Identifying evolutionary correspondences between cell types across species is a fundamental challenge in comparative genomics and evolutionary biology. Existing approaches often rely on either reference-based matching, which imposes asymmetry by designating one species as the reference, or projection-based matching, which may increase computational complexity and obscure biological interpretability at the cell-type level. Here, we present OT-MESH, an unsupervised computational framework leveraging entropy-regularized optimal transport (OT) to systematically determine cross-species cell type homologies. Our method uniquely integrates the Minimize Entropy of Sinkhorn (MESH) technique to refine the OT plan. It begins by selecting genes with high Signal-to-Noise Ratio (SNR) to capture the most informative features, from which a cost matrix is constructed using cosine distances between cell-type centroids. Importantly, the MESH procedure iteratively refines the cost matrix, leading to a transport plan with significantly enhanced sparsity and interpretability of the resulting correspondence matrices. Applied to retinal bipolar cells (BCs) and retinal ganglion cells (RGCs) from mouse and macaque, OT-MESH accurately recovers known evolutionary relationships and uncovers novel correspondences, one of which was independently validated experimentally. Thus, our framework offers a principled, scalable, symmetric, and interpretable solution for evolutionary cell type mapping, facilitating deeper insights into cellular specialization and conservation across species.
In this work, we investigate an important task named instruction-following text embedding, which generates dynamic text embeddings that adapt to user instructions, highlighting specific attributes of text. Despite recent advancements, existing approaches suffer from significant computational overhead, as they require re-encoding the entire corpus for each new instruction. To address this challenge, we propose GSTransform, a novel instruction-following text embedding framework based on Guided Space Transformation. Our key observation is that instruction-relevant information is inherently encoded in generic embeddings but remains underutilized. Instead of repeatedly encoding the corpus for each instruction, GSTransform is a lightweight transformation mechanism that adapts pre-computed embeddings in real time to align with user instructions, guided by a small amount of text data with instruction-focused label annotation. We conduct extensive experiments on three instruction-awareness downstream tasks across nine real-world datasets, demonstrating that GSTransform improves instruction-following text embedding quality over state-of-the-art methods while achieving dramatic speedups of 6~300x in real-time processing on large-scale datasets. The source code is available at https://github.com/YingchaojieFeng/GSTransform.
Large language models (LLMs) have shown great success in text modeling tasks across domains. However, natural language exhibits inherent semantic hierarchies and nuanced geometric structure, which current LLMs do not capture completely owing to their reliance on Euclidean operations. Recent studies have also shown that not respecting the geometry of token embeddings leads to training instabilities and degradation of generative capabilities. These findings suggest that shifting to non-Euclidean geometries can better align language models with the underlying geometry of text. We thus propose to operate fully in Hyperbolic space, known for its expansive, scale-free, and low-distortion properties. We thus introduce HELM, a family of HypErbolic Large Language Models, offering a geometric rethinking of the Transformer-based LLM that addresses the representational inflexibility, missing set of necessary operations, and poor scalability of existing hyperbolic LMs. We additionally introduce a Mixture-of-Curvature Experts model, HELM-MICE, where each expert operates in a distinct curvature space to encode more fine-grained geometric structure from text, as well as a dense model, HELM-D. For HELM-MICE, we further develop hyperbolic Multi-Head Latent Attention (HMLA) for efficient, reduced-KV-cache training and inference. For both models, we develop essential hyperbolic equivalents of rotary positional encodings and RMS normalization. We are the first to train fully hyperbolic LLMs at billion-parameter scale, and evaluate them on well-known benchmarks such as MMLU and ARC, spanning STEM problem-solving, general knowledge, and commonsense reasoning. Our results show consistent gains from our HELM architectures -- up to 4% -- over popular Euclidean architectures used in LLaMA and DeepSeek, highlighting the efficacy and enhanced reasoning afforded by hyperbolic geometry in large-scale LM pretraining.
