arXiv subjects

Lin Yang

Publications and source records attributed to Lin Yang.

At least 127 records · Page 7Linked to original sources

arXiv2024

PathMMU: A Massive Multimodal Expert-Level Benchmark for Understanding and Reasoning in Pathology

The emergence of large multimodal models has unlocked remarkable potential in AI, particularly in pathology. However, the lack of specialized, high-quality benchmark impeded their development and precise evaluation. To address this, we introduce PathMMU, the largest and highest-quality expert-validated pathology benchmark for Large Multimodal Models (LMMs). It comprises 33,428 multimodal multi-choice questions and 24,067 images from various sources, each accompanied by an explanation for the correct answer. The construction of PathMMU harnesses GPT-4V's advanced capabilities, utilizing over 30,000 image-caption pairs to enrich captions and generate corresponding Q&As in a cascading process. Significantly, to maximize PathMMU's authority, we invite seven pathologists to scrutinize each question under strict standards in PathMMU's validation and test sets, while simultaneously setting an expert-level performance benchmark for PathMMU. We conduct extensive evaluations, including zero-shot assessments of 14 open-sourced and 4 closed-sourced LMMs and their robustness to image corruption. We also fine-tune representative LMMs to assess their adaptability to PathMMU. The empirical findings indicate that advanced LMMs struggle with the challenging PathMMU benchmark, with the top-performing LMM, GPT-4V, achieving only a 49.8% zero-shot performance, significantly lower than the 71.8% demonstrated by human pathologists. After fine-tuning, significantly smaller open-sourced LMMs can outperform GPT-4V but still fall short of the expertise shown by pathologists. We hope that the PathMMU will offer valuable insights and foster the development of more specialized, next-generation LMMs for pathology.

cs.CV↗

arXiv2024

Mixed-halide perovskite alloys $\text{CsPb}(\text{I}_{1-x}^{}\text{Br}_x^{})_3^{}$ and $\text{CsPb}(\text{Br}_{1-x}^{}\text{Cl}_x^{})_3^{}$: New insight of configuration entropy effect from first principles and phase diagrams

Stability is one of the key issues in mixed-halide perovskite alloys which are promising in emergent optoelectronics. Previous density-functional-theory (DFT) and machine learning studies indicate that the formation-energy convex hulls of these materials are very shallow, and stable alloy compositions are rare. In this work, we revisit this problem using DFT with special focus on the effects of configuration and vibration entropies. Allowed by the $20$-atomic models for the $\text{CsPb}(\text{I}_{1-x}^{}\text{Br}_x^{})_3^{}$ and $\text{CsPb}(\text{Br}_{1-x}^{}\text{Cl}_x^{})_3^{}$ series, the partition functions and therewith thermodynamic state functions are calculated by traversing all possible mixed-halide configurations. We can thus evaluate the temperature- and system-dependent configuration entropy, which largely corrects the conventional approach based on the ideal solution model. Finally, temperature-composition phase diagrams that include $α$, $β$, $γ$ and $δ$ phases of both alloys are constructed based on the free energy data, for which the contribution of phonon vibrations is included.

cond-mat.mtrl-sci↗

arXiv2024

Tunable topological phases in nanographene-based spin-1/2 alternating-exchange Heisenberg chains

Unlocking the potential of topological order within many-body spin systems has long been a central pursuit in the realm of quantum materials. Despite extensive efforts, the quest for a versatile platform enabling site-selective spin manipulation, essential for tuning and probing diverse topological phases, has persisted. Here, we utilize on-surface synthesis to construct spin-1/2 alternating-exchange Heisenberg (AH) chains[1] with antiferromagnetic couplings $J_1$ and $J_2$ by covalently linking Clar's goblets -- nanographenes each hosting two antiferromagnetically-coupled unpaired electrons[2]. Utilizing scanning tunneling microscopy, we exert atomic-scale control over the spin chain lengths, parities and exchange-coupling terminations, and probe their magnetic response by means of inelastic tunneling spectroscopy. Our investigation confirms the gapped nature of bulk excitations in the chains, known as triplons[3]. Besides, the triplon dispersion relation is successfully extracted from the spatial variation of tunneling spectral amplitudes. Furthermore, depending on the parity and termination of chains, we observe varying numbers of in-gap $S=1/2$ edge spins, enabling the determination of the degeneracy of distinct topological ground states in the thermodynamic limit-either 1, 2, or 4. By monitoring interactions between these edge spins, we identify the exponential decay of spin correlations. Our experimental findings, corroborated by theoretical calculations, present a phase-controlled many-body platform, opening promising avenues toward the development of spin-based quantum devices.

