arXiv subjects

Linfeng Zhang

Publications and source records attributed to Linfeng Zhang.

At least 217 records · Page 12Linked to original sources

arXiv2025

SciLitLLM: How to Adapt LLMs for Scientific Literature Understanding

Scientific literature understanding is crucial for extracting targeted information and garnering insights, thereby significantly advancing scientific discovery. Despite the remarkable success of Large Language Models (LLMs), they face challenges in scientific literature understanding, primarily due to (1) a lack of scientific knowledge and (2) unfamiliarity with specialized scientific tasks. To develop an LLM specialized in scientific literature understanding, we propose a hybrid strategy that integrates continual pre-training (CPT) and supervised fine-tuning (SFT), to simultaneously infuse scientific domain knowledge and enhance instruction-following capabilities for domain-specific tasks.cIn this process, we identify two key challenges: (1) constructing high-quality CPT corpora, and (2) generating diverse SFT instructions. We address these challenges through a meticulous pipeline, including PDF text extraction, parsing content error correction, quality filtering, and synthetic instruction creation. Applying this strategy, we present a suite of LLMs: SciLitLLM, specialized in scientific literature understanding. These models demonstrate promising performance on scientific literature understanding benchmarks. Our contributions are threefold: (1) We present an effective framework that integrates CPT and SFT to adapt LLMs to scientific literature understanding, which can also be easily adapted to other domains. (2) We propose an LLM-based synthesis method to generate diverse and high-quality scientific instructions, resulting in a new instruction set -- SciLitIns -- for supervised fine-tuning in less-represented scientific domains. (3) SciLitLLM achieves promising performance improvements on scientific literature understanding benchmarks.

cs.LG↗

arXiv2025

Auto-resolving the atomic structure at van der Waals interfaces using a generative model

The high-resolution visualization of atomic structures is significant for understanding the relationship between the microscopic configurations and macroscopic properties of materials. However, a rapid, accurate, and robust approach to automatically resolve complex patterns in atomic-resolution microscopy remains difficult to implement. Here, we present a Trident strategy-enhanced disentangled representation learning method (a generative model), which utilizes a few unlabelled experimental images with abundant low-cost simulated images to generate a large corpus of annotated simulation data that closely resembles experimental results, producing a high-quality large-volume training dataset. A structural inference model is then trained via a residual neural network which can directly deduce the interlayer slip and rotation of diversified and complicated stacking patterns at van der Waals interfaces with picometer-scale accuracy across various materials (e.g. MoS2, WS2, ReS2, ReSe2, and 1T'-MoTe2) with different layer numbers , demonstrating robustness to defects, imaging quality, and surface contaminations. The framework can also identify pattern transition interfaces, quantify subtle motif variations, and discriminate moire patterns that are difficult to distinguish in frequency domains. Finally, the high-throughput processing ability of our method provides insights into a van der Waals epitaxy mode where various thermodynamically favorable slip stackings can coexist.

cond-mat.mtrl-sci↗

arXiv2025

LEGION: Learning to Ground and Explain for Synthetic Image Detection

The rapid advancements in generative technology have emerged as a double-edged sword. While offering powerful tools that enhance convenience, they also pose significant social concerns. As defenders, current synthetic image detection methods often lack artifact-level textual interpretability and are overly focused on image manipulation detection, and current datasets usually suffer from outdated generators and a lack of fine-grained annotations. In this paper, we introduce SynthScars, a high-quality and diverse dataset consisting of 12,236 fully synthetic images with human-expert annotations. It features 4 distinct image content types, 3 categories of artifacts, and fine-grained annotations covering pixel-level segmentation, detailed textual explanations, and artifact category labels. Furthermore, we propose LEGION (LEarning to Ground and explain for Synthetic Image detectiON), a multimodal large language model (MLLM)-based image forgery analysis framework that integrates artifact detection, segmentation, and explanation. Building upon this capability, we further explore LEGION as a controller, integrating it into image refinement pipelines to guide the generation of higher-quality and more realistic images. Extensive experiments show that LEGION outperforms existing methods across multiple benchmarks, particularly surpassing the second-best traditional expert on SynthScars by 3.31% in mIoU and 7.75% in F1 score. Moreover, the refined images generated under its guidance exhibit stronger alignment with human preferences. The code, model, and dataset will be released.