Large language models (LLMs) have shown great potential in decision-making due to the vast amount of knowledge stored within the models. However, these pre-trained models are prone to lack reasoning abilities and are difficult to adapt to new environments, further hindering their application to complex real-world tasks. To address these challenges, inspired by the human cognitive process, we propose Causal-aware LLMs, which integrate the structural causal model (SCM) into the decision-making process to model, update, and utilize structured knowledge of the environment in a ``learning-adapting-acting" paradigm. Specifically, in the learning stage, we first utilize an LLM to extract the environment-specific causal entities and their causal relations to initialize a structured causal model of the environment. Subsequently,in the adapting stage, we update the structured causal model through external feedback about the environment, via an idea of causal intervention. Finally, in the acting stage, Causal-aware LLMs exploit structured causal knowledge for more efficient policy-making through the reinforcement learning agent. The above processes are performed iteratively to learn causal knowledge, ultimately enabling the causal-aware LLMs to achieve a more accurate understanding of the environment and make more efficient decisions. Experimental results across 22 diverse tasks within the open-world game ``Crafter" validate the effectiveness of our proposed method.
Optimizing policies based on human preferences is key to aligning language models with human intent. This work focuses on reward modeling, a core component in reinforcement learning from human feedback (RLHF), and offline preference optimization, such as direct preference optimization. Conventional approaches typically assume accurate annotations. However, real-world preference data often contains noise due to human errors or biases. We propose a principled framework for robust policy optimization under noisy preferences, viewing reward modeling as a classification problem. This allows us to leverage symmetric losses, known for their robustness to label noise in classification, leading to our Symmetric Preference Optimization (SymPO) method. We prove that symmetric losses enable successful policy optimization even under noisy labels, as the resulting reward remains rank-preserving -- a property sufficient for policy improvement. Experiments on synthetic and real-world tasks demonstrate the effectiveness of SymPO.
As people increasingly use AI systems in work and daily life, feedback mechanisms that help them use AI responsibly are urgently needed, particularly in settings where users are not equipped to assess the quality of AI predictions. We study a realistic Machine Translation (MT) scenario where monolingual users decide whether to share an MT output, first without and then with quality feedback. We compare four types of quality feedback: explicit feedback that directly give users an assessment of translation quality using 1) error highlights and 2) LLM explanations, and implicit feedback that helps users compare MT inputs and outputs through 3) backtranslation and 4) question-answer (QA) tables. We find that all feedback types, except error highlights, significantly improve both decision accuracy and appropriate reliance. Notably, implicit feedback, especially QA tables, yields significantly greater gains than explicit feedback in terms of decision accuracy, appropriate reliance, and user perceptions, receiving the highest ratings for helpfulness and trust, and the lowest for mental burden.
Large Language Models (LLMs) need to adapt their predictions to diverse cultural contexts to benefit diverse communities across the world. While previous efforts have focused on single-LLM, single-turn approaches, we propose to exploit the complementary strengths of multiple LLMs to promote cultural adaptability. We introduce a Multi-Agent Debate framework, where two LLM-based agents debate over a cultural scenario and collaboratively reach a final decision. We propose two variants: one where either LLM agents exclusively debate and another where they dynamically choose between self-reflection and debate during their turns. We evaluate these approaches on 7 open-weight LLMs (and 21 LLM combinations) using the NormAd-ETI benchmark for social etiquette norms in 75 countries. Experiments show that debate improves both overall accuracy and cultural group parity over single-LLM baselines. Notably, multi-agent debate enables relatively small LLMs (7-9B) to achieve accuracies comparable to that of a much larger model (27B parameters).
Large language models (LLMs) have significantly advanced in reasoning tasks through reinforcement learning (RL) optimization, achieving impressive capabilities across various challenging benchmarks. However, our empirical analysis reveals a critical drawback: reasoning-oriented RL fine-tuning significantly increases the prevalence of hallucinations. We theoretically analyze the RL training dynamics, identifying high-variance gradient, entropy-induced randomness, and susceptibility to spurious local optima as key factors leading to hallucinations. To address this drawback, we propose Factuality-aware Step-wise Policy Optimization (FSPO), an innovative RL fine-tuning algorithm incorporating explicit factuality verification at each reasoning step. FSPO leverages automated verification against given evidence to dynamically adjust token-level advantage values, incentivizing factual correctness throughout the reasoning process. Experiments across mathematical reasoning and hallucination benchmarks using Qwen2.5 and Llama models demonstrate that FSPO effectively reduces hallucinations while enhancing reasoning accuracy, substantially improving both reliability and performance.
