As neural language models approach human performance on NLP benchmark tasks, their advances are widely seen as evidence of an increasingly complex understanding of syntax. This view rests upon a hypothesis that has not yet been empirically tested: that word order encodes meaning essential to performing these tasks. We refute this hypothesis in many cases: in the GLUE suite and in various genres of English text, the words in a sentence or phrase can rarely be permuted to form a phrase carrying substantially different information. Our surprising result relies on inference by iterative shuffling (IBIS), a novel, efficient procedure that finds the ordering of a bag of words having the highest likelihood under a fixed language model. IBIS can use any black-box model without additional training and is superior to existing word ordering algorithms. Coalescing our findings, we discuss how shuffling inference procedures such as IBIS can benefit language modeling and constrained generation.
Decoder-only language models, such as GPT and LLaMA, generally decode on the last layer. Motivated by human's hierarchical thinking capability, we propose that a hierarchical decoder architecture could be built with different layers decoding texts simultaneously. Due to limited time and computationally resources, we choose to adapt a pretrained language model into this form of hierarchical decoder. Language heads of the last layer are copied to different selected intermediate layers, and fine-tuned with different task inputs. By thorough experiments, we validate that these selective intermediate layers could be adapted to speak meaningful and reasonable contents, and this paradigm of hierarchical decoder can obtain state-of-the-art performances on multiple tasks such as hierarchical text classification, classification-guided generation, and hierarchical text generation. This study suggests the possibility of a generalized hierarchical reasoner, pretraining from scratch.
Large Language Models (LLMs) have advanced code generation and software automation, but are fundamentally constrained by limited inference-time context and lack of explicit code structure reasoning. We introduce Kodezi Chronos, a next-generation architecture for autonomous code understanding, debugging, and maintenance, designed to operate across ultra-long contexts comprising entire codebases, histories, and documentation, all without fixed window limits. Kodezi Chronos leverages a multi-level embedding memory engine, combining vector and graph-based indexing with continuous code-aware retrieval. This enables efficient and accurate reasoning over millions of lines of code, supporting repository-scale comprehension, multi-file refactoring, and real-time self-healing actions. Our evaluation introduces a novel Multi Random Retrieval benchmark, specifically tailored to the software engineering domain. Unlike classical retrieval benchmarks, this method requires the model to resolve arbitrarily distant and obfuscated associations across code artifacts, simulating realistic tasks such as variable tracing, dependency migration, and semantic bug localization. Chronos outperforms prior LLMs and code models, demonstrating a 23% improvement in real-world bug detection and reducing debugging cycles by up to 40% compared to traditional sequence-based approaches. By natively interfacing with IDEs and CI/CD workflows, Chronos enables seamless, autonomous software maintenance, elevating code reliability and productivity while reducing manual effort. These results mark a critical advance toward self-sustaining, continuously optimized software ecosystems.
Recent progress has been made in region-aware vision-language modeling, particularly with the emergence of the Describe Anything Model (DAM). DAM is capable of generating detailed descriptions of any specific image areas or objects without the need for additional localized image-text alignment supervision. We hypothesize that such region-level descriptive capability is beneficial for the task of Visual Question Answering (VQA), especially in challenging scenarios involving images with dense text. In such settings, the fine-grained extraction of textual information is crucial to producing correct answers. Motivated by this, we introduce DAM-QA, a framework with a tailored evaluation protocol, developed to investigate and harness the region-aware capabilities from DAM for the text-rich VQA problem that requires reasoning over text-based information within images. DAM-QA incorporates a mechanism that aggregates answers from multiple regional views of image content, enabling more effective identification of evidence that may be tied to text-related elements. Experiments on six VQA benchmarks show that our approach consistently outperforms the baseline DAM, with a notable 7+ point gain on DocVQA. DAM-QA also achieves the best overall performance among region-aware models with fewer parameters, significantly narrowing the gap with strong generalist VLMs. These results highlight the potential of DAM-like models for text-rich and broader VQA tasks when paired with efficient usage and integration strategies. Our code is publicly available at https://github.com/Linvyl/DAM-QA.git.