cs.CV↗

arXiv2025

Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling

Molecular pretrained representations (MPR) has emerged as a powerful approach for addressing the challenge of limited supervised data in applications such as drug discovery and material design. While early MPR methods relied on 1D sequences and 2D graphs, recent advancements have incorporated 3D conformational information to capture rich atomic interactions. However, these prior models treat molecules merely as discrete atom sets, overlooking the space surrounding them. We argue from a physical perspective that only modeling these discrete points is insufficient. We first present a simple yet insightful observation: naively adding randomly sampled virtual points beyond atoms can surprisingly enhance MPR performance. In light of this, we propose a principled framework that incorporates the entire 3D space spanned by molecules. We implement the framework via a novel Transformer-based architecture, dubbed SpaceFormer, with three key components: (1) grid-based space discretization; (2) grid sampling/merging; and (3) efficient 3D positional encoding. Extensive experiments show that SpaceFormer significantly outperforms previous 3D MPR models across various downstream tasks with limited data, validating the benefit of leveraging the additional 3D space beyond atoms in MPR models.

q-bio.BM↗

arXiv2025

LazyMAR: Accelerating Masked Autoregressive Models via Feature Caching

Masked Autoregressive (MAR) models have emerged as a promising approach in image generation, expected to surpass traditional autoregressive models in computational efficiency by leveraging the capability of parallel decoding. However, their dependence on bidirectional self-attention inherently conflicts with conventional KV caching mechanisms, creating unexpected computational bottlenecks that undermine their expected efficiency. To address this problem, this paper studies the caching mechanism for MAR by leveraging two types of redundancy: Token Redundancy indicates that a large portion of tokens have very similar representations in the adjacent decoding steps, which allows us to first cache them in previous steps and then reuse them in the later steps. Condition Redundancy indicates that the difference between conditional and unconditional output in classifier-free guidance exhibits very similar values in adjacent steps. Based on these two redundancies, we propose LazyMAR, which introduces two caching mechanisms to handle them one by one. LazyMAR is training-free and plug-and-play for all MAR models. Experimental results demonstrate that our method achieves 2.83 times acceleration with almost no drop in generation quality. Our codes will be released in https://github.com/feihongyan1/LazyMAR.

cs.CV↗

arXiv2025

Decouple-Then-Merge: Finetune Diffusion Models as Multi-Task Learning

Diffusion models are trained by learning a sequence of models that reverse each step of noise corruption. Typically, the model parameters are fully shared across multiple timesteps to enhance training efficiency. However, since the denoising tasks differ at each timestep, the gradients computed at different timesteps may conflict, potentially degrading the overall performance of image generation. To solve this issue, this work proposes a \textbf{De}couple-then-\textbf{Me}rge (\textbf{DeMe}) framework, which begins with a pretrained model and finetunes separate models tailored to specific timesteps. We introduce several improved techniques during the finetuning stage to promote effective knowledge sharing while minimizing training interference across timesteps. Finally, after finetuning, these separate models can be merged into a single model in the parameter space, ensuring efficient and practical inference. Experimental results show significant generation quality improvements upon 6 benchmarks including Stable Diffusion on COCO30K, ImageNet1K, PartiPrompts, and DDPM on LSUN Church, LSUN Bedroom, and CIFAR10. Code is available at \href{https://github.com/MqLeet/DeMe}{GitHub}.

cs.CV↗

arXiv2025

ProReflow: Progressive Reflow with Decomposed Velocity

Diffusion models have achieved significant progress in both image and video generation while still suffering from huge computation costs. As an effective solution, flow matching aims to reflow the diffusion process of diffusion models into a straight line for a few-step and even one-step generation. However, in this paper, we suggest that the original training pipeline of flow matching is not optimal and introduce two techniques to improve it. Firstly, we introduce progressive reflow, which progressively reflows the diffusion models in local timesteps until the whole diffusion progresses, reducing the difficulty of flow matching. Second, we introduce aligned v-prediction, which highlights the importance of direction matching in flow matching over magnitude matching. Experimental results on SDv1.5 and SDXL demonstrate the effectiveness of our method, for example, conducting on SDv1.5 achieves an FID of 10.70 on MSCOCO2014 validation set with only 4 sampling steps, close to our teacher model (32 DDIM steps, FID = 10.05).

