arXiv subjects

Songming Zhang

Publications and source records attributed to Songming Zhang.

At least 19 recordsLinked to original sources

arXiv2026

Benchmarking virtual cell models for in-the-wild perturbation response

Virtual cell (VC) models aim to predict cellular responses to any perturbations in silico and have emerged as a promising approach for drug discovery and precision medicine. Yet, a clear gap still remains: while models routinely reported impressive results on standard benchmarks, it is unclear whether their predictions are truly meaningful in practice. This is mainly due to limitations in current evaluation setups, which are often overly simplified or inconsistent, and do not reflect the complexity and variability of real biological systems. Here, we introduce a standardized and modular benchmarking framework for virtual cell prediction. Our framework evaluates diverse models under in-the-wild challenging scenarios, including unseen cell contexts, unseen perturbations, and cross-dataset generalization, which better reflect practical applications. Our analysis shows that model performance is highly context-dependent and shaped by task design and evaluation criteria. In commonly used setups, performance is often overestimated, and naive dataset aggregation can even reduce performance. When evaluated under more strict conditions, model performance drops markedly, indicating limited robustness to shifts across cellular contexts. In unseen perturbation settings, models including simple linear approaches capture global transcriptional trends but fail to recover fine-grained perturbation-specific effects. In addition, different evaluation metrics focus on different biological properties, leading to substantially different model rankings. Together, our framework provides a more reliable and biologically grounded evaluation, offering clearer guidance for applying virtual cell models in real scenarios.

q-bio.CB↗

arXiv2026

SCALE:Scalable Conditional Atlas-Level Endpoint transport for virtual cell perturbation prediction

Virtual-cell models aim to predict how cell populations respond to perturbations, but control and treated cells are measured as unpaired populations, complicating the learning of perturbation-specific effects. We present SCALE, a conditional transport model that represents cells as unordered sets and predicts treated populations without cell-level matching. A shared set-aware encoder and conditional DiT backbone learn latent transport, making endpoint supervision directly delta-aligned without an auxiliary delta objective. Across genetic, chemical, developmental and immune perturbations, SCALE recovered gene-expression changes, response directions and population structure. In CRISPR data with dominant cell-line effects, SCALE outperformed competing methods across seven metrics and maintained separation among gene-target representations rather than collapsing them into a shared region. SCALE further prioritized cytokines predicted to produce distinct immune activation and inflammatory responses. Experiments using matched PBMC samples from three donors confirmed these predicted differences. Together, SCALE enables perturbation-specific prediction from unpaired populations and supports experimental prioritization.

cs.LG↗

arXiv2026

KDFlow: A User-Friendly and Efficient Knowledge Distillation Framework for Large Language Models

Knowledge distillation (KD) is widely used to compress and post-train large language models (LLMs), yet many existing frameworks execute teacher inference with the same training-oriented backend as student optimization, leading to suboptimal efficiency. In this paper, we propose KDFlow, a novel framework for LLM distillation that features a decoupled architecture and employs SGLang for teacher inference. KDFlow combines SGLang for teacher inference with PyTorch FSDP2 for student optimization, allowing each model to run on a backend tailored to its workload. To enable efficient full-vocabulary distillation in this decoupled architecture, KDFlow transfers the teacher's final hidden states via Ray's object store and recomputes teacher logits on each student worker using a frozen copy of the teacher's output head. Furthermore, our framework supports both off-policy and on-policy distillation and incorporates cross-tokenizer algorithms through highly extensible and user-friendly APIs. Experiments show that KDFlow achieves a 1.44$\times$ to 6.36$\times$ speedup over MS-SWIFT in off-policy distillation and a 1.43$\times$ to 1.75$\times$ speedup over verl in on-policy distillation. KDFlow further scales to 64 GPUs, achieving 3.68$\times$ and 2.52$\times$ strong-scaling speedups in two representative model configurations. The code and documentation are publicly available.

cs.CL↗

arXiv2025

M-STAR: Multi-Scale Spatiotemporal Autoregression for Human Mobility Modeling

Modeling human mobility is vital for extensive applications such as transportation planning and epidemic modeling. With the rise of the Artificial Intelligence Generated Content (AIGC) paradigm, recent works explore synthetic trajectory generation using autoregressive and diffusion models. While these methods show promise for generating single-day trajectories, they remain limited by inefficiencies in long-term generation (e.g., weekly trajectories) and a lack of explicit spatiotemporal multi-scale modeling. This study proposes Multi-Scale Spatio-Temporal AutoRegression (M-STAR), a new framework that generates long-term trajectories through a coarse-to-fine spatiotemporal prediction process. M-STAR combines a Multi-scale Spatiotemporal Tokenizer that encodes hierarchical mobility patterns with a Transformer-based decoder for next-scale autoregressive prediction. Experiments on two real-world datasets show that M-STAR outperforms existing methods in fidelity and significantly improves generation speed. The data and codes are available at https://github.com/YuxiaoLuo0013/M-STAR.

