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Jiaxin Qi

Publications and source records attributed to Jiaxin Qi.

At least 19 recordsLinked to original sources
arXiv2026

SymFold: Synergizing Evolutionary and Structural Priors for Accurate Protein Inverse Folding

Protein inverse folding aims to recover amino acid sequences for a given 3D protein structure, underpinning broad applications such as enzyme engineering and drug discovery.Current methods often follow a serial pipeline, in which a structure encoder predicts a coarse sequence, which is then refined by protein language models (PLMs). However, because PLMs only perform post-hoc sequence edits, the refinement is bounded by the quality of upstream predictions.Thanks to recent multimodal protein language models (MPLMs), we could directly encode structure to generate sequences with pretrained structural knowledge, but we observe that they are not effective for inverse folding. Therefore, we introduce a symmetric dual-path architecture that both leverages PLMs for pretrained sequence evolution knowledge and MPLMs for pretrained structural knowledge to iteratively guide protein sequence generation.Through extensive experiments across standard protein inverse folding benchmarks, our method achieves state-of-the-art performance, surpassing prior approaches, and ablation studies validate the rationale of our symmetric design, revealing a promising direction for the community.

cs.AI↗
arXiv2026

PopPert: Population-level Joint-Distribution Modeling for Single-Cell Perturbation Prediction

Predicting transcriptional responses to specific perturbations is critical for understanding cellular regulatory mechanisms and accelerating drug discovery. Single-cell RNA sequencing destroys each measured cell, yielding only unpaired populations of control and perturbed cells. However, existing methods typically model perturbation prediction at the single-cell level and assume cell-to-cell correspondence, which conflicts with the unpaired nature of the observed data. To address this challenge, we propose PopPert, a framework that explicitly parameterizes population-level joint gene expression distributions for collective transcriptional state modeling. Given a control population distribution and a perturbation condition, PopPert predicts perturbation-induced changes in distribution parameters, eliminating the need for cell-level correspondence and reducing sensitivity to single-cell noise. To effectively capture gene co-expression patterns, PopPert leverages a low-rank Gaussian Copula to model cross-gene statistical dependencies and construct the joint gene expression distribution, additionally allowing sampling of synthetic perturbed single-cell profiles. Across multiple single-cell benchmarks spanning both genetic and chemical perturbations, PopPert achieves superior overall performance in differential expression recovery, perturbation effect estimation, and population-level distribution matching. These results establish population-level joint distribution learning as an effective paradigm for predicting transcriptional responses from unpaired single-cell populations. Code for PopPert is publicly available at https://github.com/whd1125/PopPert.

q-bio.GN↗
arXiv2026

A Model-Internal Protocol for Assessing Multimodal Models as Integrated Systems

As Large Vision-Language Models increasingly aim to integrate visual generation and understanding within a single parameter space, evaluating such structural unification in a cohesive manner remains a critical challenge. Current evaluation protocols predominantly treat generative and discriminative capabilities as separate tasks, leaving a gap in system-level evaluation for unified multimodal models (UMMs). In this work, we propose Self-Generative-Understanding (SGU), a novel, annotation-free evaluation framework that probes the integrated capabilities of unified models through a semantic closed-loop challenge. Without requiring new annotations, SGU leverages the dual understanding-and-generation abilities of UMMs by asking them to first perceive an image and produce a textual description, subsequently reconstruct a visual context based on that description, and finally perform reasoning over the self-generated output. This pipeline provides a zero-cost testbed that yields an integrated performance score specifically tailored for evaluating UMMs as unified systems. Extensive experiments show that even high-performing UMMs often struggle to reason over their own generated contexts, revealing limitations that are not captured by separate evaluations of understanding or generation alone. Our work provides a complementary holistic evaluation framework and offers a foundation for benchmarking the development of next-generation unified multimodal models.

