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Javen Qinfeng Shi

Publications and source records attributed to Javen Qinfeng Shi.

At least 19 recordsLinked to original sources
arXiv2026

An Identifiability Theory of Masked Prediction: Mode Blindness and Mask Schedules

Masked prediction learns to infer missing variables from visible context selected by a mask schedule. When does small excess risk guarantee recovery of the true joint distribution? We study this question on finite product spaces under masked-block log loss, with conditionals induced by a single joint distribution. To quantify recovery, we introduce an $\varepsilon$-identifiability modulus measuring the worst-case error among joint distributions with population excess risk at most $\varepsilon$. For data with separated modes pinned down by sufficiently large visible contexts, schedules that always retain such contexts can permit nonvanishing mode-weight errors while incurring exponentially small excess risk. An information decomposition explains why: the loss captures mode-weight mismatch only where the visible context leaves the mode uncertain. We prove two-sided bounds showing that, over a fixed range of mode weights, sensitivity to mode reweighting is governed by residual mode uncertainty averaged over the mask schedule. Assigning schedule mass to low-visibility masks that retain this uncertainty yields recovery bounds within the reweighting family. Beyond this family, positive full-mask probability characterizes uniform control of joint KL divergence by excess risk. Exact calculations and controlled gradient optimization validate these predictions.

cs.LG↗
arXiv2026

End-to-End Self-Supervised RGB-T Tracking without Modality Misleading

RGB-T object tracking leverages the complementary characteristics of visible and thermal infrared modalities to improve robustness under adverse conditions. Existing supervised methods typically rely on costly modality-aligned bounding box annotations, while most self-supervised approaches follow a two-stage pseudo-labeling paradigm, making tracker training sensitive to pseudo-label quality and preventing joint end-to-end optimization. In this paper, we propose ESMTrack, a fully end-to-end self-supervised RGB-T tracking framework without offline pseudo-label generation or dense frame-level bounding box annotations. Given only the standard initial-frame annotation used in visual tracking, ESMTrack learns discriminative and temporally consistent representations through two complementary objectives: a grounding triplet loss on annotated initial frames and a cross-frame temporal triplet loss on unlabeled search frames, with reliable samples selected by forward-backward consistency. To address modality dominance bias, ESMTrack employs a three-branch architecture consisting of a fusion branch and two unimodal branches for RGB and thermal inputs. We quantify modality contributions using the Average Peak-to-Correlation Energy by measuring response discrepancies between the fusion and unimodal branches. The resulting reliability estimates guide a training-time modality decoupling mechanism that suppresses dominant-modality shortcuts and adaptively weights cross-modal contrastive learning for task-level alignment. Extensive experiments on five RGB-T tracking benchmarks show that ESMTrack achieves competitive state-of-the-art performance, strong cross-dataset generalization, and real-time inference speed. The source code is available at https://github.com/LiShenglana/ESMTrack.

cs.CV↗
arXiv2026

Do-JEPA: From Masking to Intervention in Latent World Models

Latent world models are trained to predict what happens next, so nothing in their objective separates what an action caused from what merely co-occurred with it. Object-masking models such as C-JEPA intervene on what the predictor can see; we intervene on what physically happens. From one saved simulator state we run the dynamics under an action $a$ and under a reference action $a_{\varnothing}$, and train the model to predict the difference $Δz=z^{a}-z^{a_{\varnothing}}$ between the two latent futures. The resulting objective, Do-JEPA, has an effect loss, a support loss (where the action enters), a propagation loss (where its effect travels) and invariance losses (what must not change). In a synthetic system with object-aligned variables, support supervision finds the directly intervened object in 99.95% of test cases, where a sparse action mask sends the action to a nuisance slot in every case, and response-onset supervision recovers the ring-shaped propagation graph (edge AUROC 0.975 vs. 0.624). From pixels, the effect loss beats a control trained on exactly the same data: it lowers latent effect error by 28.4% on an end-to-end LeWM model and physical effect error by 13.5% when trained and tested on natural action sequences, and on three independently generated CausalWorld benchmarks it lowers responsive effect error by about 20% under physics shifts and the latent context sensitivity of predicted effects by 66%. Trained from scratch it costs factual accuracy; fine-tuning an existing model with it removes this cost. Together, these results show that intervening on the world, rather than on what the model sees, helps latent world models predict what their actions cause.

cs.CV↗
arXiv2026

I Act Therefore I Am: When Is JEPA's Action-Conditioning Enough to Learn Causal Mechanisms?

