arXiv subjects

Xiaotong Li

Publications and source records attributed to Xiaotong Li.

At least 37 records · Page 2Linked to original sources

arXiv2025

EVEv2: Improved Baselines for Encoder-Free Vision-Language Models

Existing encoder-free vision-language models (VLMs) are rapidly narrowing the performance gap with their encoder-based counterparts, highlighting the promising potential for unified multimodal systems with structural simplicity and efficient deployment. We systematically clarify the performance gap between VLMs using pre-trained vision encoders, discrete tokenizers, and minimalist visual layers from scratch, deeply excavating the under-examined characteristics of encoder-free VLMs. We develop efficient strategies for encoder-free VLMs that rival mainstream encoder-based ones. After an in-depth investigation, we launch EVEv2.0, a new and improved family of encoder-free VLMs. We show that: (i) Properly decomposing and hierarchically associating vision and language within a unified model reduces interference between modalities. (ii) A well-designed training strategy enables effective optimization for encoder-free VLMs. Through extensive evaluation, our EVEv2.0 represents a thorough study for developing a decoder-only architecture across modalities, demonstrating superior data efficiency and strong vision-reasoning capability. Code is publicly available at: https://github.com/baaivision/EVE.

cs.CV↗

arXiv2025

LEAD: Exploring Logit Space Evolution for Model Selection

The remarkable success of pretrain-then-finetune paradigm has led to a proliferation of available pre-trained models for vision tasks. This surge presents a significant challenge in efficiently choosing the most suitable pre-trained models for downstream tasks. The critical aspect of this challenge lies in effectively predicting the model transferability by considering the underlying fine-tuning dynamics. Existing methods often model fine-tuning dynamics in feature space with linear transformations, which do not precisely align with the fine-tuning objective and fail to grasp the essential nonlinearity from optimization. To this end, we present LEAD, a finetuning-aligned approach based on the network output of logits. LEAD proposes a theoretical framework to model the optimization process and derives an ordinary differential equation (ODE) to depict the nonlinear evolution toward the final logit state. Additionally, we design a class-aware decomposition method to consider the varying evolution dynamics across classes and further ensure practical applicability. Integrating the closely aligned optimization objective and nonlinear modeling capabilities derived from the differential equation, our method offers a concise solution to effectively bridge the optimization gap in a single step, bypassing the lengthy fine-tuning process. The comprehensive experiments on 24 supervised and self-supervised pre-trained models across 10 downstream datasets demonstrate impressive performances and showcase its broad adaptability even in low-data scenarios.

cs.CV↗

arXiv2025

Enhancing Safe and Controllable Protein Generation via Knowledge Preference Optimization

Protein language models have emerged as powerful tools for sequence generation, offering substantial advantages in functional optimization and denovo design. However, these models also present significant risks of generating harmful protein sequences, such as those that enhance viral transmissibility or evade immune responses. These concerns underscore critical biosafety and ethical challenges. To address these issues, we propose a Knowledge-guided Preference Optimization (KPO) framework that integrates prior knowledge via a Protein Safety Knowledge Graph. This framework utilizes an efficient graph pruning strategy to identify preferred sequences and employs reinforcement learning to minimize the risk of generating harmful proteins. Experimental results demonstrate that KPO effectively reduces the likelihood of producing hazardous sequences while maintaining high functionality, offering a robust safety assurance framework for applying generative models in biotechnology.

cs.AI↗

arXiv2025

Boosting LLM's Molecular Structure Elucidation with Knowledge Enhanced Tree Search Reasoning

Molecular structure elucidation involves deducing a molecule's structure from various types of spectral data, which is crucial in chemical experimental analysis. While large language models (LLMs) have shown remarkable proficiency in analyzing and reasoning through complex tasks, they still encounter substantial challenges in molecular structure elucidation. We identify that these challenges largely stem from LLMs' limited grasp of specialized chemical knowledge. In this work, we introduce a Knowledge-enhanced reasoning framework for Molecular Structure Elucidation (K-MSE), leveraging Monte Carlo Tree Search for test-time scaling as a plugin. Specifically, we construct an external molecular substructure knowledge base to extend the LLMs' coverage of the chemical structure space. Furthermore, we design a specialized molecule-spectrum scorer to act as a reward model for the reasoning process, addressing the issue of inaccurate solution evaluation in LLMs. Experimental results show that our approach significantly boosts performance, particularly gaining more than 20% improvement on both GPT-4o-mini and GPT-4o. Our code is available at https://github.com/HICAI-ZJU/K-MSE.