cs.CV↗
arXiv2026

Matching Matters: A Fair Quality-Efficiency Benchmark for Command-Line Agents

Rapid advances in large language models have improved the task-solving capabilities of command-line-interface (CLI)-based agents, whose CLIs determine how models invoke tools, maintain interaction history, and recover from failures. Consequently, effective matching between CLIs and LLMs has become essential. However, existing agent benchmarks largely emphasize success rate while overlooking practical objectives such as cost and efficiency, as well as the selection of LM-CLI combinations, all of which are critical in real-world deployment. We therefore introduce AgentMeter, a quality-efficiency benchmark with a new metric, the AgentMeter Score (AMS), that jointly characterizes task quality, budget sensitivity, and resource-intensive zero-reward execution, enabling a more complete assessment of deployed LM-CLI pairs. Furthermore, collected task descriptions may inadvertently favor LM-CLI pairs that are particularly compatible with their wording and structure, causing evaluation results to reflect description-specific advantages rather than general task-solving capability. We therefore propose AgentMeter-Opt, a trajectory-grounded optimization framework that constructs pair-adapted, task-preserving description variants to build a fairer evaluation set across LM-CLI pairs. Extensive experiments show that no CLI is universally optimal across language models and that task success, execution cost, and AMS identify different competitive configurations. Results on AgentMeter-Opt further reveal that task-preserving description changes affect LM-CLI pairs unevenly and can alter their relative ordering across valid description conditions. Together, AgentMeter and AgentMeter-Opt provide a practical foundation for fair and deployment-relevant evaluation of command-line agents.

cs.SE↗
arXiv2026

Beyond Gene Reconstruction: Learning Cell Representations through Complementary Transcriptomic Views

The rapid growth of single-cell transcriptomic data has enabled the development of foundation models pretrained primarily by reconstructing masked expression values. This objective encourages these models to learn gene dependencies but does not directly optimize whole-cell representations, which are essential for many downstream tasks. To bridge this gap, we propose a contrastive pretraining framework that learns cell representations through complementary transcriptomic views. Since standard contrastive learning is not readily applicable to single-cell pretraining, we introduce specific adaptations along three dimensions --- co-expression-guided gene partitioning, expression-aware contrast-set construction, and competence-gated contrastive onset. Specifically, we first construct two complementary views of each cell by partitioning its genes according to their co-expression structure. Then, to prevent the model from using gene-set identity as a shortcut, we construct hard negatives by permuting expression values while keeping gene identities unchanged. Finally, we introduce a competence-aware controller to determine how the contrastive objective is applied. Experiments on cell-type annotation and gene regulatory network inference demonstrate competitive transfer under the evaluated protocols. In the six-network GRN evaluation, our method records the highest mean AUROC and AUPRC point estimates among the compared variants, while the highest-scoring variant differs across individual networks. These results establish complementary-view contrastive learning as an effective direction for single-cell pretraining beyond gene reconstruction.

cs.LG↗
arXiv2026

A Reconstruction-Based Framework for Caption Evaluation Beyond Reference Captions

Image captioning is a primary task in vision--language research, yet assessing how faithfully a caption preserves image semantics without relying on reference captions remains unsettled. Prevailing evaluations rely on human-annotated references, whose content reflects annotator intent and captioning proficiency. In this paper, we study a reconstruction-based principle for caption evaluation: a caption is as good as its capacity to enable reconstruction of the original image. However, because captioning inherently compresses visual information, it is impossible to recover all details, and pixel-wise comparison between reconstructed and source images is neither feasible nor meaningful. Through our in-depth analysis of the nature of captions, whose fundamental purpose is to transmit the semantic content of an image, we propose a revised principle: a caption is as good as its capacity to enable a reconstruction that is semantically equivalent to the original. To assess semantic equivalence, we test whether the reconstruction matches the original image across a suite of downstream vision--language tasks, yielding a reference-free, task-conditioned caption score. We characterize component-dependent limitations and introduce the lower-cost Captioning Turing Test Dataset (CTTD) surrogate.

cs.CV↗
arXiv2026

Spatial Transcriptomics as Images for Large-Scale Pretraining

Spatial Transcriptomics (ST) profiles thousands of gene expression values at discrete spots with precise coordinates on tissue sections, preserving spatial context essential for clinical and pathological studies. With rising sequencing throughput and advancing platforms, the expanding data volumes motivate large-scale ST pretraining. However, the fundamental unit for pretraining, i.e., what constitutes a single training sample, remains ill-posed. Existing choices fall into two camps: (1) treating each spot as an independent sample, which discards spatial dependencies and collapses ST into single-cell transcriptomics; and (2) treating an entire slide as a single sample, which produces prohibitively large inputs and drastically fewer training examples, undermining effective pretraining. To address this gap, we propose treating spatial transcriptomics as croppable images. Specifically, we define a multi-channel image representation with fixed spatial size by cropping patches from raw slides, thereby preserving spatial context while substantially increasing the number of training samples. Along the channel dimension, we define gene subset selection rules to control input dimensionality and improve pretraining stability. Extensive experiments show that the proposed image-like dataset construction for ST pretraining consistently improves downstream performance, outperforming conventional pretraining schemes. Ablation studies verify that both spatial patching and channel design are necessary, establishing a unified, practical paradigm for organizing ST data and enabling large-scale pretraining.