Recent empirical and theoretical advances suggest that joint-embedding predictive architectures (JEPAs) may learn meaningful representations for action-conditioned prediction of future outcomes, thus becoming one of the foundational structures for world models. However, accurate prediction does not, in general, necessarily imply recovery of underlying causal states that give rise to the observed dynamics. This work investigates when and how JEPAs can recover the underlying causal states from observations. We first introduce a latent variable model, in which high-dimensional observations are generated from latent causal states whose dynamics are governed by action-conditioned transition mechanisms. Based on this formulation, we develop a general information-theoretic objective that combines conditional likelihood maximization for learning transition dynamics with entropy maximization for preserving latent state information. We then establish identifiability conditions under which representations learned by this general objective recover the underlying latent causal states up to component-wise invertible transformations and permutation. One key condition for such identifiability is sufficient action-induced variation in the transition mechanisms. Guided by this finding, we instantiate the general objective with an action-modulated Gaussian additive-noise model, yielding action-modulated JEPA (A-JEPA). Experiments on synthetic environments verify the theoretical findings under the identifiability conditions and robustness to moderate violations, while visual benchmarks demonstrate improved state recovery and transfer to unseen transition mechanisms.

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arXiv2026

The Geometric Mechanics of Contrastive Representation Learning: Alignment Potentials, Entropic Dispersion, and Cross-modal Divergence

While InfoNCE underlies modern contrastive learning, its geometric mechanisms remain under-characterized beyond the canonical alignment--uniformity decomposition. We develop a measure-theoretic framework in which representation measures evolve on a fixed embedding manifold. In the large-batch limit, we prove value and gradient consistency, linking the stochastic objective to explicit deterministic energy landscapes and revealing a geometric bifurcation between unimodal and symmetric multimodal regimes. In the unimodal case, the intrinsic energy is strictly convex and admits a unique Gibbs equilibrium, showing that entropy acts as a tie-breaker within the aligned basin. In the multimodal case, the intrinsic geometry becomes cross-coupled and contains a persistent negative symmetric divergence term: each modality's marginal reshapes the effective landscape of the other, allowing strong pairwise alignment to coexist with a persistent modality gap. Controlled synthetic experiments and analyses of pretrained CLIP representations support these predictions. Overall, our results shift the analytical lens from pointwise discrimination to population geometry, showing that pairwise alignment alone is insufficient to control cross-modal marginal structure.

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arXiv2026

CLAP: Isolating Content from Style through Contrastive Learning with Augmented Prompts

Contrastive vision-language models, such as CLIP, have garnered considerable attention for various downstream tasks, mainly due to the remarkable ability of the learned features for generalization. However, the features they learned often blend content and style information, which somewhat limits their generalization capabilities under distribution shifts. To address this limitation, we adopt a causal generative perspective for multimodal data and propose contrastive learning with data augmentation to disentangle content features from the original representations. To achieve this, we begin with exploring image augmentation techniques and develop a method to seamlessly integrate them into pre-trained CLIP-like models to extract pure content features. Taking a step further, recognizing the inherent semantic richness and logical structure of text data, we explore the use of text augmentation to isolate latent content from style features. This enables CLIP-like model's encoders to concentrate on latent content information, refining the learned representations by pre-trained CLIP-like models. Our extensive experiments across diverse datasets demonstrate significant improvements in zero-shot and few-shot classification tasks, alongside enhanced robustness to various perturbations. These results underscore the effectiveness of our proposed methods in refining vision-language representations and advancing the state-of-the-art in multimodal learning.

cs.CV↗
arXiv2026

Link prediction on multi-relational graphs from an influence propagation perspective

Predicting the existence and type of links (edges) between nodes in a multi-relational graph is key for applications from social interaction prediction to knowledge relationship identification. Enhancing local features with relevant global information is crucial for accurate link prediction, yet it remains challenging. We address this by modeling the relationship between node pairs as node influence. That is, whether the node influence can be propagated and what type of influence is propagated indicates where and what type the edge is, which will be the most relevant local and global information to predict the edges. To this end, we extend the Susceptible-Infectious-Recovered (SIR) epidemic model to capture the influence propagation of nodes on a large scale through sub-graph structures. Subsequently, these sub-graphs are compressed using virtual edges, thereby substantially reducing the computation associated with utilizing the global graph structure. Finally, we propose the Influential Graph Neural Predictor, referred to as IGNP, a link prediction framework guided by influence propagation. Extensive experiments demonstrate the superiority of the proposed method, which outperforms strong baselines by a large margin on the widely used and real-world datasets.

