Transcriptomic foundation models (TFMs) have recently emerged as powerful tools for analyzing gene expression in cells and tissues, supporting key tasks such as cell-type annotation, batch correction, and perturbation prediction. However, the diversity of model implementations and training strategies across recent TFMs, though promising, makes it challenging to isolate the contribution of individual design choices or evaluate their potential synergies. This hinders the field's ability to converge on best practices and limits the reproducibility of insights across studies. We present BMFM-RNA, an open-source, modular software package that unifies diverse TFM pretraining and fine-tuning objectives within a single framework. Leveraging this capability, we introduce a novel training objective, whole cell expression decoder (WCED), which captures global expression patterns using an autoencoder-like CLS bottleneck representation. In this paper, we describe the framework, supported input representations, and training objectives. We evaluated four model checkpoints pretrained on CELLxGENE using combinations of masked language modeling (MLM), WCED and multitask learning. Using the benchmarking capabilities of BMFM-RNA, we show that WCED-based models achieve performance that matches or exceeds state-of-the-art approaches like scGPT across more than a dozen datasets in both zero-shot and fine-tuning tasks. BMFM-RNA, available as part of the biomed-multi-omics project ( https://github.com/BiomedSciAI/biomed-multi-omic ), offers a reproducible foundation for systematic benchmarking and community-driven exploration of optimal TFM training strategies, enabling the development of more effective tools to leverage the latest advances in AI for understanding cell biology.
Large language model (LLM) agents have demonstrated remarkable potential in advancing scientific discovery. However, their capability in the fundamental yet crucial task of reproducing code from research papers, especially in the NLP domain, remains underexplored. This task includes unique complex reasoning challenges in the intellectual synthesis of abstract concepts and the comprehension of code repositories with interdependent files. Motivated by this gap, we present LMR-BENCH, a benchmark designed to systematically evaluate the capability of LLM agents on code reproduction from Language Modeling Research. It consists of 28 code reproduction tasks derived from 23 research papers published in top-tier NLP venues over the past five years, spanning nine fundamental categories. Models are provided with a research paper, a code repository containing one or more masked functions, and instructions for implementing these functions. We conduct extensive experiments in standard prompting and LLM agent settings with state-of-the-art LLMs, evaluating the accuracy of unit tests and performing LLM-based evaluation of code correctness. Experimental results reveal that even the most advanced models still exhibit persistent limitations in scientific reasoning and code synthesis, highlighting critical gaps in LLM agents' ability to autonomously reproduce scientific research
With the advancement of Large Language Model (LLM) for natural language processing, this paper presents an intriguing finding: a frozen pre-trained LLM layer can process visual tokens for medical image segmentation tasks. Specifically, we propose a simple hybrid structure that integrates a pre-trained, frozen LLM layer within the CNN encoder-decoder segmentation framework (LLM4Seg). Surprisingly, this design improves segmentation performance with a minimal increase in trainable parameters across various modalities, including ultrasound, dermoscopy, polypscopy, and CT scans. Our in-depth analysis reveals the potential of transferring LLM's semantic awareness to enhance segmentation tasks, offering both improved global understanding and better local modeling capabilities. The improvement proves robust across different LLMs, validated using LLaMA and DeepSeek.
