Junhao Liu

Jiayi Luo, Qiyan Liu, Tengyang Wang et al.

Autoregressive (AR) video generation has emerged as a promising paradigm for long-horizon video synthesis, where each frame is generated conditioned on previously generated tokens. To accelerate inference, the KV cache is used to avoid redundant recomputation across generation steps. Nevertheless, its growth with generation length introduces increasing memory and error accumulation, limiting the scalability of AR models to even longer sequences. Existing KV cache compression methods mitigate this issue by selectively retaining only video tokens deemed important. However, most existing methods assess token importance using short-horizon signals derived from the current or historical generation context, making these methods prone to overlooking tokens that appear unimportant at early steps but later become critical for future frames. In this work, we identify an important property of trained AR video models: although RoPE-modulated queries evolve across autoregressive steps, the underlying canonical pre-RoPE query distribution remains remarkably stable throughout the video generation process. This approximate stationarity implies that future query distributions are estimable from historical statistics, enabling principled future-aware cache decisions without any additional training. Building on this insight, we propose Future Forcing, a training-free future-aware KV cache policy for AR video generation. Specifically, Future Forcing first constructs a future query proxy from historical statistics, then scores KV cache tokens by their importance under this proxy, and finally merges redundant token pairs within the affine subspace induced by the future query. Extensive experiments show that Future Forcing improves long-horizon consistency under limited KV caches, achieving up to 1.49 improvement in subject consistency on VBench-Long for 60s generation over existing AR video KV cache policies.

Lei Zhang, Yunshui Li, Ziqiang Liu et al.

With the advancement of large language models (LLMs) and the expansion of their context windows, existing long-context benchmarks fall short in effectively evaluating the models' comprehension and reasoning abilities in extended texts. Moreover, conventional benchmarks relying on F1 metrics often inaccurately score responses: they may undervalue correct answers that differ from the reference responses and overvalue incorrect ones that resemble the reference texts. In response to these limitations, we introduce Marathon, a novel evaluation benchmark that adopts a multiple-choice question format. It is specifically designed to overcome the constraints of previous benchmarks and provide a rapid, precise, and unbiased appraisal of the long-context comprehension skills of large language models. We conducted comprehensive evaluations on the Marathon benchmark with a range of state-of-the-art LLMs and assessed the effectiveness of various optimization strategies tailored for long-context generation. We anticipate that the Marathon benchmark and its associated leaderboard will enable a more precise and equitable evaluation of LLMs' capabilities in understanding and reasoning over extended contexts. Marathon is available at https://github.com/Hambaobao/Marathon.

Tianchi Li, Zhenyu Yan, Junhao Liu et al.

We propose a novel framework that provides constructive feedback to an LLM in the "guess-and-check" paradigm by formally verifying its own thinking process and detecting local reasoning errors. We apply this framework to the loop invariant synthesis problem. We prompt the model to produce a step-by-step natural language proof justifying its thinking process for the failed verification condition of its generated loop invariants. Then, we use an LLM to translate the reasoning steps into first-order logic implications, which can be checked automatically. An invalid implication pinpoints the exact logical flaw in the LLM's thinking process, which we then use to construct targeted feedback for refinement. We have implemented our approach in a tool called LORIS and evaluated it on a main benchmark suite of 460 C programs and an additional benchmark suite of 50 C programs each of which involves non-linear properties. On the main benchmark suite, LORIS solved 445 of the programs, and achieved an overall success rate of $93.1\%$. LORIS also demonstrates robustness on the challenging non-linear benchmark suite.

Jiahao Zhao, Feng Jiang, Shaowei Qin et al.

Large language models (LLMs) are increasingly applied in scientific research, offering new capabilities for knowledge discovery and reasoning. In single-cell biology, however, evaluation practices for both general and specialized LLMs remain inadequate: existing benchmarks are fragmented across tasks, adopt formats such as multiple-choice classification that diverge from real-world usage, and rely on metrics lacking interpretability and biological grounding. We present SC-ARENA, a natural language evaluation framework tailored to single-cell foundation models. SC-ARENA formalizes a virtual cell abstraction that unifies evaluation targets by representing both intrinsic attributes and gene-level interactions. Within this paradigm, we define five natural language tasks (cell type annotation, captioning, generation, perturbation prediction, and scientific QA) that probe core reasoning capabilities in cellular biology. To overcome the limitations of brittle string-matching metrics, we introduce knowledge-augmented evaluation, which incorporates external ontologies, marker databases, and scientific literature to support biologically faithful and interpretable judgments. Experiments and analysis across both general-purpose and domain-specialized LLMs demonstrate that (i) under the Virtual Cell unified evaluation paradigm, current models achieve uneven performance on biologically complex tasks, particularly those demanding mechanistic or causal understanding; and (ii) our knowledge-augmented evaluation framework ensures biological correctness, provides interpretable, evidence-grounded rationales, and achieves high discriminative capacity, overcoming the brittleness and opacity of conventional metrics. SC-Arena thus provides a unified and interpretable framework for assessing LLMs in single-cell biology, pointing toward the development of biology-aligned, generalizable foundation models.

