised Reinforcement Learning for Reasoning Models' Instruction Following Arxiv: http://arxiv.org/abs/2508.02150v1 Abstract: Reasoning models excel in complex problem solving but exhibit a concerning trade off between reasoning capabilities and instruction following abilities. Existing approaches for improving instruction following rely on stronger external models, creating methodological bottlenecks and practical limitations including increased costs and accessibility constraints. We propose a self-supervised RL framework that leverages reasoning models' own internal signals to improve instruction following capabilities without external supervision. Extensive experiments demonstrate that our framework significantly improves instruction following capabilities while maintaining reasoning performance, offering a scalable and cost-effective approach to enhance instruction following in reasoning models. The data and code are publicly available at https://github.com/Rainier-rq/verl-if.

🤗 Upvotes: 21 | cs.CR, cs.AI Authors: Sajana Weerawardhena, Paul Kassianik, Blaine Nelson, Baturay Saglam, Anu Vellore, Aman Priyanshu, Supriti Vijay, Massimo Aufiero, Arthur Goldblatt, Fraser Burch, Ed Li, Jianliang He, Dhruv Kedia, Kojin Oshiba, Zhouran Yang, Yaron Singer, Amin Karbasi Title: Llama-3.1-FoundationAI-SecurityLLM-8B-Instruct Technical Report Arxiv: http://arxiv.org/abs/2508.01059v1 Abstract: Large language models (LLMs) have shown remarkable success across many domains, yet their integration into cybersecurity applications remains limited due to a lack of general-purpose cybersecurity data, representational complexity, and safety and regulatory concerns. To address this gap, we previously introduced Foundation-Sec-8B, a cybersecurity-focused LLM suitable for fine-tuning on downstream tasks. That model, however, was not designed for chat-style interactions or instruction-following. In this report, we release Foundation-Sec-8B-Instruct: a model specifically trained for general-purpose cybersecurity dialogue. Built on Foundation-Sec-8B, it combines domain-specific knowledge with instruction-following, conversational capabilities, and alignment with human preferences to produce high-quality, relevant responses. Comprehensive evaluations show that Foundation-Sec-8B-Instruct outperforms Llama 3.1-8B-Instruct on a range of cybersecurity tasks while matching its instruction-following performance. It is also competitive with GPT-4o-mini on cyber threat intelligence and instruction-following tasks. We envision Foundation-Sec-8B-Instruct becoming an indispensable assistant in the daily workflows of cybersecurity professionals. We release the model publicly at https://huggingface.co/fdtn-ai/Foundation-Sec-8B-Instruct.

🤗 Upvotes: 39 | cs.CL Authors: Jinsong Li, Xiaoyi Dong, Yuhang Zang, Yuhang Cao, Jiaqi Wang, Dahua Lin Title: Beyond Fixed: Variable-Length Denoising for Diffusion Large Language Models Arxiv: http://arxiv.org/abs/2508.00819v1 Abstract: Diffusion Large Language Models (DLLMs) are emerging as a powerful alternative to the dominant Autoregressive Large Language Models, offering efficient parallel generation and capable global context modeling. However, the practical application of DLLMs is hindered by a critical architectural constraint: the need for a statically predefined generation length. This static length allocation leads to a problematic trade-off: insufficient lengths cripple performance on complex tasks, while excessive lengths incur significant computational overhead and sometimes result in performance degradation. While the inference framework is rigid, we observe that the model itself possesses internal signals that correlate with the optimal response length for a given task. To bridge this gap, we leverage these latent signals and introduce DAEDAL, a novel training-free denoising strategy that enables Dynamic Adaptive Length Expansion for Diffusion Large Language Models. DAEDAL operates in two phases: 1) Before the denoising process, DAEDAL starts from a short initial length and iteratively expands it to a coarse task-appropriate length, guided by a sequence completion metric. 2) During the denoising process, DAEDAL dynamically intervenes by pinpointing and expanding insufficient generation regions through mask token insertion, ensuring the final output is fully developed. Extensive experiments on DLLMs demonstrate that DAEDAL achieves performance comparable, and in some cases superior, to meticulously tuned fixed-length baselines, while simultaneously enhancing computational efficiency by achieving a higher effective token ratio. By resolving the static length constraint, DAEDAL unlocks new potential for DLLMs, bridging a critical gap with their Autoregressive counterparts and paving the way for more efficient and capable generation.

🤗 Upvotes: 38 | cs.AI, cs.CL Authors: Tianqing Fang, Zhisong Zhang, Xiaoyang Wang, Rui Wang, Can Qin, Yuxuan Wan, Jun-Yu Ma, Ce Zhang, Jiaqi Chen, Xiyun Li, Hongming Zhang, Haitao Mi, Dong Yu Title: Cognitive Kernel-Pro: A Framework for Deep Research Agents and Agent Foundation Models Training Arxiv: http://arxiv.org/abs/2508.00414v1 Abstract: General AI Agents are increasingly recognized as foundational frameworks for the next generation of artificial intelligence, enabling complex reasoning, web interaction, coding, and autonomous research capabilities. However, current agent systems are either closed-source or heavily reliant on a variety of paid APIs and proprietary tools, limiting accessibility and reproducibility for the research community. In this work, we present \textbf{Cognitive Kernel-Pro}, a fully open-source and (to the maximum extent) free multi-module agent framework designed to democratize the development and evaluation of advanced AI agents. Within Cognitive Kernel-Pro, we systematically investigate the curation of high-quality training data for Agent Foundation Models, focusing on the construction of queries, trajectories, and verifiable answers across four key domains: web, file, code, and general reasoning. Furthermore, we explore novel strategies for agent test-time reflection and voting to enhance agent robustness and performance. We evaluate Cognitive Kernel-Pro on GAIA, achieving state-of-the-art results among open-source and free agents. Notably, our 8B-parameter open-source model surpasses previous leading systems such as WebDancer and WebSailor, establishing a new performance standard for accessible, high-capability AI agents. Code is available at https://github.com/Tencent/CognitiveKernel-Pro