cs.GR↗

arXiv2025

Dataset Distillation with Neural Characteristic Function: A Minmax Perspective

Dataset distillation has emerged as a powerful approach for reducing data requirements in deep learning. Among various methods, distribution matching-based approaches stand out for their balance of computational efficiency and strong performance. However, existing distance metrics used in distribution matching often fail to accurately capture distributional differences, leading to unreliable measures of discrepancy. In this paper, we reformulate dataset distillation as a minmax optimization problem and introduce Neural Characteristic Function Discrepancy (NCFD), a comprehensive and theoretically grounded metric for measuring distributional differences. NCFD leverages the Characteristic Function (CF) to encapsulate full distributional information, employing a neural network to optimize the sampling strategy for the CF's frequency arguments, thereby maximizing the discrepancy to enhance distance estimation. Simultaneously, we minimize the difference between real and synthetic data under this optimized NCFD measure. Our approach, termed Neural Characteristic Function Matching (\mymethod{}), inherently aligns the phase and amplitude of neural features in the complex plane for both real and synthetic data, achieving a balance between realism and diversity in synthetic samples. Experiments demonstrate that our method achieves significant performance gains over state-of-the-art methods on both low- and high-resolution datasets. Notably, we achieve a 20.5\% accuracy boost on ImageSquawk. Our method also reduces GPU memory usage by over 300$\times$ and achieves 20$\times$ faster processing speeds compared to state-of-the-art methods. To the best of our knowledge, this is the first work to achieve lossless compression of CIFAR-100 on a single NVIDIA 2080 Ti GPU using only 2.3 GB of memory.

cs.CV↗

arXiv2025

DeePMD-kit v3: A Multiple-Backend Framework for Machine Learning Potentials

In recent years, machine learning potentials (MLPs) have become indispensable tools in physics, chemistry, and materials science, driving the development of software packages for molecular dynamics (MD) simulations and related applications. These packages, typically built on specific machine learning frameworks such as TensorFlow, PyTorch, or JAX, face integration challenges when advanced applications demand communication across different frameworks. The previous TensorFlow-based implementation of DeePMD-kit exemplified these limitations. In this work, we introduce DeePMD-kit version 3, a significant update featuring a multi-backend framework that supports TensorFlow, PyTorch, JAX, and PaddlePaddle backends, and demonstrate the versatility of this architecture through the integration of other MLPs packages and of Differentiable Molecular Force Field. This architecture allows seamless backend switching with minimal modifications, enabling users and developers to integrate DeePMD-kit with other packages using different machine learning frameworks. This innovation facilitates the development of more complex and interoperable workflows, paving the way for broader applications of MLPs in scientific research.

physics.chem-ph↗

arXiv2025

Gnothi Seauton: Empowering Faithful Self-Interpretability in Black-Box Transformers

The debate between self-interpretable models and post-hoc explanations for black-box models is central to Explainable AI (XAI). Self-interpretable models, such as concept-based networks, offer insights by connecting decisions to human-understandable concepts but often struggle with performance and scalability. Conversely, post-hoc methods like Shapley values, while theoretically robust, are computationally expensive and resource-intensive. To bridge the gap between these two lines of research, we propose a novel method that combines their strengths, providing theoretically guaranteed self-interpretability for black-box models without compromising prediction accuracy. Specifically, we introduce a parameter-efficient pipeline, AutoGnothi, which integrates a small side network into the black-box model, allowing it to generate Shapley value explanations without changing the original network parameters. This side-tuning approach significantly reduces memory, training, and inference costs, outperforming traditional parameter-efficient methods, where full fine-tuning serves as the optimal baseline. AutoGnothi enables the black-box model to predict and explain its predictions with minimal overhead. Extensive experiments show that AutoGnothi offers accurate explanations for both vision and language tasks, delivering superior computational efficiency with comparable interpretability.