Single-trajectory reinforcement learning (RL) methods aim to optimize policies from datasets consisting of (prompt, response, reward) triplets, where scalar rewards are directly available. This supervision format is highly practical, as it mirrors real-world human feedback, such as thumbs-up/down signals, and avoids the need for structured preference annotations. In contrast, pairwise preference-based methods like Direct Preference Optimization (DPO) rely on datasets with both preferred and dispreferred responses, which are harder to construct and less natural to collect. Among single-trajectory approaches, Direct Reward Optimization (DRO) has shown strong empirical performance due to its simplicity and stability. However, DRO requires approximating a value function, which introduces several limitations: high off-policy variance, coupling between policy and value learning, and a lack of absolute supervision on the policy itself. We introduce Reward Partitioning Optimization (RPO), a new method that resolves these limitations by removing the need to model the value function. Instead, RPO normalizes observed rewards using a partitioning approach estimated directly from data. This leads to a straightforward supervised learning objective on the policy, with no auxiliary models and no joint optimization. RPO provides direct and stable supervision on the policy, making it robust and easy to implement in practice. We validate RPO on scalar-feedback language modeling tasks using Flan-T5 encoder-decoder models. Our results demonstrate that RPO outperforms existing single-trajectory baselines such as DRO and Kahneman-Tversky Optimization (KTO). These findings confirm that RPO is a simple, effective, and theoretically grounded method for single-trajectory policy optimization.
Large Language Models (LLMs) are powerful tools with profound societal impacts, yet their ability to generate responses to diverse and uncontrolled inputs leaves them vulnerable to adversarial attacks. While existing defenses often struggle to generalize across varying attack types, recent advancements in representation engineering offer promising alternatives. In this work, we propose a defense framework that formulates model defense as a contrastive representation learning (CRL) problem. Our method finetunes a model using a triplet-based loss combined with adversarial hard negative mining to encourage separation between benign and harmful representations. Our experimental results across multiple models demonstrate that our approach outperforms prior representation engineering-based defenses, improving robustness against both input-level and embedding-space attacks without compromising standard performance. Our code is available at https://github.com/samuelsimko/crl-llm-defense
Long-context understanding is crucial for many NLP applications, yet transformers struggle with efficiency due to the quadratic complexity of self-attention. Sparse attention methods alleviate this cost but often impose static, predefined masks, failing to capture heterogeneous attention patterns. This results in suboptimal token interactions, limiting adaptability and retrieval accuracy in long-sequence tasks. This work introduces a dynamic sparse attention mechanism that assigns adaptive masks at the attention-map level, preserving heterogeneous patterns across layers and heads. Unlike existing approaches, our method eliminates the need for fine-tuning and predefined mask structures while maintaining computational efficiency. By learning context-aware attention structures, it achieves high alignment with full-attention models, ensuring minimal performance degradation while reducing memory and compute overhead. This approach provides a scalable alternative to full attention, enabling the practical deployment of large-scale Large Language Models (LLMs) without sacrificing retrieval performance. DAM is available at: https://github.com/HanzhiZhang-Ulrica/DAM.
Remote sensing has become critical for understanding environmental dynamics, urban planning, and disaster management. However, traditional remote sensing workflows often rely on explicit segmentation or detection methods, which struggle to handle complex, implicit queries that require reasoning over spatial context, domain knowledge, and implicit user intent. Motivated by this, we introduce a new task, \ie, geospatial pixel reasoning, which allows implicit querying and reasoning and generates the mask of the target region. To advance this task, we construct and release the first large-scale benchmark dataset called EarthReason, which comprises 5,434 manually annotated image masks with over 30,000 implicit question-answer pairs. Moreover, we propose SegEarth-R1, a simple yet effective language-guided segmentation baseline that integrates a hierarchical visual encoder, a large language model (LLM) for instruction parsing, and a tailored mask generator for spatial correlation. The design of SegEarth-R1 incorporates domain-specific adaptations, including aggressive visual token compression to handle ultra-high-resolution remote sensing images, a description projection module to fuse language and multi-scale features, and a streamlined mask prediction pipeline that directly queries description embeddings. Extensive experiments demonstrate that SegEarth-R1 achieves state-of-the-art performance on both reasoning and referring segmentation tasks, significantly outperforming traditional and LLM-based segmentation methods. Our data and code will be released at https://github.com/earth-insights/SegEarth-R1.