Face anti-spoofing (FAS) aims to construct a robust system that can withstand diverse attacks. While recent efforts have concentrated mainly on cross-domain generalization, two significant challenges persist: limited semantic understanding of attack types and training redundancy across domains. We address the first by integrating vision-language models (VLMs) to enhance the perception of visual input. For the second challenge, we employ a meta-domain strategy to learn a unified model that generalizes well across multiple domains. Our proposed InstructFLIP is a novel instruction-tuned framework that leverages VLMs to enhance generalization via textual guidance trained solely on a single domain. At its core, InstructFLIP explicitly decouples instructions into content and style components, where content-based instructions focus on the essential semantics of spoofing, and style-based instructions consider variations related to the environment and camera characteristics. Extensive experiments demonstrate the effectiveness of InstructFLIP by outperforming SOTA models in accuracy and substantially reducing training redundancy across diverse domains in FAS. Project website is available at https://kunkunlin1221.github.io/InstructFLIP.
Language Model (LM) pipelines can dynamically refine their outputs against programmatic constraints. However, their effectiveness collapses when faced with competing soft constraints, leading to inefficient backtracking loops where satisfying one constraint violates another. We introduce Meta Self-Refining, a framework that equips LM pipelines with a meta-corrective layer to repair these competitions at runtime/inference-time. Our approach monitors the pipeline's execution history to detect oscillatory failures. Upon detection, it invokes a meta-repairer LM that analyzes the holistic state of the backtracking attempts and synthesizes a strategic instruction to balance the competing requirements. This self-repair instruction guides the original LM out of a failing refining loop towards a successful output. Our results show Meta Self-Refining can successfully repair these loops, leading to more efficient LM programs.
Scientific databases aggregate vast amounts of quantitative data alongside descriptive text. In biochemistry, molecule screening assays evaluate the functional responses of candidate molecules against disease targets. Unstructured text that describes the biological mechanisms through which these targets operate, experimental screening protocols, and other attributes of assays offer rich information for new drug discovery campaigns but has been untapped because of that unstructured format. We present Assay2Mol, a large language model-based workflow that can capitalize on the vast existing biochemical screening assays for early-stage drug discovery. Assay2Mol retrieves existing assay records involving targets similar to the new target and generates candidate molecules using in-context learning with the retrieved assay screening data. Assay2Mol outperforms recent machine learning approaches that generate candidate ligand molecules for target protein structures, while also promoting more synthesizable molecule generation.
While tokenization is a key step in language modeling, with effects on model training and performance, it remains unclear how to effectively evaluate tokenizer quality. One proposed dimension of tokenizer quality is the extent to which tokenizers preserve linguistically meaningful subwords, aligning token boundaries with morphological boundaries within a word. We expand MorphScore (Arnett & Bergen, 2025), which previously covered 22 languages, to support a total of 70 languages. The updated MorphScore offers more flexibility in evaluation and addresses some of the limitations of the original version. We then correlate our alignment scores with downstream task performance for five pre-trained languages models on seven tasks, with at least one task in each of the languages in our sample. We find that morphological alignment does not explain very much variance in model performance, suggesting that morphological alignment alone does not measure dimensions of tokenization quality relevant to model performance.
Sparsifying neural networks often suffers from seemingly inevitable performance degradation, and it remains challenging to restore the original performance despite much recent progress. Motivated by recent studies in robust optimization, we aim to tackle this problem by finding subnetworks that are both sparse and flat at the same time. Specifically, we formulate pruning as a sparsity-constrained optimization problem where flatness is encouraged as an objective. We solve it explicitly via an augmented Lagrange dual approach and extend it further by proposing a generalized projection operation, resulting in novel pruning methods called SAFE and its extension, SAFE$^+$. Extensive evaluations on standard image classification and language modeling tasks reveal that SAFE consistently yields sparse networks with improved generalization performance, which compares competitively to well-established baselines. In addition, SAFE demonstrates resilience to noisy data, making it well-suited for real-world conditions.
We present a multi-agent system for automation of scientific research tasks, cmbagent. The system is formed by about 30 Large Language Model (LLM) agents and implements a Planning & Control strategy to orchestrate the agentic workflow, with no human-in-the-loop at any point. Each agent specializes in a different task (performing retrieval on scientific papers and codebases, writing code, interpreting results, critiquing the output of other agents) and the system is able to execute code locally. We successfully apply cmbagent to carry out a PhD level cosmology task (the measurement of cosmological parameters using supernova data) and evaluate its performance on two benchmark sets, finding superior performance over state-of-the-art LLMs. The source code is available on GitHub, demonstration videos are also available, and the system is deployed on HuggingFace and will be available on the cloud.