To address the computational and storage challenges posed by large-scale datasets in deep learning, dataset distillation has been proposed to synthesize a compact dataset that replaces the original while maintaining comparable model performance. Unlike optimization-based approaches that require costly bi-level optimization, distribution matching (DM) methods improve efficiency by aligning the distributions of synthetic and original data, thereby eliminating nested optimization. DM achieves high computational efficiency and has emerged as a promising solution. However, existing DM methods, constrained to Euclidean space, treat data as independent and identically distributed points, overlooking complex geometric and hierarchical relationships. To overcome this limitation, we propose a novel hyperbolic dataset distillation method, termed HDD. Hyperbolic space, characterized by negative curvature and exponential volume growth with distance, naturally models hierarchical and tree-like structures. HDD embeds features extracted by a shallow network into the Lorentz hyperbolic space, where the discrepancy between synthetic and original data is measured by the hyperbolic (geodesic) distance between their centroids. By optimizing this distance, the hierarchical structure is explicitly integrated into the distillation process, guiding synthetic samples to gravitate towards the root-centric regions of the original data distribution while preserving their underlying geometric characteristics. Furthermore, we find that pruning in hyperbolic space requires only 20% of the distilled core set to retain model performance, while significantly improving training stability. Notably, HDD is seamlessly compatible with most existing DM methods, and extensive experiments on different datasets validate its effectiveness.
The availability of Large Language Models (LLMs) presents a unique opportunity to reinvigorate research on Knowledge Engineering (KE) automation, a trend already evident in recent efforts developing LLM-based methods and tools for the automatic generation of Competency Questions (CQs). However, the evaluation of these tools lacks standardisation. This undermines the methodological rigour and hinders the replication and comparison of results. To address this gap, we introduce Bench4KE, an extensible API-based benchmarking system for KE automation. Its first release focuses on evaluating tools that generate CQs automatically. CQs are natural language questions used by ontology engineers to define the functional requirements of an ontology. Bench4KE provides a curated gold standard consisting of CQ datasets from four real-world ontology projects. It uses a suite of similarity metrics to assess the quality of the CQs generated. We present a comparative analysis of four recent CQ generation systems, which are based on LLMs, establishing a baseline for future research. Bench4KE is also designed to accommodate additional KE automation tasks, such as SPARQL query generation, ontology testing and drafting. Code and datasets are publicly available under the Apache 2.0 license.
Recent advancements in Generative AI and Large Language Models (LLMs) have enabled the creation of highly realistic synthetic content, raising concerns about the potential for malicious use, such as misinformation and manipulation. Moreover, detecting Machine-Generated Text (MGT) remains challenging due to the lack of robust benchmarks that assess generalization to real-world scenarios. In this work, we present a pipeline to test the resilience of state-of-the-art MGT detectors (e.g., Mage, Radar, LLM-DetectAIve) to linguistically informed adversarial attacks. To challenge the detectors, we fine-tune language models using Direct Preference Optimization (DPO) to shift the MGT style toward human-written text (HWT). This exploits the detectors' reliance on stylistic clues, making new generations more challenging to detect. Additionally, we analyze the linguistic shifts induced by the alignment and which features are used by detectors to detect MGT texts. Our results show that detectors can be easily fooled with relatively few examples, resulting in a significant drop in detection performance. This highlights the importance of improving detection methods and making them robust to unseen in-domain texts.
Time series forecasting (TSF) is a fundamental and widely studied task, spanning methods from classical statistical approaches to modern deep learning and multimodal language modeling. Despite their effectiveness, these methods often follow a fast thinking paradigm emphasizing pattern extraction and direct value mapping, while overlooking explicit reasoning over temporal dynamics and contextual dependencies. Meanwhile, emerging slow-thinking LLMs (e.g., ChatGPT-o1, DeepSeek-R1) have demonstrated impressive multi-step reasoning capabilities across diverse domains, suggesting a new opportunity for reframing TSF as a structured reasoning task. This motivates a key question: can slow-thinking LLMs effectively reason over temporal patterns to support time series forecasting, even in zero-shot manner? To investigate this, in this paper, we propose TimeReasoner, an extensive empirical study that formulates TSF as a conditional reasoning task. We design a series of prompting strategies to elicit inference-time reasoning from pretrained slow-thinking LLMs and evaluate their performance across diverse TSF benchmarks. Our findings reveal that slow-thinking LLMs exhibit non-trivial zero-shot forecasting capabilities, especially in capturing high-level trends and contextual shifts. While preliminary, our study surfaces important insights into the reasoning behaviors of LLMs in temporal domains highlighting both their potential and limitations. We hope this work catalyzes further research into reasoning-based forecasting paradigms and paves the way toward more interpretable and generalizable TSF frameworks.