cs.AI↗

arXiv2025

Think Natively: Unlocking Multilingual Reasoning with Consistency-Enhanced Reinforcement Learning

Large Reasoning Models (LRMs) have achieved remarkable performance on complex reasoning tasks by adopting the ``think-then-answer'' paradigm, which enhances both accuracy and interpretability. However, current LRMs exhibit two critical limitations when processing non-English languages: (1) They often struggle to maintain input-output language consistency; (2) They generally perform poorly with wrong reasoning paths and lower answer accuracy compared to English. These limitations significantly compromise the interpretability of reasoning processes and degrade the user experience for non-English speakers, hindering the global deployment of LRMs. To address these limitations, we propose M-Thinker, which is trained by the GRPO algorithm that involves a Language Consistency (LC) reward and a novel Cross-lingual Thinking Alignment (CTA) reward. Specifically, the LC reward defines a strict constraint on the language consistency between the input, thought, and answer. Besides, the CTA reward compares the model's non-English reasoning paths with its English reasoning path to transfer its own reasoning capability from English to non-English languages. Through an iterative RL procedure, our M-Thinker-1.5B/4B/7B models not only achieve nearly 100% language consistency and superior performance on two multilingual benchmarks (MMATH and PolyMath), but also exhibit excellent generalization on out-of-domain languages.

cs.CL↗

arXiv2025

CM-Align: Consistency-based Multilingual Alignment for Large Language Models

Current large language models (LLMs) generally show a significant performance gap in alignment between English and other languages. To bridge this gap, existing research typically leverages the model's responses in English as a reference to select the best/worst responses in other languages, which are then used for Direct Preference Optimization (DPO) training. However, we argue that there are two limitations in the current methods that result in noisy multilingual preference data and further limited alignment performance: 1) Not all English responses are of high quality, and using a response with low quality may mislead the alignment for other languages. 2) Current methods usually use biased or heuristic approaches to construct multilingual preference pairs. To address these limitations, we design a consistency-based data selection method to construct high-quality multilingual preference data for improving multilingual alignment (CM-Align). Specifically, our method includes two parts: consistency-guided English reference selection and cross-lingual consistency-based multilingual preference data construction. Experimental results on three LLMs and three common tasks demonstrate the effectiveness and superiority of our method, which further indicates the necessity of constructing high-quality preference data.

cs.CL↗

arXiv2025

Less, but Better: Efficient Multilingual Expansion for LLMs via Layer-wise Mixture-of-Experts

Continually expanding new languages for existing large language models (LLMs) is a promising yet challenging approach to building powerful multilingual LLMs. The biggest challenge is to make the model continuously learn new languages while preserving the proficient ability of old languages. To achieve this, recent work utilizes the Mixture-of-Experts (MoE) architecture to expand new languages by adding new experts and avoid catastrophic forgetting of old languages by routing corresponding tokens to the original model backbone (old experts). Although intuitive, this kind of method is parameter-costly when expanding new languages and still inevitably impacts the performance of old languages. To address these limitations, we analyze the language characteristics of different layers in LLMs and propose a layer-wise expert allocation algorithm (LayerMoE) to determine the appropriate number of new experts for each layer. Specifically, we find different layers in LLMs exhibit different representation similarities between languages and then utilize the similarity as the indicator to allocate experts for each layer, i.e., the higher similarity, the fewer experts. Additionally, to further mitigate the forgetting of old languages, we add a classifier in front of the router network on the layers with higher similarity to guide the routing of old language tokens. Experimental results show that our method outperforms the previous state-of-the-art baseline with 60% fewer experts in the single-expansion setting and with 33.3% fewer experts in the lifelong-expansion setting, demonstrating the effectiveness of our method.

cs.CL↗

arXiv2025

A Dual-Space Framework for General Knowledge Distillation of Large Language Models