Sequence models like Transformers and RNNs often overallocate attention to irrelevant context, leading to noisy intermediate representations. This degrades LLM capabilities by promoting hallucinations, weakening long-range and retrieval abilities, and reducing robustness. Recent work has shown that differential design can mitigate this issue in Transformers, improving their effectiveness across various applications. In this paper, we explore whether these techniques, originally developed for Transformers, can be applied to Mamba, a recent architecture based on selective state-space layers that achieves Transformer-level performance with greater efficiency. We show that a naive adaptation of differential design to Mamba is insufficient and requires careful architectural modifications. To address this, we introduce a novel differential mechanism for Mamba, empirically validated on language modeling benchmarks, demonstrating improved retrieval capabilities and superior performance over vanilla Mamba. Finally, we conduct extensive ablation studies and empirical analyses to justify our design choices and provide evidence that our approach effectively mitigates the overallocation problem in Mamba-based models. Our code is publicly available.
We introduce DeSTA2.5-Audio, a general-purpose Large Audio Language Model (LALM) designed for robust auditory perception and instruction-following, without requiring task-specific audio instruction-tuning. Recent LALMs typically augment Large Language Models (LLMs) with auditory capabilities by training on large-scale, manually curated or LLM-synthesized audio-instruction datasets. However, these approaches have often suffered from the catastrophic forgetting of the LLM's original language abilities. To address this, we revisit the data construction pipeline and propose DeSTA, a self-generated cross-modal alignment strategy in which the backbone LLM generates its own training targets. This approach preserves the LLM's native language proficiency while establishing effective audio-text alignment, thereby enabling zero-shot generalization without task-specific tuning. Using DeSTA, we construct DeSTA-AQA5M, a large-scale, task-agnostic dataset containing 5 million training samples derived from 7,000 hours of audio spanning 50 diverse datasets, including speech, environmental sounds, and music. DeSTA2.5-Audio achieves state-of-the-art or competitive performance across a wide range of audio-language benchmarks, including Dynamic-SUPERB, MMAU, SAKURA, Speech-IFEval, and VoiceBench. Comprehensive comparative studies demonstrate that our self-generated strategy outperforms widely adopted data construction and training strategies in both auditory perception and instruction-following capabilities. Our findings underscore the importance of carefully designed data construction in LALM development and offer practical insights for building robust, general-purpose LALMs.
In today's digital world, casual user-generated content often contains subtle cues that may inadvertently expose sensitive personal attributes. Such risks underscore the growing importance of effective text anonymization to safeguard individual privacy. However, existing methods either rely on rigid replacements that damage utility or cloud-based LLMs that are costly and pose privacy risks. To address these issues, we explore the use of locally deployed smaller-scale language models (SLMs) for anonymization. Yet training effective SLMs remains challenging due to limited high-quality supervision. To address the challenge, we propose AgentStealth, a self-reinforcing LLM anonymization framework.First, we introduce an adversarial anonymization workflow enhanced by In-context Contrastive Learning and Adaptive Utility-Aware Control. Second, we perform supervised adaptation of SLMs using high-quality data collected from the workflow, which includes both anonymization and attack signals. Finally, we apply online reinforcement learning where the model leverages its internal adversarial feedback to iteratively improve anonymization performance. Experiments on two datasets show that our method outperforms baselines in both anonymization effectiveness (+12.3%) and utility (+6.8%). Our lightweight design supports direct deployment on edge devices, avoiding cloud reliance and communication-based privacy risks. Our code is open-source at https://github.com/tsinghua-fib-lab/AgentStealth.
Large Language Model-based Multi-Agent Systems (MASs) have demonstrated strong advantages in addressing complex real-world tasks. However, due to the introduction of additional attack surfaces, MASs are particularly vulnerable to misinformation injection. To facilitate a deeper understanding of misinformation propagation dynamics within these systems, we introduce MisinfoTask, a novel dataset featuring complex, realistic tasks designed to evaluate MAS robustness against such threats. Building upon this, we propose ARGUS, a two-stage, training-free defense framework leveraging goal-aware reasoning for precise misinformation rectification within information flows. Our experiments demonstrate that in challenging misinformation scenarios, ARGUS exhibits significant efficacy across various injection attacks, achieving an average reduction in misinformation toxicity of approximately 28.17% and improving task success rates under attack by approximately 10.33%. Our code and dataset is available at: https://github.com/zhrli324/ARGUS.