cs.SI↗
arXiv2026

Boundary Embedding Shaping with Adaptive Contrastive Learning for Graph Structural Disentanglement

Graph neural networks (GNNs) excel at aggregating neighbor information for classification, yet their performance is hindered by graph structural entanglement, where spurious correlations from semantically irrelevant neighbors contaminate node embeddings. This challenge is most acute for nodes near class boundaries in the embedding space, where amplified structural noise blurs decision boundaries and destabilizes predictions. Existing robust GNN methods largely treat all nodes uniformly, ignoring boundary vulnerabilities. In this paper, to improve classification performance, we tackle graph structural disentanglement by identifying boundary-region entanglement as the primary bottleneck and propose Boundary Embedding Shaping (BES), an adaptive contrastive learning GNN plug-in module that selectively suppresses spurious structural noise at decision boundaries with minimal model parameter perturbation. Extensive experiments demonstrate that BES consistently improves boundary discrimination and outperforms existing leading methods. Notably, BES boosts GCN performance by an average of 3.3% in node classification (up to 5.0% on WikiCS) and achieves superior accuracy in link prediction.

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arXiv2026

Learning Latent Dynamical Causal Processes for Single-Cell Perturbation Prediction

Single-cell perturbation prediction aims to infer how cells respond to unseen interventions and to achieve out-of-distribution (OOD) generalization, providing a computational route to understanding how perturbations reshape cellular programs over time. Existing machine learning methods have made important progress, but typically capture only one side of the response. Latent causal approaches seek mechanisms that support generalization and interpretation, yet often treat perturbation effects as static outcomes. Temporal models describe how gene expression changes across time, but usually do not explicitly recover the latent causal generative mechanisms driving these changes. In practice, perturbation effects are both latent and dynamical: interventions act through unobserved cellular programs, whose states evolve over time and give rise to observed expression profiles. Motivated by this view, we propose a latent dynamical causal generative model for single-cell perturbation data that jointly captures latent cellular programs, perturbation-conditioned mechanisms, and temporal evolution. We further provide an identifiability analysis showing that, under suitable conditions, the latent causal variables are recoverable up to standard equivalence classes. Guided by this analysis, we develop CITE-VAE, a learning framework for recovering latent cellular programs and their perturbation-driven dynamics from single-cell sequencing data. Experiments on Causal-3DIdent validate the theoretical results and the effectiveness of the proposed method in controlled settings. Additional experiments on real-world CRISPR-based single-cell perturbation data show improved generalization to unseen perturbations compared with state-of-the-art baselines, highlighting the practical robustness of our approach.

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arXiv2026

What Makes a Representation Good for Single-Cell Perturbation Prediction?

Single-cell perturbation modeling is fundamental for understanding and predicting cellular responses to genetic perturbations. However, existing approaches, from causal representation learning to foundation models, often struggle with an overlooked challenge: gene expression is dominated by perturbation-invariant information, while perturbation-specific signals are intrinsically sparse. As a result, learned representations either entangle invariant and perturbation-specific information, leading to spurious and non-generalizable predictors, or suppress perturbation-specific signals altogether, rendering them ineffective for prediction. To address this, we propose PerturbedVAE, a general framework designed to resolve this signal imbalance. The framework explicitly separates perturbation-specific information from dominant invariant structure and recovers causal representations to effectively utilize such information for prediction. We further provide an identifiability analysis that characterizes the conditions under which sparse perturbation effects can be reliably recovered, thereby clarifying how the framework can be concretely specified under such conditions. Empirically, PerturbedVAE achieves state-of-the-art performance on a widely used benchmark across multiple evaluation settings, yielding significant gains on out-of-distribution combinatorial predictions and uncovering interpretable perturbation-response programs.

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arXiv2026

Chem4DLLM: 4D Multimodal LLMs for Chemical Dynamics Understanding

Existing chemical understanding tasks primarily rely on static molecular representations, limiting their ability to model inherently dynamic phenomena such as bond breaking or conformational changes, which are essential for a chemist to understand chemical reactions. To address this gap, we introduce Chemical Dynamics Understanding (ChemDU), a new task that translates 4D molecular trajectories into interpretable natural-language explanations. ChemDU focuses on fundamental dynamic scenarios, including gas-phase and catalytic reactions, and requires models to reason about key events along molecular trajectories, such as bond formation and dissociation, and to generate coherent, mechanistically grounded narratives. To benchmark this capability, we construct Chem4DBench, the first dataset pairing 4D molecular trajectories with expert-authored explanations across these settings. We further propose Chem4DLLM, a unified model that integrates an equivariant graph encoder with a pretrained large language model to explicitly capture molecular geometry and rotational dynamics. We hope that ChemDU, together with Chem4DBench and Chem4DLLM, will stimulate further research in dynamic chemical understanding and multimodal scientific reasoning.