Junhao Liu, Zhenhao Xu, Yuxin Fang et al.

Recently, there have been notable advancements in large language models (LLMs), demonstrating their growing abilities in complex reasoning. However, existing research largely overlooks a thorough and systematic comparison of these models' reasoning processes and outputs, particularly regarding their self-reflection pattern (also termed "Aha moment") and the interconnections across diverse domains. This paper proposes a novel framework for analyzing the reasoning characteristics of four cutting-edge large reasoning models (GPT-o1, DeepSeek-R1, Kimi-k1.5, and Grok-3) using keywords statistic and LLM-as-a-judge paradigm. Our approach connects their internal thinking processes with their final outputs. A diverse dataset consists of real-world scenario-based questions covering logical deduction, causal inference, and multi-step problem-solving. Additionally, a set of metrics is put forward to assess both the coherence of reasoning and the accuracy of the outputs. The research results uncover various patterns of how these models balance exploration and exploitation, deal with problems, and reach conclusions during the reasoning process. Through quantitative and qualitative comparisons, disparities among these models are identified in aspects such as the depth of reasoning, the reliance on intermediate steps, and the degree of similarity between their thinking processes and output patterns and those of GPT-o1. This work offers valuable insights into the trade-off between computational efficiency and reasoning robustness and provides practical recommendations for enhancing model design and evaluation in practical applications. We publicly release our project at: https://github.com/ChangWenhan/FromThinking2Output

Junhao Liu, Xin Zhang

Existing local model-agnostic explanation techniques are ineffective for machine learning models that consider inputs of variable lengths, as they do not consider temporal information embedded in these models. To address this limitation, we propose \textsc{ReX}, a general framework for incorporating temporal information in these techniques. Our key insight is that these techniques typically learn a model surrogate by sampling model inputs and outputs, and we can incorporate temporal information in a uniform way by only changing the sampling process and the surrogate features. We instantiate our approach on three popular explanation techniques: Anchors, LIME, and Kernel SHAP. To evaluate the effectiveness of \textsc{ReX}, we apply our approach to six models in three different tasks. Our evaluation results demonstrate that our approach 1) significantly improves the fidelity of explanations, making model-agnostic techniques outperform a state-of-the-art model-specific technique on its target model, and 2) helps end users better understand the models' behaviors.

Zhenhao Xu, Wenhan Chang, Yichuan Chen et al.

Large Reasoning Models (LRMs) improve performance on complex tasks, but they also make safety control harder at deployment time. In black-box settings, defenders cannot modify model weights and must instead intervene at inference time. This setting creates three practical challenges: harmful intent may be hidden by educational or role-play framing, deep safety analysis can introduce non-trivial latency, and long adversarial contexts can dilute the local cues that simpler filters rely on. These challenges can expose an apparent thinking--output gap, where the model appears cautious during reasoning but still produces an unsafe final answer. To address this problem, we propose Safety Context Injection (SCI), an inference-time framework that separates safety assessment from task generation and prepends a structured external risk report as injected safety context for the protected model. The framework is instantiated in two complementary variants: Static Model Filtering (SMF), a lightweight one-pass guard for fast deployment, and Dynamic Agents Filtering (DAF), an agentic-loop-based analyzer that iteratively gathers and synthesizes evidence for ambiguous or long-context attacks. Across AdvBench and GPTFuzz, spanning base and reasoning models under five jailbreak families, both variants reduce attack success rate and toxicity in the evaluated settings. SMF offers an efficient low-latency option, while DAF is more effective when harmful intent is semantically disguised or dispersed across long contexts.

Lei Zhang, Yunshui Li, Jiaming Li et al.