cs.LG↗

arXiv2025

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis; improving peptide and protein identification and quantification; characterizing protein-protein interactions and protein complexes; advancing spatial and perturbation proteomics; integrating multi-omics data; and ultimately enabling AI-empowered virtual cells.

q-bio.OT↗

arXiv2025

Accelerating Diffusion Transformers with Token-wise Feature Caching

Diffusion transformers have shown significant effectiveness in both image and video synthesis at the expense of huge computation costs. To address this problem, feature caching methods have been introduced to accelerate diffusion transformers by caching the features in previous timesteps and reusing them in the following timesteps. However, previous caching methods ignore that different tokens exhibit different sensitivities to feature caching, and feature caching on some tokens may lead to 10$\times$ more destruction to the overall generation quality compared with other tokens. In this paper, we introduce token-wise feature caching, allowing us to adaptively select the most suitable tokens for caching, and further enable us to apply different caching ratios to neural layers in different types and depths. Extensive experiments on PixArt-$α$, OpenSora, and DiT demonstrate our effectiveness in both image and video generation with no requirements for training. For instance, 2.36$\times$ and 1.93$\times$ acceleration are achieved on OpenSora and PixArt-$α$ with almost no drop in generation quality.

cs.LG↗

arXiv2025

Learning local equivariant representations for quantum operators

Predicting quantum operator matrices such as Hamiltonian, overlap, and density matrices in the density functional theory (DFT) framework is crucial for material science. Current methods often focus on individual operators and struggle with efficiency and scalability for large systems. Here we introduce a novel deep learning model, SLEM (strictly localized equivariant message-passing) for predicting multiple quantum operators, that achieves state-of-the-art accuracy while dramatically improving computational efficiency. SLEM's key innovation is its strict locality-based design for equivariant representations of quantum tensors while preserving physical symmetries. This enables complex many-body dependency without expanding the effective receptive field, leading to superior data efficiency and transferability. Using an innovative SO(2) convolution and invariant overlap parameterization, SLEM reduces the computational complexity of high-order tensor products and is therefore capable of handling systems requiring the $f$ and $g$ orbitals in their basis sets. We demonstrate SLEM's capabilities across diverse 2D and 3D materials, achieving high accuracy even with limited training data. SLEM's design facilitates efficient parallelization, potentially extending DFT simulations to systems with device-level sizes, opening new possibilities for large-scale quantum simulations and high-throughput materials discovery.

cond-mat.mtrl-sci↗

arXiv2025

The OpenLAM Challenges

Inspired by the success of Large Language Models (LLMs), the development of Large Atom Models (LAMs) has gained significant momentum in scientific computation. Since 2022, the Deep Potential team has been actively pretraining LAMs and launched the OpenLAM Initiative to develop an open-source foundation model spanning the periodic table. A core objective is establishing comprehensive benchmarks for reliable LAM evaluation, addressing limitations in existing datasets. As a first step, the LAM Crystal Philately competition has collected over 19.8 million valid structures, including 1 million on the OpenLAM convex hull, driving advancements in generative modeling and materials science applications.

cs.LG↗

arXiv2025

Intelligent System for Automated Molecular Patent Infringement Assessment

Automated drug discovery offers significant potential for accelerating the development of novel therapeutics by substituting labor-intensive human workflows with machine-driven processes. However, molecules generated by artificial intelligence may unintentionally infringe on existing patents, posing legal and financial risks that impede the full automation of drug discovery pipelines. This paper introduces PatentFinder, a novel multi-agent and tool-enhanced intelligence system that can accurately and comprehensively evaluate small molecules for patent infringement. PatentFinder features five specialized agents that collaboratively analyze patent claims and molecular structures with heuristic and model-based tools, generating interpretable infringement reports. To support systematic evaluation, we curate MolPatent-240, a benchmark dataset tailored for patent infringement assessment algorithms. On this benchmark, PatentFinder outperforms baseline methods that rely solely on large language models or specialized chemical tools, achieving a 13.8% improvement in F1-score and a 12% increase in accuracy. Additionally, PatentFinder autonomously generates detailed and interpretable patent infringement reports, showcasing enhanced accuracy and improved interpretability. The high accuracy and interpretability of PatentFinder make it a valuable and reliable tool for automating patent infringement assessments, offering a practical solution for integrating patent protection analysis into the drug discovery pipeline.