Recently, Large Language Models (LLMs) have made significant progress in IQ-related domains that require careful thinking, such as mathematics and coding. However, enhancing LLMs' cognitive development in social domains, particularly from a post-training perspective, remains underexplored. Recognizing that the social world follows a distinct timeline and requires a richer blend of cognitive modes (from intuitive reactions (System 1) and surface-level thinking to deliberate thinking (System 2)) than mathematics, which primarily relies on System 2 cognition (careful, step-by-step reasoning), we introduce Temporal-aware Hierarchical Cognitive Reinforcement Learning (TimeHC-RL) for enhancing LLMs' social intelligence. In our experiments, we systematically explore improving LLMs' social intelligence and validate the effectiveness of the TimeHC-RL method, through five other post-training paradigms and two test-time intervention paradigms on eight datasets with diverse data patterns. Experimental results reveal the superiority of our proposed TimeHC-RL method compared to the widely adopted System 2 RL method. It gives the 7B backbone model wings, enabling it to rival the performance of advanced models like DeepSeek-R1 and OpenAI-O3. Additionally, the systematic exploration from post-training and test-time interventions perspectives to improve LLMs' social intelligence has uncovered several valuable insights.
In this paper, we investigate code-integrated reasoning, where models generate code when necessary and integrate feedback by executing it through a code interpreter. To acquire this capability, models must learn when and how to use external code tools effectively, which is supported by tool-augmented reinforcement learning (RL) through interactive learning. Despite its benefits, tool-augmented RL can still suffer from potential instability in the learning dynamics. In light of this challenge, we present a systematic approach to improving the training effectiveness and stability of tool-augmented RL for code-integrated reasoning. Specifically, we develop enhanced training strategies that balance exploration and stability, progressively building tool-use capabilities while improving reasoning performance. Through extensive experiments on five mainstream mathematical reasoning benchmarks, our model demonstrates significant performance improvements over multiple competitive baselines. Furthermore, we conduct an in-depth analysis of the mechanism and effect of code-integrated reasoning, revealing several key insights, such as the extension of model's capability boundaries and the simultaneous improvement of reasoning efficiency through code integration. All data and code for reproducing this work are available at: https://github.com/RUCAIBox/CIR.
Large language models (LLMs) have emerged as powerful tools but pose significant safety risks through harmful outputs and vulnerability to adversarial attacks. We propose SaP, short for Safety Polytope, a geometric approach to LLM safety that learns and enforces multiple safety constraints directly in the model's representation space. We develop a framework that identifies safe and unsafe regions via the polytope's facets, enabling both detection and correction of unsafe outputs through geometric steering. Unlike existing approaches that modify model weights, SaP operates post-hoc in the representation space, preserving model capabilities while enforcing safety constraints. Experiments across multiple LLMs demonstrate that our method can effectively detect unethical inputs, reduce adversarial attack success rates while maintaining performance on standard tasks, thus highlighting the importance of having an explicit geometric model for safety. Analysis of the learned polytope facets reveals emergence of specialization in detecting different semantic notions of safety, providing interpretable insights into how safety is captured in LLMs' representation space.
Despite recent advancements in offline multi-task reinforcement learning (MTRL) have harnessed the powerful capabilities of the Transformer architecture, most approaches focus on a limited number of tasks, with scaling to extremely massive tasks remaining a formidable challenge. In this paper, we first revisit the key impact of task numbers on current MTRL method, and further reveal that naively expanding the parameters proves insufficient to counteract the performance degradation as the number of tasks escalates. Building upon these insights, we propose M3DT, a novel mixture-of-experts (MoE) framework that tackles task scalability by further unlocking the model's parameter scalability. Specifically, we enhance both the architecture and the optimization of the agent, where we strengthen the Decision Transformer (DT) backbone with MoE to reduce task load on parameter subsets, and introduce a three-stage training mechanism to facilitate efficient training with optimal performance. Experimental results show that, by increasing the number of experts, M3DT not only consistently enhances its performance as model expansion on the fixed task numbers, but also exhibits remarkable task scalability, successfully extending to 160 tasks with superior performance.