Knowledge distillation (KD) is a promising solution to compress large language models (LLMs) by transferring their knowledge to smaller models. During this process, white-box KD methods usually minimize the distance between the output distributions of the teacher model and the student model to transfer more information. However, we reveal that the current white-box KD framework exhibits two limitations: a) bridging probability distributions from different output spaces will limit the similarity between the teacher model and the student model; b) this framework cannot be applied to LLMs with different vocabularies. One of the root causes for these limitations is that the distributions from the teacher and the student for KD are output by different prediction heads, which yield distributions in different output spaces and dimensions. Therefore, in this paper, we propose a dual-space knowledge distillation (DSKD) framework that unifies the prediction heads of the teacher and the student models for KD. Specifically, we first introduce two projectors with ideal initialization to project the teacher/student hidden states into the student/teacher representation spaces. After this, the hidden states from different models can share the same head and unify the output spaces of the distributions. Furthermore, we develop an exact token alignment (ETA) algorithm to align the same tokens in two differently-tokenized sequences. Based on the above, our DSKD framework is a general KD framework that supports both off-policy and on-policy KD, and KD between any two LLMs regardless of their vocabularies. Extensive experiments on instruction-following, mathematical reasoning, and code generation benchmarks show that DSKD significantly outperforms existing methods based on the current white-box KD framework and surpasses other cross-tokenizer KD methods for LLMs with different vocabularies.

cs.CL↗

arXiv2025

AlignDistil: Token-Level Language Model Alignment as Adaptive Policy Distillation

In modern large language models (LLMs), LLM alignment is of crucial importance and is typically achieved through methods such as reinforcement learning from human feedback (RLHF) and direct preference optimization (DPO). However, in most existing methods for LLM alignment, all tokens in the response are optimized using a sparse, response-level reward or preference annotation. The ignorance of token-level rewards may erroneously punish high-quality tokens or encourage low-quality tokens, resulting in suboptimal performance and slow convergence speed. To address this issue, we propose AlignDistil, an RLHF-equivalent distillation method for token-level reward optimization. Specifically, we introduce the reward learned by DPO into the RLHF objective and theoretically prove the equivalence between this objective and a token-level distillation process, where the teacher distribution linearly combines the logits from the DPO model and a reference model. On this basis, we further bridge the accuracy gap between the reward from the DPO model and the pure reward model, by building a contrastive DPO reward with a normal and a reverse DPO model. Moreover, to avoid under- and over-optimization on different tokens, we design a token adaptive logit extrapolation mechanism to construct an appropriate teacher distribution for each token. Experimental results demonstrate the superiority of our AlignDistil over existing methods and showcase fast convergence due to its token-level distributional reward optimization.

cs.CL↗

arXiv2024

GATES: Graph Attention Network with Global Expression Fusion for Deciphering Spatial Transcriptome Architectures

Single-cell spatial transcriptomics (ST) offers a unique approach to measuring gene expression profiles and spatial cell locations simultaneously. However, most existing ST methods assume that cells in closer spatial proximity exhibit more similar gene expression patterns. Such assumption typically results in graph structures that prioritize local spatial information while overlooking global patterns, limiting the ability to fully capture the broader structural features of biological tissues. To overcome this limitation, we propose GATES (Graph Attention neTwork with global Expression fuSion), a novel model designed to capture structural details in spatial transcriptomics data. GATES first constructs an expression graph that integrates local and global information by leveraging both spatial proximity and gene expression similarity. The model then employs an autoencoder with adaptive attention to assign proper weights for neighboring nodes, enhancing its capability of feature extraction. By fusing features of both the spatial and expression graphs, GATES effectively balances spatial context with gene expression data. Experimental results across multiple datasets demonstrate that GATES significantly outperforms existing methods in identifying spatial domains, highlighting its potential for analyzing complex biological tissues. Our code can be accessed on GitHub at https://github.com/xiaoxiongtao/GATES.

q-bio.GN↗

arXiv2024

Dual-Space Knowledge Distillation for Large Language Models

Knowledge distillation (KD) is known as a promising solution to compress large language models (LLMs) via transferring their knowledge to smaller models. During this process, white-box KD methods usually minimize the distance between the output distributions of the two models so that more knowledge can be transferred. However, in the current white-box KD framework, the output distributions are from the respective output spaces of the two models, using their own prediction heads. We argue that the space discrepancy will lead to low similarity between the teacher model and the student model on both representation and distribution levels. Furthermore, this discrepancy also hinders the KD process between models with different vocabularies, which is common for current LLMs. To address these issues, we propose a dual-space knowledge distillation (DSKD) framework that unifies the output spaces of the two models for KD. On the basis of DSKD, we further develop a cross-model attention mechanism, which can automatically align the representations of the two models with different vocabularies. Thus, our framework is not only compatible with various distance functions for KD (e.g., KL divergence) like the current framework, but also supports KD between any two LLMs regardless of their vocabularies. Experiments on task-agnostic instruction-following benchmarks show that DSKD significantly outperforms the current white-box KD framework with various distance functions, and also surpasses existing KD methods for LLMs with different vocabularies.