cs.CL↗

arXiv2025

Composite Indicator-Guided Infilling Sampling for Expensive Multi-Objective Optimization

In expensive multi-objective optimization, where the evaluation budget is strictly limited, selecting promising candidate solutions for expensive fitness evaluations is critical for accelerating convergence and improving algorithmic performance. However, designing an optimization strategy that effectively balances convergence, diversity, and distribution remains a challenge. To tackle this issue, we propose a composite indicator-based evolutionary algorithm (CI-EMO) for expensive multi-objective optimization. In each generation of the optimization process, CI-EMO first employs NSGA-III to explore the solution space based on fitness values predicted by surrogate models, generating a candidate population. Subsequently, we design a novel composite performance indicator to guide the selection of candidates for real fitness evaluation. This indicator simultaneously considers convergence, diversity, and distribution to improve the efficiency of identifying promising candidate solutions, which significantly improves algorithm performance. The composite indicator-based candidate selection strategy is easy to achieve and computes efficiency. Component analysis experiments confirm the effectiveness of each element in the composite performance indicator. Comparative experiments on three benchmark test sets and real-world problems demonstrate that the proposed algorithm outperforms five state-of-the-art expensive multi-objective optimization algorithms.

cs.NE↗

arXiv2025

Beyond Entropy: Region Confidence Proxy for Wild Test-Time Adaptation

Wild Test-Time Adaptation (WTTA) is proposed to adapt a source model to unseen domains under extreme data scarcity and multiple shifts. Previous approaches mainly focused on sample selection strategies, while overlooking the fundamental problem on underlying optimization. Initially, we critically analyze the widely-adopted entropy minimization framework in WTTA and uncover its significant limitations in noisy optimization dynamics that substantially hinder adaptation efficiency. Through our analysis, we identify region confidence as a superior alternative to traditional entropy, however, its direct optimization remains computationally prohibitive for real-time applications. In this paper, we introduce a novel region-integrated method ReCAP that bypasses the lengthy process. Specifically, we propose a probabilistic region modeling scheme that flexibly captures semantic changes in embedding space. Subsequently, we develop a finite-to-infinite asymptotic approximation that transforms the intractable region confidence into a tractable and upper-bounded proxy. These innovations significantly unlock the overlooked potential dynamics in local region in a concise solution. Our extensive experiments demonstrate the consistent superiority of ReCAP over existing methods across various datasets and wild scenarios.

cs.CV↗

arXiv2025

Tempo: Helping Data Scientists and Domain Experts Collaboratively Specify Predictive Modeling Tasks

Temporal predictive models have the potential to improve decisions in health care, public services, and other domains, yet they often fail to effectively support decision-makers. Prior literature shows that many misalignments between model behavior and decision-makers' expectations stem from issues of model specification, namely how, when, and for whom predictions are made. However, model specifications for predictive tasks are highly technical and difficult for non-data-scientist stakeholders to interpret and critique. To address this challenge we developed Tempo, an interactive system that helps data scientists and domain experts collaboratively iterate on model specifications. Using Tempo's simple yet precise temporal query language, data scientists can quickly prototype specifications with greater transparency about pre-processing choices. Moreover, domain experts can assess performance within data subgroups to validate that models behave as expected. Through three case studies, we demonstrate how Tempo helps multidisciplinary teams quickly prune infeasible specifications and identify more promising directions to explore.

cs.HC↗

arXiv2025

Explicit positivity preserving numerical method for linear stochastic volatility models driven by $α$-stable process

In this paper, we introduce a linear stochastic volatility model driven by $α$-stable processes, which admits a unique positive solution. To preserve positivity, we modify the classical forward Euler-Maruyama scheme and analyze its numerical properties. The scheme achieves a strong convergence order of $1/α$. Numerical simulations are presented at the end to verify theoretical results.