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arXiv2026

I Predict Therefore I Am: Is Next Token Prediction Enough to Learn Human-Interpretable Concepts from Data?

Recent empirical evidence shows that LLM representations encode human-interpretable concepts. Nevertheless, the mechanisms by which these representations emerge remain largely unexplored. To shed further light on this, we introduce a novel generative model that generates tokens on the basis of such concepts formulated as latent discrete variables. Under mild conditions, even when the mapping from the latent space to the observed space is non-invertible, we establish rigorous identifiability result: the representations learned by LLMs through next-token prediction can be approximately modeled as the logarithm of the posterior probabilities of these latent discrete concepts given input context, up to an linear transformation. This theoretical finding: 1) provides evidence that LLMs capture essential underlying generative factors, 2) offers a unified and principled perspective for understanding the linear representation hypothesis, and 3) motivates a theoretically grounded approach for evaluating sparse autoencoders. Empirically, we validate our theoretical results through evaluations on both simulation data and the Pythia, Llama, and DeepSeek model families.

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arXiv2026

Beyond DAGs: A Latent Partial Causal Model for Multimodal Learning

Directed Acyclic Graphs (DAGs) are a standard tool in causal modeling, but their suitability for capturing the complexity of large-scale multimodal data is questionable. In practice, real-world multimodal datasets are often collected from heterogeneous generative processes that do not conform to a single DAG. Instead, they may involve multiple, and even opposing, DAG structures with inverse causal directions. To address this gap, in this work, we first propose a novel latent partial causal model tailored for multimodal data representation learning, featuring two latent coupled variables parts connected by an undirected edge, to represent the transfer of knowledge across modalities. Under specific statistical assumptions, we establish an identifiability result, demonstrating that representations learned by MultiModal Contrastive Learning (MMCL) correspond to the latent coupled variables up to a trivial transformation. This result deepens our understanding of the why MMCL works, highlights its potential for representation disentanglement, and expands the utility of pre-trained models like CLIP. Synthetic experiments confirm the robustness of our findings, even when the assumptions are partially violated. Most importantly, experiments on a pre-trained CLIP model embodies disentangled representations, enabling few-shot learning and improving domain generalization across diverse real-world datasets. Together, these contributions push the boundaries of MMCL, both in theory and in practical applications.

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arXiv2026

Identifying Weight-Variant Latent Causal Models

The task of causal representation learning aims to uncover latent higher-level causal variables that affect lower-level observations. Identifying the true latent causal variables from observed data, while allowing instantaneous causal relations among latent variables, remains a challenge, however. To this end, we start with the analysis of three intrinsic indeterminacies in identifying latent variables from observations: transitivity, permutation indeterminacy, and scaling indeterminacy. We find that transitivity acts as a key role in impeding the identifiability of latent causal variables. To address the unidentifiable issue due to transitivity, we introduce a novel identifiability condition where the underlying latent causal model satisfies a linear-Gaussian model, in which the causal coefficients and the distribution of Gaussian noise are modulated by an additional observed variable. Under certain assumptions, including the existence of a reference condition under which latent causal influences vanish, we can show that the latent causal variables can be identified up to trivial permutation and scaling, and that partial identifiability results can still be obtained when this reference condition is violated for a subset of latent variables. Furthermore, based on these theoretical results, we propose a novel method, termed Structural caUsAl Variational autoEncoder (SuaVE), which directly learns causal representations and causal relationships among them, together with the mapping from the latent causal variables to the observed ones. Experimental results on synthetic and real data demonstrate the identifiability and consistency results and the efficacy of SuaVE in learning causal representations.

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arXiv2026

Towards Identifiable Latent Additive Noise Models

Causal representation learning (CRL) offers the promise of uncovering the underlying causal model by which observed data was generated, but the practical applicability of existing methods remains limited by the strong assumptions required for identifiability and by challenges in applying them to real-world settings. Most current approaches are applicable only to relatively restrictive model classes, such as linear or polynomial models, which limits their flexibility and robustness in practice. One promising approach to this problem seeks to address these issues by leveraging changes in causal influences among latent variables. In this vein we propose a more general and relaxed framework than typically applied, formulated by imposing constraints on the function classes applied. Within this framework, we establish partial identifiability results under weaker conditions, including scenarios where only a subset of causal influences change. We then extend our analysis to a broader class of latent post-nonlinear models. Building on these theoretical insights, we develop a flexible method for learning latent causal representations. We demonstrate the effectiveness of our approach on synthetic and semi-synthetic datasets, and further showcase its applicability in a case study on human motion analysis, a complex real-world domain that also highlights the potential to broaden the practical reach of identifiable CRL models.