Some recently developed code large language models (Code LLMs) have been pre-trained on repository-level code data (Repo-Code LLMs), enabling these models to recognize repository structures and utilize cross-file information for code completion. However, in real-world development scenarios, simply concatenating the entire code repository often exceeds the context window limits of these Repo-Code LLMs, leading to significant performance degradation. In this study, we conducted extensive preliminary experiments and analyses on six Repo-Code LLMs. The results indicate that maintaining the topological dependencies of files and increasing the code file content in the completion prompts can improve completion accuracy; pruning the specific implementations of functions in all dependent files does not significantly reduce the accuracy of completions. Based on these findings, we proposed a strategy named Hierarchical Context Pruning (HCP) to construct completion prompts with high informational code content. The HCP models the code repository at the function level, maintaining the topological dependencies between code files while removing a large amount of irrelevant code content, significantly reduces the input length for repository-level code completion. We applied the HCP strategy in experiments with six Repo-Code LLMs, and the results demonstrate that our proposed method can significantly enhance completion accuracy while substantially reducing the length of input. Our code and data are available at https://github.com/Hambaobao/HCP-Coder.

Jian Wang, Junhao Liu, Wei Bi et al.

Neural network models usually suffer from the challenge of incorporating commonsense knowledge into the open-domain dialogue systems. In this paper, we propose a novel knowledge-aware dialogue generation model (called TransDG), which transfers question representation and knowledge matching abilities from knowledge base question answering (KBQA) task to facilitate the utterance understanding and factual knowledge selection for dialogue generation. In addition, we propose a response guiding attention and a multi-step decoding strategy to steer our model to focus on relevant features for response generation. Experiments on two benchmark datasets demonstrate that our model has robust superiority over compared methods in generating informative and fluent dialogues. Our code is available at https://github.com/siat-nlp/TransDG.

Yunshui Li, Binyuan Hui, Xiaobo Xia et al. · tsinghua

Contemporary practices in instruction tuning often hinge on enlarging data scaling without a clear strategy for ensuring data quality, inadvertently introducing noise that may compromise model performance. To address this challenge, we introduce \textsc{Nuggets}, a novel and efficient methodology that leverages one-shot learning to discern and select high-quality instruction data from extensive datasets. \textsc{Nuggets} assesses the potential of individual instruction examples to act as effective one-shot learning instances, thereby identifying those that can significantly improve performance across diverse tasks. \textsc{Nuggets} utilizes a scoring system based on the impact of candidate examples on the perplexity of a diverse anchor set, facilitating the selection of the most advantageous data for instruction tuning. Through comprehensive evaluations on two benchmarks, including MT-Bench and Alpaca-Eval, we show that instruction tuning with the top 1\% of examples curated by \textsc{Nuggets} substantially outperforms conventional methods employing the entire dataset.

Guangyi Zhang, Yi Dai, Yiyun He et al.

Single-cell ATAC-seq (scATAC-seq) enables high-resolution mapping of chromatin accessibility, yet privacy regulations and data size constraints hinder multi-institutional sharing. Federated learning (FL) offers a privacy-preserving alternative, but faces three fundamental barriers in scATAC-seq analysis: ultra-high dimensionality, extreme sparsity, and severe cross-institutional heterogeneity. We propose FL-Sailer, the first FL framework designed for scATAC-seq data. FL-Sailer integrates two key innovations: (i) adaptive leverage score sampling, which selects biologically interpretable features while reducing dimensionality by 80%, and (ii) an invariant VAE architecture, which disentangles biological signals from technical confounders via mutual information minimization. We provide a convergence guarantee, showing that FL-Sailer converges to an approximate solution of the original high-dimensional problem with bounded error. Extensive experiments on synthetic and real epigenomic datasets demonstrate that FL-Sailer not only enables previously infeasible multi-institutional collaborations but also surpasses centralized methods by leveraging adaptive sampling as an implicit regularizer to suppress technical noise. Our work establishes that federated learning, when tailored to domain-specific challenges, can become a superior paradigm for collaborative epigenomic research.

Haonan Yu, Junhao Liu, Zhenyu Yan et al.