Large language models (LLMs) have achieved remarkable performance, yet their capability on long-context reasoning is often constrained by the excessive memory required to store the Key-Value (KV) cache. This makes KV cache compression an essential step toward enabling efficient long-context reasoning. Recent methods have explored reducing the hidden dimensions of the KV cache, but many introduce additional computation through projection layers or suffer from significant performance degradation under high compression ratios. To address these challenges, we propose ReCalKV, a post-training KV cache compression method that reduces the hidden dimensions of the KV cache. We develop distinct compression strategies for Keys and Values based on their different roles and varying importance in the attention mechanism. For Keys, we propose Head-wise Similarity-aware Reordering (HSR), which clusters similar heads and applies grouped SVD to the key projection matrix, reducing additional computation while preserving accuracy. For Values, we propose Offline Calibration and Matrix Fusion (OCMF) to preserve accuracy without extra computational overhead. Experiments show that ReCalKV outperforms existing low-rank compression methods, achieving high compression ratios with minimal performance loss. The code and models will be available at: https://github.com/XIANGLONGYAN/ReCalKV.
Reinforcement learning (RL) has become a dominant paradigm for training large language models (LLMs), particularly for reasoning tasks. Effective RL for LLMs requires massive parallelization and poses an urgent need for efficient training systems. Most existing large-scale RL systems for LLMs are synchronous, alternating generation and training in a batch setting where rollouts in each training batch are generated by the same model. This approach stabilizes RL training but suffers from severe system-level inefficiency: generation must wait until the longest output in the batch is completed before model updates, resulting in GPU underutilization. We present AReaL, a fully asynchronous RL system that completely decouples generation from training. Rollout workers in AReaL continuously generate new outputs without waiting, while training workers update the model whenever a batch of data is collected. AReaL also incorporates a collection of system-level optimizations, leading to substantially higher GPU utilization. To stabilize RL training, AReaL balances the workload of rollout and training workers to control data staleness, and adopts a staleness-enhanced PPO variant to better handle outdated training samples. Extensive experiments on math and code reasoning benchmarks show that AReaL achieves up to 2.77$\times$ training speedup compared to synchronous systems with the same number of GPUs and matched or improved final performance. The code of AReaL is available at https://github.com/inclusionAI/AReaL/.
Neural Algorithmic Reasoning (NAR) trains neural networks to simulate classical algorithms, enabling structured and interpretable reasoning over complex data. While prior research has predominantly focused on learning exact algorithms for polynomial-time-solvable problems, extending NAR to harder problems remains an open challenge. In this work, we introduce a general NAR framework grounded in the primal-dual paradigm, a classical method for designing efficient approximation algorithms. By leveraging a bipartite representation between primal and dual variables, we establish an alignment between primal-dual algorithms and Graph Neural Networks. Furthermore, we incorporate optimal solutions from small instances to greatly enhance the model's reasoning capabilities. Our empirical results demonstrate that our model not only simulates but also outperforms approximation algorithms for multiple tasks, exhibiting robust generalization to larger and out-of-distribution graphs. Moreover, we highlight the framework's practical utility by integrating it with commercial solvers and applying it to real-world datasets.
Deep neural networks often develop spurious bias, reliance on correlations between non-essential features and classes for predictions. For example, a model may identify objects based on frequently co-occurring backgrounds rather than intrinsic features, resulting in degraded performance on data lacking these correlations. Existing mitigation approaches typically depend on external annotations of spurious correlations, which may be difficult to obtain and are not relevant to the spurious bias in a model. In this paper, we take a step towards self-guided mitigation of spurious bias by proposing NeuronTune, a post hoc method that directly intervenes in a model's internal decision process. Our method probes in a model's latent embedding space to identify and regulate neurons that lead to spurious prediction behaviors. We theoretically justify our approach and show that it brings the model closer to an unbiased one. Unlike previous methods, NeuronTune operates without requiring spurious correlation annotations, making it a practical and effective tool for improving model robustness. Experiments across different architectures and data modalities demonstrate that our method significantly mitigates spurious bias in a self-guided way.