cs.LG↗

arXiv2025

Cyber Risk Assessment for Capital Management

This paper introduces a two-pillar cyber risk management framework to address the pervasive challenges in managing cyber risk. The first pillar, cyber risk assessment, combines insurance frequency-severity models with cybersecurity cascade models to capture the unique nature of cyber risk. The second pillar, cyber capital management, facilitates informed allocation of capital for a balanced cyber risk management strategy, including cybersecurity investments, insurance coverage, and reserves. A case study, based on historical cyber incident data and realistic assumptions, demonstrates the necessity of comprehensive cost-benefit analysis for budget-constrained companies with competing objectives in cyber risk management. In addition, sensitivity analysis highlights the dependence of the optimal strategy on factors such as the price of cybersecurity controls and their effectiveness. The framework's implementation across a diverse range of companies yields general insights on cyber risk management.

q-fin.RM↗

arXiv2024

Token Pruning for Caching Better: 9 Times Acceleration on Stable Diffusion for Free

Stable Diffusion has achieved remarkable success in the field of text-to-image generation, with its powerful generative capabilities and diverse generation results making a lasting impact. However, its iterative denoising introduces high computational costs and slows generation speed, limiting broader adoption. The community has made numerous efforts to reduce this computational burden, with methods like feature caching attracting attention due to their effectiveness and simplicity. Nonetheless, simply reusing features computed at previous timesteps causes the features across adjacent timesteps to become similar, reducing the dynamics of features over time and ultimately compromising the quality of generated images. In this paper, we introduce a dynamics-aware token pruning (DaTo) approach that addresses the limitations of feature caching. DaTo selectively prunes tokens with lower dynamics, allowing only high-dynamic tokens to participate in self-attention layers, thereby extending feature dynamics across timesteps. DaTo combines feature caching with token pruning in a training-free manner, achieving both temporal and token-wise information reuse. Applied to Stable Diffusion on the ImageNet, our approach delivered a 9$\times$ speedup while reducing FID by 0.33, indicating enhanced image quality. On the COCO-30k, we observed a 7$\times$ acceleration coupled with a notable FID reduction of 2.17.

cs.CV↗

arXiv2024

SAVEn-Vid: Synergistic Audio-Visual Integration for Enhanced Understanding in Long Video Context

Endeavors have been made to explore Large Language Models for video analysis (Video-LLMs), particularly in understanding and interpreting long videos. However, existing Video-LLMs still face challenges in effectively integrating the rich and diverse audio-visual information inherent in long videos, which is crucial for comprehensive understanding. This raises the question: how can we leverage embedded audio-visual information to enhance long video understanding? Therefore, (i) we introduce SAVEn-Vid, the first-ever long audio-visual video dataset comprising over 58k audio-visual instructions. (ii) From the model perspective, we propose a time-aware Audio-Visual Large Language Model (AV-LLM), SAVEnVideo, fine-tuned on SAVEn-Vid. (iii) Besides, we present AVBench, a benchmark containing 2,500 QAs designed to evaluate models on enhanced audio-visual comprehension tasks within long video, challenging their ability to handle intricate audio-visual interactions. Experiments on AVBench reveal the limitations of current AV-LLMs. Experiments also demonstrate that SAVEnVideo outperforms the best Video-LLM by 3.61% on the zero-shot long video task (Video-MME) and surpasses the leading audio-visual LLM by 1.29% on the zero-shot audio-visual task (Music-AVQA). Consequently, at the 7B parameter scale, SAVEnVideo can achieve state-of-the-art performance. Our dataset and code will be released at https://ljungang.github.io/SAVEn-Vid/ upon acceptance.

cs.CV↗