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arXiv2026

Concept Component Analysis: A Principled Approach for Concept Extraction in LLMs

Developing human understandable interpretation of large language models (LLMs) becomes increasingly critical for their deployment in essential domains. Mechanistic interpretability seeks to mitigate the issues through extracts human-interpretable process and concepts from LLMs' activations. Sparse autoencoders (SAEs) have emerged as a popular approach for extracting interpretable and monosemantic concepts by decomposing the LLM internal representations into a dictionary. Despite their empirical progress, SAEs suffer from a fundamental theoretical ambiguity: the well-defined correspondence between LLM representations and human-interpretable concepts remains unclear. This lack of theoretical grounding gives rise to several methodological challenges, including difficulties in principled method design and evaluation criteria. In this work, we show that, under mild assumptions, LLM representations can be approximated as a {linear mixture} of the log-posteriors over concepts given the input context, through the lens of a latent variable model where concepts are treated as latent variables. This motivates a principled framework for concept extraction, namely Concept Component Analysis (ConCA), which aims to recover the log-posterior of each concept from LLM representations through a {unsupervised} linear unmixing process. We explore a specific variant, termed sparse ConCA, which leverages a sparsity prior to address the inherent ill-posedness of the unmixing problem. We implement 12 sparse ConCA variants and demonstrate their ability to extract meaningful concepts across multiple LLMs, offering theory-backed advantages over SAEs.

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arXiv2025

On the Value of Cross-Modal Misalignment in Multimodal Representation Learning

Multimodal representation learning, exemplified by multimodal contrastive learning (MMCL) using image-text pairs, aims to learn powerful representations by aligning cues across modalities. This approach relies on the core assumption that the exemplar image-text pairs constitute two representations of an identical concept. However, recent research has revealed that real-world datasets often exhibit cross-modal misalignment. There are two distinct viewpoints on how to address this issue: one suggests mitigating the misalignment, and the other leveraging it. We seek here to reconcile these seemingly opposing perspectives, and to provide a practical guide for practitioners. Using latent variable models we thus formalize cross-modal misalignment by introducing two specific mechanisms: Selection bias, where some semantic variables are absent in the text, and perturbation bias, where semantic variables are altered -- both leading to misalignment in data pairs. Our theoretical analysis demonstrates that, under mild assumptions, the representations learned by MMCL capture exactly the information related to the subset of the semantic variables invariant to selection and perturbation biases. This provides a unified perspective for understanding misalignment. Based on this, we further offer actionable insights into how misalignment should inform the design of real-world ML systems. We validate our theoretical findings via extensive empirical studies on both synthetic data and real image-text datasets, shedding light on the nuanced impact of cross-modal misalignment on multimodal representation learning.

cs.LG↗
arXiv2025

Causal Disentanglement and Cross-Modal Alignment for Enhanced Few-Shot Learning

Few-shot learning (FSL) often requires effective adaptation of models using limited labeled data. However, most existing FSL methods rely on entangled representations, requiring the model to implicitly recover the unmixing process to obtain disentangled representations using only limited supervision, which hinders effective adaptation. Recent theoretical studies show that multimodal contrastive learning methods, such as CLIP, can disentangle latent representations up to linear transformations. In light of this, we propose the Causal CLIP Adapter (CCA), a novel framework that explicitly disentangles visual features extracted from CLIP using unsupervised Independent Component Analysis (ICA). This removes the need to learn the unmixing process from the labeled data, thereby reducing the number of trainable parameters and mitigating overfitting. Taking a step further, while ICA can obtain visual disentangled representations, it may also disrupt CLIP's intra- and inter-modal alignment. To counteract this, CCA further leverages CLIP's inherent cross-modal alignment by enhancing it in two ways: unidirectionally, through fine-tuning a CLIP-based text classifier, and bidirectionally, via a cross-attention mechanism that enriches visual and textual representations through mutual interaction. Both unimodal and cross-modal classification outputs can be effectively combined linearly to improve classification accuracy. Extensive experiments on 11 benchmark datasets demonstrate that our method consistently outperforms state-of-the-art approaches in terms of few-shot performance and robustness to distributional shifts, while maintaining computational efficiency. Code will be available at https://github.com/tianjiao-j/CCA.

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