cs.CL↗

arXiv2024

Multilingual Knowledge Editing with Language-Agnostic Factual Neurons

Multilingual knowledge editing (MKE) aims to simultaneously update factual knowledge across multiple languages within large language models (LLMs). Previous research indicates that the same knowledge across different languages within LLMs exhibits a degree of shareability. However, most existing MKE methods overlook the connections of the same knowledge between different languages, resulting in knowledge conflicts and limited edit performance. To address this issue, we first investigate how LLMs process multilingual factual knowledge and discover that the same factual knowledge in different languages generally activates a shared set of neurons, which we call language-agnostic factual neurons (LAFNs). These neurons represent the same factual knowledge shared across languages and imply the semantic connections among multilingual knowledge. Inspired by this finding, we propose a new MKE method by Locating and Updating Language-Agnostic Factual Neurons (LU-LAFNs) to edit multilingual knowledge simultaneously, which avoids knowledge conflicts and thus improves edit performance. Experimental results on Bi-ZsRE and MzsRE benchmarks demonstrate that our method achieves the best edit performance, indicating the effectiveness and importance of modeling the semantic connections among multilingual knowledge.

cs.CL↗

arXiv2023

Mixture Data for Training Cannot Ensure Out-of-distribution Generalization

Deep neural networks often face generalization problems to handle out-of-distribution (OOD) data, and there remains a notable theoretical gap between the contributing factors and their respective impacts. Literature evidence from in-distribution data has suggested that generalization error can shrink if the size of mixture data for training increases. However, when it comes to OOD samples, this conventional understanding does not hold anymore -- Increasing the size of training data does not always lead to a reduction in the test generalization error. In fact, diverse trends of the errors have been found across various shifting scenarios including those decreasing trends under a power-law pattern, initial declines followed by increases, or continuous stable patterns. Previous work has approached OOD data qualitatively, treating them merely as samples unseen during training, which are hard to explain the complicated non-monotonic trends. In this work, we quantitatively redefine OOD data as those situated outside the convex hull of mixed training data and establish novel generalization error bounds to comprehend the counterintuitive observations better. Our proof of the new risk bound agrees that the efficacy of well-trained models can be guaranteed for unseen data within the convex hull; More interestingly, but for OOD data beyond this coverage, the generalization cannot be ensured, which aligns with our observations. Furthermore, we attempted various OOD techniques to underscore that our results not only explain insightful observations in recent OOD generalization work, such as the significance of diverse data and the sensitivity to unseen shifts of existing algorithms, but it also inspires a novel and effective data selection strategy.

cs.LG↗

arXiv2023

ShiftKD: Benchmarking Knowledge Distillation under Distribution Shift

Knowledge Distillation (KD) transfers knowledge from large models to small models and has recently achieved remarkable success. However, the reliability of existing KD methods in real-world applications, especially under distribution shift, remains underexplored. Distribution shift refers to the data distribution drifts between the training and testing phases, and this can adversely affect the efficacy of KD. In this paper, we propose a unified and systematic framework \textsc{ShiftKD} to benchmark KD against two general distributional shifts: diversity and correlation shift. The evaluation benchmark covers more than 30 methods from algorithmic, data-driven, and optimization perspectives for five benchmark datasets. Our development of \textsc{ShiftKD} conducts extensive experiments and reveals strengths and limitations of current SOTA KD methods. More importantly, we thoroughly analyze key factors in student model training process, including data augmentation, pruning methods, optimizers, and evaluation metrics. We believe \textsc{ShiftKD} could serve as an effective benchmark for assessing KD in real-world scenarios, thus driving the development of more robust KD methods in response to evolving demands. The code will be made available upon publication.

cs.LG↗

arXiv2023

A Quality-based Syntactic Template Retriever for Syntactically-controlled Paraphrase Generation