cs.CV↗
arXiv2026

Intrinsic Gradient Suppression for Label-Noise Prompt Tuning in Vision-Language Models

Contrastive vision-language models like CLIP exhibit remarkable zero-shot generalization. However, prompt tuning remains highly sensitive to label noise, as mislabeled samples generate disproportionately large gradients that can overwhelm pre-trained priors. We argue that because CLIP already provides a near-optimal initialization, adaptation should be inherently conservative, particularly against the extreme gradient updates common in noisy settings. To this end, we propose Double-Softmax Prompt Tuning (DSPT), a hyperparameter-free method for intrinsic gradient suppression. By applying a sequential probabilistic normalization, DSPT induces a self-adaptive saturation zone that suppresses gradients from high-error noisy samples while maintaining informative updates. We also provide both theoretical analysis and empirical evidence about how this mechanism achieves adaptive suppression. This design transforms ``gradient vanishing'', traditionally a training bottleneck, into a principled noise-filtering shield for label-noise prompt tuning. Extensive experiments confirm that this simple, drop-in design achieves state-of-the-art robustness across various noisy benchmarks, outperforming methods with complex architectures and handcrafted hyperparameters.

cs.CV↗
arXiv2026

Towards Universal Gene Regulatory Network Inference: Unlocking Generalizable Regulatory Knowledge in Single-cell Foundation Models

Gene Regulatory Network (GRN) inference is essential for understanding complex cellular mechanisms, rendered tractable through single-cell transcriptomic data. With the emergence of single-cell Foundation Models (scFMs), enhanced transcriptomic encoding is widely expected to revolutionize GRN inference. However, we observe that their performance remains far from satisfactory. The primary reason is that the standard reconstruction-based pre-training objectives often fail to explicitly capture latent regulatory signals. To bridge this gap, we first introduce a GRN generalization benchmark designed to evaluate regulatory predictions on unseen genes and datasets, which relies on the zero-shot capabilities of scFMs and is inherently challenging for traditional methods. Furthermore, to unlock the regulatory knowledge within the foundation models, we propose two novel methods, Virtual Value Perturbation and Gradient Trajectory, to distill implicit regulatory information from scFMs into highly generalizable inter-gene features. Extensive experiments demonstrate that our approach significantly outperforms existing methods, establishing a new paradigm for leveraging the potential of scFMs in universal GRN inference.

cs.LG↗
arXiv2026

Long-CODE: Isolating Pure Long-Context as an Orthogonal Dimension in Video Evaluation

As video generation models achieve unprecedented capabilities, the demand for robust video evaluation metrics becomes increasingly critical. Traditional metrics are intrinsically tailored for short-video evaluation, predominantly assessing frame-level visual quality and localized temporal smoothness. However, as state-of-the-art video generation models scale to generate longer videos, these metrics fail to capture essential long-range characteristics, such as narrative richness and global causal consistency. Recognizing that short-term visual perception and long-context attributes are fundamentally orthogonal dimensions, we argue that long-video metrics should be disentangled from short-video assessments. In this paper, we focus on the rigorous justification and design of a dedicated framework for long-video evaluation. We first introduce a suite of long-video attribute corruption tests, exposing the critical limitations of existing hort-video metrics from their insensitivity to structural inconsistencies, such as shot-level perturbations and narrative shuffling. To bridge this gap, we design a novel long-video metric based on shot dynamics, which is highly sensitive to the long-range testing framework. Furthermore, we introduce Long-CODE (Long-Context as an Orthogonal Dimension for video Evaluation), a specialized dataset designed to benchmark long-video evaluation, with human annotations isolated specifically to genuine long-range characteristics. Extensive experiments show that our proposed metrics achieve state-of-the-art correlation with human judgments. Ultimately, our metric and benchmark seamlessly complement existing short-video standards, establishing a holistic and unbiased evaluation paradigm for video generation models.