🤗 Upvotes: 33 | cs.CV Authors: Shuai Wang, Ziteng Gao, Chenhui Zhu, Weilin Huang, Limin Wang Title: PixNerd: Pixel Neural Field Diffusion Arxiv: http://arxiv.org/abs/2507.23268v2 Abstract: The current success of diffusion transformers heavily depends on the compressed latent space shaped by the pre-trained variational autoencoder(VAE). However, this two-stage training paradigm inevitably introduces accumulated errors and decoding artifacts. To address the aforementioned problems, researchers return to pixel space at the cost of complicated cascade pipelines and increased token complexity. In contrast to their efforts, we propose to model the patch-wise decoding with neural field and present a single-scale, single-stage, efficient, end-to-end solution, coined as pixel neural field diffusion~(PixelNerd). Thanks to the efficient neural field representation in PixNerd, we directly achieved 2.15 FID on ImageNet $256\times256$ and 2.84 FID on ImageNet $512\times512$ without any complex cascade pipeline or VAE. We also extend our PixNerd framework to text-to-image applications. Our PixNerd-XXL/16 achieved a competitive 0.73 overall score on the GenEval benchmark and 80.9 overall score on the DPG benchmark.

🤗 Upvotes: 65 | cs.AI, cs.CL Authors: Luoxin Chen, Jinming Gu, Liankai Huang, Wenhao Huang, Zhicheng Jiang, Allan Jie, Xiaoran Jin, Xing Jin, Chenggang Li, Kaijing Ma, Cheng Ren, Jiawei Shen, Wenlei Shi, Tong Sun, He Sun, Jiahui Wang, Siran Wang, Zhihong Wang, Chenrui Wei, Shufa Wei, Yonghui Wu, Yuchen Wu, Yihang Xia, Huajian Xin, Fan Yang, Huaiyuan Ying, Hongyi Yuan, Zheng Yuan, Tianyang Zhan, Chi Zhang, Yue Zhang, Ge Zhang, Tianyun Zhao, Jianqiu Zhao, Yichi Zhou, Thomas Hanwen Zhu Title: Seed-Prover: Deep and Broad Reasoning for Automated Theorem Proving Arxiv: http://arxiv.org/abs/2507.23726v1 Abstract: LLMs have demonstrated strong mathematical reasoning abilities by leveraging reinforcement learning with long chain-of-thought, yet they continue to struggle with theorem proving due to the lack of clear supervision signals when solely using natural language. Dedicated domain-specific languages like Lean provide clear supervision via formal verification of proofs, enabling effective training through reinforcement learning. In this work, we propose \textbf{Seed-Prover}, a lemma-style whole-proof reasoning model. Seed-Prover can iteratively refine its proof based on Lean feedback, proved lemmas, and self-summarization. To solve IMO-level contest problems, we design three test-time inference strategies that enable both deep and broad reasoning. Seed-Prover proves $78.1\%$ of formalized past IMO problems, saturates MiniF2F, and achieves over 50\% on PutnamBench, outperforming the previous state-of-the-art by a large margin. To address the lack of geometry support in Lean, we introduce a geometry reasoning engine \textbf{Seed-Geometry}, which outperforms previous formal geometry engines. We use these two systems to participate in IMO 2025 and fully prove 5 out of 6 problems. This work represents a significant advancement in automated mathematical reasoning, demonstrating the effectiveness of formal verification with long chain-of-thought reasoning.

🤗 Upvotes: 28 | cs.CV, cs.AI, cs.MM Authors: Miaosen Zhang, Ziqiang Xu, Jialiang Zhu, Qi Dai, Kai Qiu, Yifan Yang, Chong Luo, Tianyi Chen, Justin Wagle, Tim Franklin, Baining Guo Title: Phi-Ground Tech Report: Advancing Perception in GUI Grounding Arxiv: http://arxiv.org/abs/2507.23779v1 Abstract: With the development of multimodal reasoning models, Computer Use Agents (CUAs), akin to Jarvis from \textit{"Iron Man"}, are becoming a reality. GUI grounding is a core component for CUAs to execute actual actions, similar to mechanical control in robotics, and it directly leads to the success or failure of the system. It determines actions such as clicking and typing, as well as related parameters like the coordinates for clicks. Current end-to-end grounding models still achieve less than 65\% accuracy on challenging benchmarks like ScreenSpot-pro and UI-Vision, indicating they are far from being ready for deployment. % , as a single misclick can result in unacceptable consequences. In this work, we conduct an empirical study on the training of grounding models, examining details from data collection to model training. Ultimately, we developed the \textbf{Phi-Ground} model family, which achieves state-of-the-art performance across all five grounding benchmarks for models under $10B$ parameters in agent settings. In the end-to-end model setting, our model still achieves SOTA results with scores of \textit{\textbf{43.2}} on ScreenSpot-pro and \textit{\textbf{27.2}} on UI-Vision. We believe that the various details discussed in this paper, along with our successes and failures, not only clarify the construction of grounding models but also benefit other perception tasks. Project homepage: \href{https://zhangmiaosen2000.github.io/Phi-Ground/}{https://zhangmiaosen2000.github.io/Phi-Ground/}