Watermarking the outputs of generative models has emerged as a promising approach for tracking their provenance. Despite significant interest in autoregressive image generation models and their potential for misuse, no prior work has attempted to watermark their outputs at the token level. In this work, we present the first such approach by adapting language model watermarking techniques to this setting. We identify a key challenge: the lack of reverse cycle-consistency (RCC), wherein re-tokenizing generated image tokens significantly alters the token sequence, effectively erasing the watermark. To address this and to make our method robust to common image transformations, neural compression, and removal attacks, we introduce (i) a custom tokenizer-detokenizer finetuning procedure that improves RCC, and (ii) a complementary watermark synchronization layer. As our experiments demonstrate, our approach enables reliable and robust watermark detection with theoretically grounded p-values.
This paper presents improved native unified multimodal models, \emph{i.e.,} Show-o2, that leverage autoregressive modeling and flow matching. Built upon a 3D causal variational autoencoder space, unified visual representations are constructed through a dual-path of spatial (-temporal) fusion, enabling scalability across image and video modalities while ensuring effective multimodal understanding and generation. Based on a language model, autoregressive modeling and flow matching are natively applied to the language head and flow head, respectively, to facilitate text token prediction and image/video generation. A two-stage training recipe is designed to effectively learn and scale to larger models. The resulting Show-o2 models demonstrate versatility in handling a wide range of multimodal understanding and generation tasks across diverse modalities, including text, images, and videos. Code and models are released at https://github.com/showlab/Show-o.
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}.
Large language models (LLMs) have shown remarkable capabilities in language understanding and generation. However, such impressive capability typically comes with a substantial model size, which presents significant challenges in deployment and inference. While structured pruning of model parameters offers a promising way to reduce computational costs at deployment time, current methods primarily focus on single model pruning. In this work, we develop a novel strategy to compress models by strategically combining or merging layers from finetuned model variants, which preserves the original model's abilities by aggregating capabilities accentuated in different finetunes. We pose the optimal tailoring of these LLMs as a zero-order optimization problem, adopting a search space that supports three different operations: (1) Layer removal, (2) Layer selection from different candidate models, and (3) Layer merging. Our experiments demonstrate that this approach leads to competitive model pruning, for example, for the Llama2-13B model families, our compressed models maintain approximately 97.3\% of the original performance while removing $\sim25\%$ of parameters, significantly outperforming previous state-of-the-art methods. The code is available at https://github.com/Guinan-Su/auto-merge-llm.
With rapidly evolving media narratives, it has become increasingly critical to not just extract narratives from a given corpus but rather investigate, how they develop over time. While popular narrative extraction methods such as Large Language Models do well in capturing typical narrative elements or even the complex structure of a narrative, applying them to an entire corpus comes with obstacles, such as a high financial or computational cost. We propose a combination of the language understanding capabilities of Large Language Models with the large scale applicability of topic models to dynamically model narrative shifts across time using the Narrative Policy Framework. We apply a topic model and a corresponding change point detection method to find changes that concern a specific topic of interest. Using this model, we filter our corpus for documents that are particularly representative of that change and feed them into a Large Language Model that interprets the change that happened in an automated fashion and distinguishes between content and narrative shifts. We employ our pipeline on a corpus of The Wall Street Journal news paper articles from 2009 to 2023. Our findings indicate that a Large Language Model can efficiently extract a narrative shift if one exists at a given point in time, but does not perform as well when having to decide whether a shift in content or a narrative shift took place.
Large reasoning models (LRMs) achieve impressive reasoning capabilities by generating lengthy chain-of-thoughts, but this "overthinking" incurs high latency and cost without commensurate accuracy gains. In this work, we introduce AALC, a lightweight, accuracy-aware length reward integrated into reinforcement learning that dynamically balances correctness and brevity during training. By incorporating validation accuracy into the reward and employing a smooth, dynamically scheduled length penalty, AALC delays length penalty until target performance is met. Through extensive experiments across standard and out-of-distribution math benchmarks, we show that our approach reduces response length by over 50% while maintaining or even improving the original accuracy. Furthermore, qualitative analysis reveals that our method curbs redundant reasoning patterns such as excessive subgoal setting and verification, leading to structurally refined outputs rather than naive truncation. We also identify that efficiency gains are accompanied by reduced interpretability: models trained with AALC omit some narrative framing and explanatory context. These findings highlight the potential of reward-based strategies to guide LRMs toward more efficient, generalizable reasoning paths.