Precise behavioral control of large language models (LLMs) is critical for complex applications. However, existing methods often incur high training costs, lack natural language controllability, or compromise semantic coherence. To bridge this gap, we propose WASD (unWeaving Actionable Sufficient Directives), a novel framework that explains model behavior by identifying sufficient neural conditions for token generation. Our method represents candidate conditions as neuron-activation predicates and iteratively searches for a minimal set that guarantees the current output under input perturbations. Experiments on SST-2 and CounterFact with the Gemma-2-2B model demonstrate that our approach produces explanations that are more stable, accurate, and concise than conventional attribution graphs. Moreover, through a case study on controlling cross-lingual output generation, we validated the practical effectiveness of WASD in controlling model behavior.

Junhao Liu, Haonan Yu, Zhenyu Yan et al.

As Large Language Models (LLMs) scale to handle massive context windows, achieving surgical feature-level interpretation is essential for high-stakes tasks like legal auditing and code debugging. However, existing local model-agnostic explanation methods face a critical dilemma in these scenarios: feature-based methods suffer from attribution dilution due to high feature dimensionality, thus failing to provide faithful explanations. In this paper, we propose Focus-LIME, a coarse-to-fine framework designed to restore the tractability of surgical interpretation. Focus-LIME utilizes a proxy model to curate the perturbation neighborhood, allowing the target model to perform fine-grained attribution exclusively within the optimized context. Empirical evaluations on long-context benchmarks demonstrate that our method makes surgical explanations practicable and provides faithful explanations to users.

Junhao Liu, Siwei Xu, Lei Zhang et al.

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues and uncover underlying disease mechanisms. Among all the analytical steps, assigning individual cells to specific types is fundamental for understanding cellular heterogeneity. However, this process is usually labor-intensive and requires extensive expert knowledge. Recent advances in large language models (LLMs) have demonstrated their ability to efficiently process and synthesize vast corpora of text to automatically extract essential biological knowledge, such as marker genes, potentially promoting more efficient and automated cell type annotations. To thoroughly evaluate the capability of modern instruction-tuned LLMs in automating the cell type identification process, we introduce SOAR, a comprehensive benchmarking study of LLMs for cell type annotation tasks in single-cell genomics. Specifically, we assess the performance of 8 instruction-tuned LLMs across 11 datasets, spanning multiple cell types and species. Our study explores the potential of LLMs to accurately classify and annotate cell types in single-cell RNA sequencing (scRNA-seq) data, while extending their application to multiomics data through cross-modality translation. Additionally, we evaluate the effectiveness of chain-of-thought (CoT) prompting techniques in generating detailed biological insights during the annotation process. The results demonstrate that LLMs can provide robust interpretations of single-cell data without requiring additional fine-tuning, advancing the automation of cell type annotation in genomics research.

Junhao Liu, Haonan Yu, Xin Zhang

With Large language models (LLMs) becoming increasingly prevalent in various applications, the need for interpreting their predictions has become a critical challenge. As LLMs vary in architecture and some are closed-sourced, model-agnostic techniques show great promise without requiring access to the model's internal parameters. However, existing model-agnostic techniques need to invoke LLMs many times to gain sufficient samples for generating faithful explanations, which leads to high economic costs. In this paper, we show that it is practical to generate faithful explanations for large-scale LLMs by sampling from some budget-friendly models through a series of empirical studies. Moreover, we show that such proxy explanations also perform well on downstream tasks. Our analysis provides a new paradigm of model-agnostic explanation methods for LLMs, by including information from budget-friendly models.

Haonan Yu, Junhao Liu, Xin Zhang

Anchors is a popular local model-agnostic explanation technique whose applicability is limited by its computational inefficiency. To address this limitation, we propose a pre-training-based approach to accelerate Anchors without compromising the explanation quality. Our approach leverages the iterative nature of Anchors' algorithm which gradually refines an explanation until it is precise enough for a given input by providing a general explanation that is obtained through pre-training as Anchors' initial explanation. Specifically, we develop a two-step rule transformation process: the horizontal transformation adapts a pre-trained explanation to the current input by replacing features, and the vertical transformation refines the general explanation until it is precise enough for the input. We evaluate our method across tabular, text, and image datasets, demonstrating that it significantly reduces explanation generation time while maintaining fidelity and interpretability, thereby enabling the practical adoption of Anchors in time-sensitive applications.