cs.CV↗
arXiv2026

In Search of Lost DNA Sequence Pretraining

DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have overwhelmingly emphasized pretraining scale and custom downstream evaluation datasets, while neglecting some essential components of the pretraining paradigm. In this paper, we reveal three critical yet heretofore overlooked problems in DNA pretraining: inappropriate downstream datasets, inherent flaws in the neighbor-masking strategy, and the lack of detailed discussion on vocabulary. Therefore, we undertake comprehensive investigations and propose principled guidelines, including selection criteria for evaluation datasets, guiding task design, and in-depth vocabulary analysis. Extensive experiments validate the significance of our identified problems and support the rationale behind our recommendations. Finally, we introduce a standardized testbed that enables reproducible and rigorous benchmarking of DNA pretraining methods to advance the development of genomic foundation models.

cs.LG↗
arXiv2026

CCCaption: Dual-Reward Reinforcement Learning for Complete and Correct Image Captioning

Image captioning remains a fundamental task for vision language understanding, yet ground-truth supervision still relies predominantly on human-annotated references. Because human annotations reflect subjective preferences and expertise, ground-truth captions are often incomplete or even incorrect, which in turn limits caption models. We argue that caption quality should be assessed by two objective aspects: completeness (does the caption cover all salient visual facts?) and correctness (are the descriptions true with respect to the image?). To this end, we introduce CCCaption: a dual-reward reinforcement learning framework with a dedicated fine-tuning corpus that explicitly optimizes these properties to generate \textbf{C}omplete and \textbf{C}orrect \textbf{Captions}. For completeness, we use diverse LVLMs to disentangle the image into a set of visual queries, and reward captions that answer more of these queries, with a dynamic query sampling strategy to improve training efficiency. For correctness, we penalize captions that contain hallucinations by validating the authenticity of sub-caption queries, which are derived from the caption decomposition. Our symmetric dual-reward optimization jointly maximizes completeness and correctness, guiding models toward captions that better satisfy these objective criteria. Extensive experiments across standard captioning benchmarks show consistent improvements, offering a principled path to training caption models beyond human-annotation imitation.

cs.CV↗
arXiv2026

Scaling Test-Time Robustness of Vision-Language Models via Self-Critical Inference Framework

The emergence of Large Language Models (LLMs) has driven rapid progress in multi-modal learning, particularly in the development of Large Vision-Language Models (LVLMs). However, existing LVLM training paradigms place excessive reliance on the LLM component, giving rise to two critical robustness challenges: language bias and language sensitivity. To address both issues simultaneously, we propose a novel Self-Critical Inference (SCI) framework that extends Visual Contrastive Decoding by conducting multi-round counterfactual reasoning through both textual and visual perturbations. This process further introduces a new strategy for improving robustness by scaling the number of counterfactual rounds. Moreover, we also observe that failure cases of LVLMs differ significantly across models, indicating that fixed robustness benchmarks may not be able to capture the true reliability of LVLMs. To this end, we propose the Dynamic Robustness Benchmark (DRBench), a model-specific evaluation framework targeting both language bias and sensitivity issues. Extensive experiments show that SCI consistently outperforms baseline methods on DRBench, and that increasing the number of inference rounds further boosts robustness beyond existing single-step counterfactual reasoning methods.

cs.CV↗
arXiv2026

Experience is the Best Teacher: Motivating Effective Exploration in Reinforcement Learning for LLMs

Reinforcement Learning (RL) with rubric-based rewards has recently shown remarkable progress in enhancing general reasoning capabilities of Large Language Models (LLMs), yet still suffers from ineffective exploration confined to curent policy distribution. In fact, RL optimization can be viewed as steering the policy toward an ideal distribution that maximizes the rewards, while effective exploration should align efforts with desired target. Leveraging this insight, we propose HeRL, a Hindsight experience guided Reinforcement Learning framework to bootstrap effective exploration by explicitly telling LLMs the desired behaviors specified in rewards. Concretely, HeRL treats failed trajectories along with their unmet rubrics as hindsight experience, which serves as in-context guidance for the policy to explore desired responses beyond its current distribution. Additionally, we introduce a bonus reward to incentivize responses with greater potential for improvement under such guidance. HeRL facilitates effective learning from desired high quality samples without repeated trial-and-error from scratch, yielding a more accurate estimation of the expected gradient theoretically. Extensive experiments across various benchmarks demonstrate that HeRL achieves superior performance gains over baselines, and can further benefit from experience guided self-improvement at test time. Our code is available at https://github.com/sikelifei/HeRL.