Background: The positive predictive value (PPV) of large language model (LLM)-based proofreading for radiology reports is limited due to the low error prevalence. Purpose: To assess whether a three-pass LLM framework enhances PPV and reduces operational costs compared with baseline approaches. Materials and Methods: A retrospective analysis was performed on 1,000 consecutive radiology reports (250 each: radiography, ultrasonography, CT, MRI) from the MIMIC-III database. Two external datasets (CheXpert and Open-i) were validation sets. Three LLM frameworks were tested: (1) single-prompt detector; (2) extractor plus detector; and (3) extractor, detector, and false-positive verifier. Precision was measured by PPV and absolute true positive rate (aTPR). Efficiency was calculated from model inference charges and reviewer remuneration. Statistical significance was tested using cluster bootstrap, exact McNemar tests, and Holm-Bonferroni correction. Results: Framework PPV increased from 0.063 (95% CI, 0.036-0.101, Framework 1) to 0.079 (0.049-0.118, Framework 2), and significantly to 0.159 (0.090-0.252, Framework 3; P<.001 vs. baselines). aTPR remained stable (0.012-0.014; P>=.84). Operational costs per 1,000 reports dropped to USD 5.58 (Framework 3) from USD 9.72 (Framework 1) and USD 6.85 (Framework 2), reflecting reductions of 42.6% and 18.5%, respectively. Human-reviewed reports decreased from 192 to 88. External validation supported Framework 3's superior PPV (CheXpert 0.133, Open-i 0.105) and stable aTPR (0.007). Conclusion: A three-pass LLM framework significantly enhanced PPV and reduced operational costs, maintaining detection performance, providing an effective strategy for AI-assisted radiology report quality assurance.
Large language model-based machine learning (ML) agents have shown great promise in automating ML research. However, existing agents typically operate in isolation on a given research problem, without engaging with the broader research community, where human researchers often gain insights and contribute by sharing knowledge. To bridge this gap, we introduce MLE-Live, a live evaluation framework designed to assess an agent's ability to communicate with and leverage collective knowledge from a simulated Kaggle research community. Building on this framework, we propose CoMind, a novel agent that excels at exchanging insights and developing novel solutions within a community context. CoMind achieves state-of-the-art performance on MLE-Live and outperforms 79.2% human competitors on average across four ongoing Kaggle competitions. Our code is released at https://github.com/comind-ml/CoMind.
Different base language model families, such as Llama and Qwen, exhibit divergent behaviors during post-training with reinforcement learning (RL), especially on reasoning-intensive tasks. What makes a base language model suitable for reinforcement learning? Gaining deeper insight into this question is essential for developing RL-scalable foundation models of the next generation. In this work, we investigate how mid-training strategies shape RL dynamics, focusing on two representative model families: Qwen and Llama. Our study reveals that (1) high-quality mathematical corpora, such as MegaMath-Web-Pro, significantly improve both base model and RL performance, while existing alternatives (e.g., FineMath-4plus) fail to do so; (2) further adding QA-style data, particularly long chain-of-thought (CoT) reasoning examples, enhances RL outcomes, and instruction data further unlocks this effect; (3) while long-CoT improves reasoning depth, it can also induce verbosity of model responses and unstability of RL training, underscoring the importance of data formatting; (4) scaling mid-training consistently leads to stronger downstream RL performance. Building on these insights, we introduce a two-stage mid-training strategy, Stable-then-Decay, in which base models are first trained on 200B tokens with a constant learning rate, followed by 20B tokens across three CoT-focused branches with learning rate decay. This yields OctoThinker, a family of models demonstrating strong RL compatibility and closing the performance gap with more RL-friendly model families, i.e., Qwen. We hope our work will help shape pre-training strategies for foundation models in the RL era. To support further research, we release our open-source models along with a curated math reasoning-intensive corpus of over 70 billion tokens (i.e., MegaMath-Web-Pro-Max).