Junhao Liu, Haonan Yu, Xin Zhang

With the rapid advancements of various machine learning models, there is a significant demand for model-agnostic explanation techniques, which can explain these models across different architectures. Mainstream model-agnostic explanation techniques generate local explanations based on basic features (e.g., words for text models and (super-)pixels for image models). However, these explanations often do not align with the decision-making processes of the target models and end-users, resulting in explanations that are unfaithful and difficult for users to understand. On the other hand, concept-based techniques provide explanations based on high-level features (e.g., topics for text models and objects for image models), but most are model-specific or require additional pre-defined external concept knowledge. To address this limitation, we propose \toolname, a general framework to provide concept-based local explanations for any machine learning models. Our key insight is that we can automatically extract high-level concepts from large pre-trained models, and uniformly extend existing local model-agnostic techniques to provide unified concept-based explanations. We have instantiated \toolname on four different types of explanation techniques: LIME, Kernel SHAP, Anchor, and LORE, and applied these techniques to text and image models. Our evaluation results demonstrate that 1) compared to the vanilla versions, \toolname offers more faithful explanations and makes them more understandable to users, and 2) by offering multiple forms of explanations, \toolname outperforms state-of-the-art concept-based explanation techniques specifically designed for text and image models, respectively.

Yunshui Li, Junhao Liu, Chengming Li et al.

In this paper, we propose a selfdistillation framework with meta learning(MetaSD) for knowledge graph completion with dynamic pruning, which aims to learn compressed graph embeddings and tackle the longtail samples. Specifically, we first propose a dynamic pruning technique to obtain a small pruned model from a large source model, where the pruning mask of the pruned model could be updated adaptively per epoch after the model weights are updated. The pruned model is supposed to be more sensitive to difficult to memorize samples(e.g., longtail samples) than the source model. Then, we propose a onestep meta selfdistillation method for distilling comprehensive knowledge from the source model to the pruned model, where the two models coevolve in a dynamic manner during training. In particular, we exploit the performance of the pruned model, which is trained alongside the source model in one iteration, to improve the source models knowledge transfer ability for the next iteration via meta learning. Extensive experiments show that MetaSD achieves competitive performance compared to strong baselines, while being 10x smaller than baselines.

Lingdong Kong, Prakhar Ganesh, Tan Wang et al.

We unveil a long-standing problem in the prevailing co-saliency detection systems: there is indeed inconsistency between training and testing. Constructing a high-quality co-saliency detection dataset involves time-consuming and labor-intensive pixel-level labeling, which has forced most recent works to rely instead on semantic segmentation or saliency detection datasets for training. However, the lack of proper co-saliency and the absence of multiple foreground objects in these datasets can lead to spurious variations and inherent biases learned by models. To tackle this, we introduce the idea of counterfactual training through context adjustment and propose a "cost-free" group-cut-paste (GCP) procedure to leverage off-the-shelf images and synthesize new samples. Following GCP, we collect a novel dataset called Context Adjustment Training (CAT). CAT consists of 33,500 images, which is four times larger than the current co-saliency detection datasets. All samples are automatically annotated with high-quality mask annotations, object categories, and edge maps. Extensive experiments on recent benchmarks are conducted, show that CAT can improve various state-of-the-art models by a large margin (5% ~ 25%). We hope that the scale, diversity, and quality of our dataset can benefit researchers in this area and beyond. Our dataset will be publicly accessible through our project page.

Junhao Liu, Linjun Shou, Jian Pei et al.

Cross-lingual Machine Reading Comprehension (CLMRC) remains a challenging problem due to the lack of large-scale annotated datasets in low-source languages, such as Arabic, Hindi, and Vietnamese. Many previous approaches use translation data by translating from a rich-source language, such as English, to low-source languages as auxiliary supervision. However, how to effectively leverage translation data and reduce the impact of noise introduced by translation remains onerous. In this paper, we tackle this challenge and enhance the cross-lingual transferring performance by a novel augmentation approach named Language Branch Machine Reading Comprehension (LBMRC). A language branch is a group of passages in one single language paired with questions in all target languages. We train multiple machine reading comprehension (MRC) models proficient in individual language based on LBMRC. Then, we devise a multilingual distillation approach to amalgamate knowledge from multiple language branch models to a single model for all target languages. Combining the LBMRC and multilingual distillation can be more robust to the data noises, therefore, improving the model's cross-lingual ability. Meanwhile, the produced single multilingual model is applicable to all target languages, which saves the cost of training, inference, and maintenance for multiple models. Extensive experiments on two CLMRC benchmarks clearly show the effectiveness of our proposed method.