math.PR↗

arXiv2025

Infinity-MM: Scaling Multimodal Performance with Large-Scale and High-Quality Instruction Data

Recently, Vision-Language Models (VLMs) have achieved remarkable progress in multimodal tasks, and multimodal instruction data serves as the foundation for enhancing VLM capabilities. Despite the availability of several open-source multimodal datasets, limitations in the scale and quality of open-source instruction data hinder the performance of VLMs trained on these datasets, leading to a significant gap compared to models trained on closed-source data. To address this challenge, we introduce Infinity-MM, a large-scale multimodal instruction dataset. We collected the available multimodal instruction datasets and performed unified preprocessing, resulting in a dataset with over 40 million samples that ensures diversity and accuracy. Furthermore, to enable large-scale expansion of instruction data and support the continuous acquisition of high-quality data, we propose a synthetic instruction generation method based on a tagging system and open-source VLMs. By establishing correspondences between different types of images and associated instruction types, this method can provide essential guidance during data synthesis. Leveraging this high-quality data, we have trained a 2-billion-parameter Vision-Language Model, Aquila-VL-2B, which achieves state-of-the-art (SOTA) performance among models of similar scale. The data is available at: https://huggingface.co/datasets/BAAI/Infinity-MM.

cs.CL↗

arXiv2024

DenseFusion-1M: Merging Vision Experts for Comprehensive Multimodal Perception

Existing Multimodal Large Language Models (MLLMs) increasingly emphasize complex understanding of various visual elements, including multiple objects, text information, and spatial relations. Their development for comprehensive visual perception hinges on the availability of high-quality image-text datasets that offer diverse visual elements and throughout image descriptions. However, the scarcity of such hyper-detailed datasets currently hinders progress within the MLLM community. The bottleneck stems from the limited perceptual capabilities of current caption engines, which fall short in providing complete and accurate annotations. To facilitate the cutting-edge research of MLLMs on comprehensive vision perception, we thereby propose Perceptual Fusion, using a low-budget but highly effective caption engine for complete and accurate image descriptions. Specifically, Perceptual Fusion integrates diverse perception experts as image priors to provide explicit information on visual elements and adopts an efficient MLLM as a centric pivot to mimic advanced MLLMs' perception abilities. We carefully select 1M highly representative images from uncurated LAION dataset and generate dense descriptions using our engine, dubbed DenseFusion-1M. Extensive experiments validate that our engine outperforms its counterparts, where the resulting dataset significantly improves the perception and cognition abilities of existing MLLMs across diverse vision-language benchmarks, especially with high-resolution images as inputs. The dataset and code are publicly available at https://github.com/baaivision/DenseFusion.

cs.CV↗

arXiv2024

Unveiling Encoder-Free Vision-Language Models

Existing vision-language models (VLMs) mostly rely on vision encoders to extract visual features followed by large language models (LLMs) for visual-language tasks. However, the vision encoders set a strong inductive bias in abstracting visual representation, e.g., resolution, aspect ratio, and semantic priors, which could impede the flexibility and efficiency of the VLMs. Training pure VLMs that accept the seamless vision and language inputs, i.e., without vision encoders, remains challenging and rarely explored. Empirical observations reveal that direct training without encoders results in slow convergence and large performance gaps. In this work, we bridge the gap between encoder-based and encoder-free models, and present a simple yet effective training recipe towards pure VLMs. Specifically, we unveil the key aspects of training encoder-free VLMs efficiently via thorough experiments: (1) Bridging vision-language representation inside one unified decoder; (2) Enhancing visual recognition capability via extra supervision. With these strategies, we launch EVE, an encoder-free vision-language model that can be trained and forwarded efficiently. Notably, solely utilizing 35M publicly accessible data, EVE can impressively rival the encoder-based VLMs of similar capacities across multiple vision-language benchmarks. It significantly outperforms the counterpart Fuyu-8B with mysterious training procedures and undisclosed training data. We believe that EVE provides a transparent and efficient route for developing a pure decoder-only architecture across modalities. Our code and models are publicly available at: https://github.com/baaivision/EVE.