Existing syntactically-controlled paraphrase generation (SPG) models perform promisingly with human-annotated or well-chosen syntactic templates. However, the difficulty of obtaining such templates actually hinders the practical application of SPG models. For one thing, the prohibitive cost makes it unfeasible to manually design decent templates for every source sentence. For another, the templates automatically retrieved by current heuristic methods are usually unreliable for SPG models to generate qualified paraphrases. To escape this dilemma, we propose a novel Quality-based Syntactic Template Retriever (QSTR) to retrieve templates based on the quality of the to-be-generated paraphrases. Furthermore, for situations requiring multiple paraphrases for each source sentence, we design a Diverse Templates Search (DTS) algorithm, which can enhance the diversity between paraphrases without sacrificing quality. Experiments demonstrate that QSTR can significantly surpass existing retrieval methods in generating high-quality paraphrases and even perform comparably with human-annotated templates in terms of reference-free metrics. Additionally, human evaluation and the performance on downstream tasks using our generated paraphrases for data augmentation showcase the potential of our QSTR and DTS algorithm in practical scenarios.

cs.CL↗

arXiv2023

Towards Understanding and Improving Knowledge Distillation for Neural Machine Translation

Knowledge distillation (KD) is a promising technique for model compression in neural machine translation. However, where the knowledge hides in KD is still not clear, which may hinder the development of KD. In this work, we first unravel this mystery from an empirical perspective and show that the knowledge comes from the top-1 predictions of teachers, which also helps us build a potential connection between word- and sequence-level KD. Further, we point out two inherent issues in vanilla word-level KD based on this finding. Firstly, the current objective of KD spreads its focus to whole distributions to learn the knowledge, yet lacks special treatment on the most crucial top-1 information. Secondly, the knowledge is largely covered by the golden information due to the fact that most top-1 predictions of teachers overlap with ground-truth tokens, which further restricts the potential of KD. To address these issues, we propose a novel method named \textbf{T}op-1 \textbf{I}nformation \textbf{E}nhanced \textbf{K}nowledge \textbf{D}istillation (TIE-KD). Specifically, we design a hierarchical ranking loss to enforce the learning of the top-1 information from the teacher. Additionally, we develop an iterative KD procedure to infuse more additional knowledge by distilling on the data without ground-truth targets. Experiments on WMT'14 English-German, WMT'14 English-French and WMT'16 English-Romanian demonstrate that our method can respectively boost Transformer$_{base}$ students by +1.04, +0.60 and +1.11 BLEU scores and significantly outperform the vanilla word-level KD baseline. Besides, our method shows higher generalizability on different teacher-student capacity gaps than existing KD techniques.

cs.CL↗

arXiv2022

Improved Data Augmentation for Translation Suggestion

Translation suggestion (TS) models are used to automatically provide alternative suggestions for incorrect spans in sentences generated by machine translation. This paper introduces the system used in our submission to the WMT'22 Translation Suggestion shared task. Our system is based on the ensemble of different translation architectures, including Transformer, SA-Transformer, and DynamicConv. We use three strategies to construct synthetic data from parallel corpora to compensate for the lack of supervised data. In addition, we introduce a multi-phase pre-training strategy, adding an additional pre-training phase with in-domain data. We rank second and third on the English-German and English-Chinese bidirectional tasks, respectively.

cs.CL↗

arXiv2022

Conditional Bilingual Mutual Information Based Adaptive Training for Neural Machine Translation

Token-level adaptive training approaches can alleviate the token imbalance problem and thus improve neural machine translation, through re-weighting the losses of different target tokens based on specific statistical metrics (e.g., token frequency or mutual information). Given that standard translation models make predictions on the condition of previous target contexts, we argue that the above statistical metrics ignore target context information and may assign inappropriate weights to target tokens. While one possible solution is to directly take target contexts into these statistical metrics, the target-context-aware statistical computing is extremely expensive, and the corresponding storage overhead is unrealistic. To solve the above issues, we propose a target-context-aware metric, named conditional bilingual mutual information (CBMI), which makes it feasible to supplement target context information for statistical metrics. Particularly, our CBMI can be formalized as the log quotient of the translation model probability and language model probability by decomposing the conditional joint distribution. Thus CBMI can be efficiently calculated during model training without any pre-specific statistical calculations and large storage overhead. Furthermore, we propose an effective adaptive training approach based on both the token- and sentence-level CBMI. Experimental results on WMT14 English-German and WMT19 Chinese-English tasks show our approach can significantly outperform the Transformer baseline and other related methods.

cs.CL↗