Recent advances in multimodal generative models have unlocked photorealistic, instruction-aligned image generation, yet leading systems like GPT-4o-Image remain proprietary and inaccessible. To democratize these capabilities, we present ShareGPT-4o-Image, the first dataset comprising 45K text-to-image and 46K text-and-image-to-image data, all synthesized using GPT-4o's image generation capabilities for distilling its advanced image generation abilities. Leveraging this dataset, we develop Janus-4o, a multimodal large language model capable of both text-to-image and text-and-image-to-image generation. Janus-4o not only significantly improves text-to-image generation over its predecessor, Janus-Pro, but also newly supports text-and-image-to-image generation. Notably, it achieves impressive performance in text-and-image-to-image generation from scratch, using only 91K synthetic samples and 6 hours of training on an 8 A800-GPU machine. We hope the release of ShareGPT-4o-Image and Janus-4o will foster open research in photorealistic, instruction-aligned image generation.
Multivariate time series anomaly detection (MTS-AD) is critical in domains like healthcare, cybersecurity, and industrial monitoring, yet remains challenging due to complex inter-variable dependencies, temporal dynamics, and sparse anomaly labels. We introduce mTSBench, the largest benchmark to date for MTS-AD and unsupervised model selection, spanning 344 labeled time series across 19 datasets and 12 diverse application domains. mTSBench evaluates 24 anomaly detection methods, including large language model (LLM)-based detectors for multivariate time series, and systematically benchmarks unsupervised model selection techniques under standardized conditions. Consistent with prior findings, our results confirm that no single detector excels across datasets, underscoring the importance of model selection. However, even state-of-the-art selection methods remain far from optimal, revealing critical gaps. mTSBench provides a unified evaluation suite to enable rigorous, reproducible comparisons and catalyze future advances in adaptive anomaly detection and robust model selection.
In this paper, we explore the use of a text-only, autoregressive language modeling approach for the extraction of referring expressions from visually grounded dialogue. More specifically, the aim is to investigate the extent to which the linguistic context alone can inform the detection of mentions that have a (visually perceivable) referent in the visual context of the conversation. To this end, we adapt a pretrained large language model (LLM) to perform a relatively course-grained annotation of mention spans in unfolding conversations by demarcating mention span boundaries in text via next-token prediction. Our findings indicate that even when using a moderately sized LLM, relatively small datasets, and parameter-efficient fine-tuning, a text-only approach can be effective, highlighting the relative importance of the linguistic context for this task. Nevertheless, we argue that the task represents an inherently multimodal problem and discuss limitations fundamental to unimodal approaches.
Fine-tuning vision language models (VLMs) has achieved remarkable performance across various downstream tasks; yet, it requires access to model gradients through backpropagation (BP), making them unsuitable for memory-constrained, inference-only edge devices. To address this limitation, previous work has explored various BP-free fine-tuning methods. However, these approaches often rely on high-variance evolutionary strategies (ES) or zeroth-order (ZO) optimization, and often fail to achieve satisfactory performance. In this paper, we propose a hybrid Sharpness-aware Zeroth-order optimization (SharpZO) approach, specifically designed to enhance the performance of ZO VLM fine-tuning via a sharpness-aware warm-up training. SharpZO features a two-stage optimization process: a sharpness-aware ES stage that globally explores and smooths the loss landscape to construct a strong initialization, followed by a fine-grained local search via sparse ZO optimization. The entire optimization relies solely on forward passes. Detailed theoretical analysis and extensive experiments on CLIP models demonstrate that SharpZO significantly improves accuracy and convergence speed, achieving up to 7% average gain over state-of-the-art forward-only methods.
Given the growing influence of language model-based agents on high-stakes societal decisions, from public policy to healthcare, ensuring their beneficial impact requires understanding the far-reaching implications of their suggestions. We propose a proof-of-concept framework that projects how model-generated advice could propagate through societal systems on a macroscopic scale over time, enabling more robust alignment. To assess the long-term safety awareness of language models, we also introduce a dataset of 100 indirect harm scenarios, testing models' ability to foresee adverse, non-obvious outcomes from seemingly harmless user prompts. Our approach achieves not only over 20% improvement on the new dataset but also an average win rate exceeding 70% against strong baselines on existing safety benchmarks (AdvBench, SafeRLHF, WildGuardMix), suggesting a promising direction for safer agents.
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.