cs.CV↗

arXiv2024

Toward Scalable Image Feature Compression: A Content-Adaptive and Diffusion-Based Approach

Traditional image codecs emphasize signal fidelity and human perception, often at the expense of machine vision tasks. Deep learning methods have demonstrated promising coding performance by utilizing rich semantic embeddings optimized for both human and machine vision. However, these compact embeddings struggle to capture fine details such as contours and textures, resulting in imperfect reconstructions. Furthermore, existing learning-based codecs lack scalability. To address these limitations, this paper introduces a content-adaptive diffusion model for scalable image compression. The proposed method encodes fine textures through a diffusion process, enhancing perceptual quality while preserving essential features for machine vision tasks. The approach employs a Markov palette diffusion model combined with widely used feature extractors and image generators, enabling efficient data compression. By leveraging collaborative texture-semantic feature extraction and pseudo-label generation, the method accurately captures texture information. A content-adaptive Markov palette diffusion model is then applied to represent both low-level textures and high-level semantic content in a scalable manner. This framework offers flexible control over compression ratios by selecting intermediate diffusion states, eliminating the need for retraining deep learning models at different operating points. Extensive experiments demonstrate the effectiveness of the proposed framework in both image reconstruction and downstream machine vision tasks such as object detection, segmentation, and facial landmark detection, achieving superior perceptual quality compared to state-of-the-art methods.

cs.CV↗

arXiv2024

Scientific Large Language Models: A Survey on Biological & Chemical Domains

Large Language Models (LLMs) have emerged as a transformative power in enhancing natural language comprehension, representing a significant stride toward artificial general intelligence. The application of LLMs extends beyond conventional linguistic boundaries, encompassing specialized linguistic systems developed within various scientific disciplines. This growing interest has led to the advent of scientific LLMs, a novel subclass specifically engineered for facilitating scientific discovery. As a burgeoning area in the community of AI for Science, scientific LLMs warrant comprehensive exploration. However, a systematic and up-to-date survey introducing them is currently lacking. In this paper, we endeavor to methodically delineate the concept of "scientific language", whilst providing a thorough review of the latest advancements in scientific LLMs. Given the expansive realm of scientific disciplines, our analysis adopts a focused lens, concentrating on the biological and chemical domains. This includes an in-depth examination of LLMs for textual knowledge, small molecules, macromolecular proteins, genomic sequences, and their combinations, analyzing them in terms of model architectures, capabilities, datasets, and evaluation. Finally, we critically examine the prevailing challenges and point out promising research directions along with the advances of LLMs. By offering a comprehensive overview of technical developments in this field, this survey aspires to be an invaluable resource for researchers navigating the intricate landscape of scientific LLMs.

cs.CL↗

arXiv2023

The semi-implicit Euler-Maruyama method for nonlinear non-autonomous stochastic differential equations driven by a class of Lévy processes

The strong convergence of the semi-implicit Euler-Maruyama (EM) method for stochastic differential equations with non-linear coefficients driven by a class of Lévy processes is investigated. The dependence of the convergence order of the numerical scheme on the parameters of the class of Lévy processes is discovered, which is different from existing results. In addition, the existence and uniqueness of numerical invariant measure of the semi-implicit EM method is studied and its convergence to the underlying invariant measure is also proved. Numerical examples are provided to confirm our theoretical results.

math.NA↗

arXiv2023

InstructProtein: Aligning Human and Protein Language via Knowledge Instruction

Large Language Models (LLMs) have revolutionized the field of natural language processing, but they fall short in comprehending biological sequences such as proteins. To address this challenge, we propose InstructProtein, an innovative LLM that possesses bidirectional generation capabilities in both human and protein languages: (i) taking a protein sequence as input to predict its textual function description and (ii) using natural language to prompt protein sequence generation. To achieve this, we first pre-train an LLM on both protein and natural language corpora, enabling it to comprehend individual languages. Then supervised instruction tuning is employed to facilitate the alignment of these two distinct languages. Herein, we introduce a knowledge graph-based instruction generation framework to construct a high-quality instruction dataset, addressing annotation imbalance and instruction deficits in existing protein-text corpus. In particular, the instructions inherit the structural relations between proteins and function annotations in knowledge graphs, which empowers our model to engage in the causal modeling of protein functions, akin to the chain-of-thought processes in natural languages. Extensive experiments on bidirectional protein-text generation tasks show that InstructProtein outperforms state-of-the-art LLMs by large margins. Moreover, InstructProtein serves as a pioneering step towards text-based protein function prediction and sequence design, effectively bridging the gap between protein and human language understanding.