cs.AI↗
arXiv2026

A Comprehensive Benchmark for Electrocardiogram Time-Series

Electrocardiogram~(ECG), a key bioelectrical time-series signal, is crucial for assessing cardiac health and diagnosing various diseases. Given its time-series format, ECG data is often incorporated into pre-training datasets for large-scale time-series model training. However, existing studies often overlook its unique characteristics and specialized downstream applications, which differ significantly from other time-series data, leading to an incomplete understanding of its properties. In this paper, we present an in-depth investigation of ECG signals and establish a comprehensive benchmark, which includes (1) categorizing its downstream applications into four distinct evaluation tasks, (2) identifying limitations in traditional evaluation metrics for ECG analysis, and introducing a novel metric; (3) benchmarking state-of-the-art time-series models and proposing a new architecture. Extensive experiments demonstrate that our proposed benchmark is comprehensive and robust. The results validate the effectiveness of the proposed metric and model architecture, which establish a solid foundation for advancing research in ECG signal analysis.

eess.SP↗
arXiv2025

Two Causal Principles for Improving Visual Dialog

This paper unravels the design tricks adopted by us, the champion team MReaL-BDAI, for Visual Dialog Challenge 2019: two causal principles for improving Visual Dialog (VisDial). By "improving", we mean that they can promote almost every existing VisDial model to the state-of-the-art performance on the leader-board. Such a major improvement is only due to our careful inspection on the causality behind the model and data, finding that the community has overlooked two causalities in VisDial. Intuitively, Principle 1 suggests: we should remove the direct input of the dialog history to the answer model, otherwise a harmful shortcut bias will be introduced; Principle 2 says: there is an unobserved confounder for history, question, and answer, leading to spurious correlations from training data. In particular, to remove the confounder suggested in Principle 2, we propose several causal intervention algorithms, which make the training fundamentally different from the traditional likelihood estimation. Note that the two principles are model-agnostic, so they are applicable in any VisDial model. The code is available at https://github.com/simpleshinobu/visdial-principles.

cs.CV↗
arXiv2025

Gene Incremental Learning for Single-Cell Transcriptomics

Classes, as fundamental elements of Computer Vision, have been extensively studied within incremental learning frameworks. In contrast, tokens, which play essential roles in many research fields, exhibit similar characteristics of growth, yet investigations into their incremental learning remain significantly scarce. This research gap primarily stems from the holistic nature of tokens in language, which imposes significant challenges on the design of incremental learning frameworks for them. To overcome this obstacle, in this work, we turn to a type of token, gene, for a large-scale biological dataset--single-cell transcriptomics--to formulate a pipeline for gene incremental learning and establish corresponding evaluations. We found that the forgetting problem also exists in gene incremental learning, thus we adapted existing class incremental learning methods to mitigate the forgetting of genes. Through extensive experiments, we demonstrated the soundness of our framework design and evaluations, as well as the effectiveness of our method adaptations. Finally, we provide a complete benchmark for gene incremental learning in single-cell transcriptomics.

cs.LG↗
arXiv2025

Invariant Feature Learning for Generalized Long-Tailed Classification

Existing long-tailed classification (LT) methods only focus on tackling the class-wise imbalance that head classes have more samples than tail classes, but overlook the attribute-wise imbalance. In fact, even if the class is balanced, samples within each class may still be long-tailed due to the varying attributes. Note that the latter is fundamentally more ubiquitous and challenging than the former because attributes are not just implicit for most datasets, but also combinatorially complex, thus prohibitively expensive to be balanced. Therefore, we introduce a novel research problem: Generalized Long-Tailed classification (GLT), to jointly consider both kinds of imbalances. By "generalized", we mean that a GLT method should naturally solve the traditional LT, but not vice versa. Not surprisingly, we find that most class-wise LT methods degenerate in our proposed two benchmarks: ImageNet-GLT and MSCOCO-GLT. We argue that it is because they over-emphasize the adjustment of class distribution while neglecting to learn attribute-invariant features. To this end, we propose an Invariant Feature Learning (IFL) method as the first strong baseline for GLT. IFL first discovers environments with divergent intra-class distributions from the imperfect predictions and then learns invariant features across them. Promisingly, as an improved feature backbone, IFL boosts all the LT line-up: one/two-stage re-balance, augmentation, and ensemble. Codes and benchmarks are available on Github: https://github.com/KaihuaTang/Generalized-Long-Tailed-Benchmarks.pytorch

cs.CV↗