Can we leverage LLMs to model the process of discovering novel language model (LM) architectures? Inspired by real research, we propose a multi-agent LLM approach that simulates the conventional stages of research, from ideation and literature search (proposal stage) to design implementation (code generation), generative pre-training, and downstream evaluation (verification). Using ideas from scaling laws, our system, Genesys, employs a Ladder of Scales approach; new designs are proposed, adversarially reviewed, implemented, and selectively verified at increasingly larger model scales (14M$\sim$350M parameters) with a narrowing budget (the number of models we can train at each scale). To help make discovery efficient and factorizable, Genesys uses a novel genetic programming backbone, which we show has empirical advantages over commonly used direct prompt generation workflows (e.g., $\sim$86\% percentage point improvement in successful design generation, a key bottleneck). We report experiments involving 1,162 newly discovered designs (1,062 fully verified through pre-training) and find the best designs to be highly competitive with known architectures (e.g., outperform GPT2, Mamba2, etc., on 6/9 common benchmarks). We couple these results with comprehensive system-level ablations and formal results, which give broader insights into the design of effective autonomous discovery systems.
Retrieval-Augmented Generation (RAG) addresses limitations of large language models (LLMs) by leveraging a vector database to provide more accurate and up-to-date information. When a user submits a query, RAG executes a vector search to find relevant documents, which are then used to generate a response. However, ensuring the relevance of retrieved documents with a query would be a big challenge. To address this, a secondary model, known as a relevant grader, can be served to verify its relevance. To reduce computational requirements of a relevant grader, a lightweight small language model is preferred. In this work, we finetuned llama-3.2-1b as a relevant grader and achieved a significant increase in precision from 0.1301 to 0.7750. Its precision is comparable to that of llama-3.1-70b. Our code is available at https://github.com/taeheej/Lightweight-Relevance-Grader-in-RAG.
Tokenization imposes a fixed granularity on the input text, freezing how a language model operates on data and how far in the future it predicts. Byte Pair Encoding (BPE) and similar schemes split text once, build a static vocabulary, and leave the model stuck with that choice. We relax this rigidity by introducing an autoregressive U-Net that learns to embed its own tokens as it trains. The network reads raw bytes, pools them into words, then pairs of words, then up to 4 words, giving it a multi-scale view of the sequence. At deeper stages, the model must predict further into the future -- anticipating the next few words rather than the next byte -- so deeper stages focus on broader semantic patterns while earlier stages handle fine details. When carefully tuning and controlling pretraining compute, shallow hierarchies tie strong BPE baselines, and deeper hierarchies have a promising trend. Because tokenization now lives inside the model, the same system can handle character-level tasks and carry knowledge across low-resource languages.
While research on dialogue response generation has primarily focused on generating coherent responses conditioning on textual context, the critical question of when to respond grounded on the temporal context remains underexplored. To bridge this gap, we propose a novel task called timely dialogue response generation and introduce the TimelyChat benchmark, which evaluates the capabilities of language models to predict appropriate time intervals and generate time-conditioned responses. Additionally, we construct a large-scale training dataset by leveraging unlabeled event knowledge from a temporal commonsense knowledge graph and employing a large language model (LLM) to synthesize 55K event-driven dialogues. We then train Timer, a dialogue agent designed to proactively predict time intervals and generate timely responses that align with those intervals. Experimental results show that Timer outperforms prompting-based LLMs and other fine-tuned baselines in both turn-level and dialogue-level evaluations. We publicly release our data, model, and code.