q-bio.BM↗

arXiv2023

Exploring Model Transferability through the Lens of Potential Energy

Transfer learning has become crucial in computer vision tasks due to the vast availability of pre-trained deep learning models. However, selecting the optimal pre-trained model from a diverse pool for a specific downstream task remains a challenge. Existing methods for measuring the transferability of pre-trained models rely on statistical correlations between encoded static features and task labels, but they overlook the impact of underlying representation dynamics during fine-tuning, leading to unreliable results, especially for self-supervised models. In this paper, we present an insightful physics-inspired approach named PED to address these challenges. We reframe the challenge of model selection through the lens of potential energy and directly model the interaction forces that influence fine-tuning dynamics. By capturing the motion of dynamic representations to decline the potential energy within a force-driven physical model, we can acquire an enhanced and more stable observation for estimating transferability. The experimental results on 10 downstream tasks and 12 self-supervised models demonstrate that our approach can seamlessly integrate into existing ranking techniques and enhance their performances, revealing its effectiveness for the model selection task and its potential for understanding the mechanism in transfer learning. Code will be available at https://github.com/lixiaotong97/PED.

cs.CV↗

arXiv2023

Masked Image Modeling with Denoising Contrast

Since the development of self-supervised visual representation learning from contrastive learning to masked image modeling (MIM), there is no significant difference in essence, that is, how to design proper pretext tasks for vision dictionary look-up. MIM recently dominates this line of research with state-of-the-art performance on vision Transformers (ViTs), where the core is to enhance the patch-level visual context capturing of the network via denoising auto-encoding mechanism. Rather than tailoring image tokenizers with extra training stages as in previous works, we unleash the great potential of contrastive learning on denoising auto-encoding and introduce a pure MIM method, ConMIM, to produce simple intra-image inter-patch contrastive constraints as the sole learning objectives for masked patch prediction. We further strengthen the denoising mechanism with asymmetric designs, including image perturbations and model progress rates, to improve the network pre-training. ConMIM-pretrained models with various scales achieve competitive results on downstream image classification, semantic segmentation, object detection, and instance segmentation tasks, e.g., on ImageNet-1K classification, we achieve 83.9% top-1 accuracy with ViT-Small and 85.3% with ViT-Base without extra data for pre-training.

cs.CV↗

arXiv2023

Modeling Uncertain Feature Representation for Domain Generalization

Though deep neural networks have achieved impressive success on various vision tasks, obvious performance degradation still exists when models are tested in out-of-distribution scenarios. In addressing this limitation, we ponder that the feature statistics (mean and standard deviation), which carry the domain characteristics of the training data, can be properly manipulated to improve the generalization ability of deep learning models. Existing methods commonly consider feature statistics as deterministic values measured from the learned features and do not explicitly model the uncertain statistics discrepancy caused by potential domain shifts during testing. In this paper, we improve the network generalization ability by modeling domain shifts with uncertainty (DSU), i.e., characterizing the feature statistics as uncertain distributions during training. Specifically, we hypothesize that the feature statistic, after considering the potential uncertainties, follows a multivariate Gaussian distribution. During inference, we propose an instance-wise adaptation strategy that can adaptively deal with the unforeseeable shift and further enhance the generalization ability of the trained model with negligible additional cost. We also conduct theoretical analysis on the aspects of generalization error bound and the implicit regularization effect, showing the efficacy of our method. Extensive experiments demonstrate that our method consistently improves the network generalization ability on multiple vision tasks, including image classification, semantic segmentation, instance retrieval, and pose estimation. Our methods are simple yet effective and can be readily integrated into networks without additional trainable parameters or loss constraints. Code will be released in https://github.com/lixiaotong97/DSU.

cs.CV↗