cond-mat.mtrl-sci↗

arXiv2024

PathAsst: A Generative Foundation AI Assistant Towards Artificial General Intelligence of Pathology

As advances in large language models (LLMs) and multimodal techniques continue to mature, the development of general-purpose multimodal large language models (MLLMs) has surged, offering significant applications in interpreting natural images. However, the field of pathology has largely remained untapped, particularly in gathering high-quality data and designing comprehensive model frameworks. To bridge the gap in pathology MLLMs, we present PathAsst, a multimodal generative foundation AI assistant to revolutionize diagnostic and predictive analytics in pathology. The development of PathAsst involves three pivotal steps: data acquisition, CLIP model adaptation, and the training of PathAsst's multimodal generative capabilities. Firstly, we collect over 207K high-quality pathology image-text pairs from authoritative sources. Leveraging the advanced power of ChatGPT, we generate over 180K instruction-following samples. Furthermore, we devise additional instruction-following data specifically tailored for invoking eight pathology-specific sub-models we prepared, allowing the PathAsst to effectively collaborate with these models, enhancing its diagnostic ability. Secondly, by leveraging the collected data, we construct PathCLIP, a pathology-dedicated CLIP, to enhance PathAsst's capabilities in interpreting pathology images. Finally, we integrate PathCLIP with the Vicuna-13b and utilize pathology-specific instruction-tuning data to enhance the multimodal generation capacity of PathAsst and bolster its synergistic interactions with sub-models. The experimental results of PathAsst show the potential of harnessing AI-powered generative foundation model to improve pathology diagnosis and treatment processes.

cs.CV↗

arXiv2024

Try with Simpler -- An Evaluation of Improved Principal Component Analysis in Log-based Anomaly Detection

The rapid growth of deep learning (DL) has spurred interest in enhancing log-based anomaly detection. This approach aims to extract meaning from log events (log message templates) and develop advanced DL models for anomaly detection. However, these DL methods face challenges like heavy reliance on training data, labels, and computational resources due to model complexity. In contrast, traditional machine learning and data mining techniques are less data-dependent and more efficient but less effective than DL. To make log-based anomaly detection more practical, the goal is to enhance traditional techniques to match DL's effectiveness. Previous research in a different domain (linking questions on Stack Overflow) suggests that optimized traditional techniques can rival state-of-the-art DL methods. Drawing inspiration from this concept, we conducted an empirical study. We optimized the unsupervised PCA (Principal Component Analysis), a traditional technique, by incorporating lightweight semantic-based log representation. This addresses the issue of unseen log events in training data, enhancing log representation. Our study compared seven log-based anomaly detection methods, including four DL-based, two traditional, and the optimized PCA technique, using public and industrial datasets. Results indicate that the optimized unsupervised PCA technique achieves similar effectiveness to advanced supervised/semi-supervised DL methods while being more stable with limited training data and resource-efficient. This demonstrates the adaptability and strength of traditional techniques through small yet impactful adaptations.

cs.LG↗

arXiv2024

Unleashing the Power of Prompt-driven Nucleus Instance Segmentation

Nucleus instance segmentation in histology images is crucial for a broad spectrum of clinical applications. Current dominant algorithms rely on regression of nuclear proxy maps. Distinguishing nucleus instances from the estimated maps requires carefully curated post-processing, which is error-prone and parameter-sensitive. Recently, the Segment Anything Model (SAM) has earned huge attention in medical image segmentation, owing to its impressive generalization ability and promptable property. Nevertheless, its potential on nucleus instance segmentation remains largely underexplored. In this paper, we present a novel prompt-driven framework that consists of a nucleus prompter and SAM for automatic nucleus instance segmentation. Specifically, the prompter learns to generate a unique point prompt for each nucleus while the SAM is fine-tuned to output the corresponding mask for the prompted nucleus. Furthermore, we propose the inclusion of adjacent nuclei as negative prompts to enhance the model's capability to identify overlapping nuclei. Without complicated post-processing, our proposed method sets a new state-of-the-art performance on three challenging benchmarks. Code is available at \url{github.com/windygoo/PromptNucSeg}

cs.CV↗

arXiv2024

A star-based method for precise flux calibration of the Chinese Space Station Telescope (CSST) slitless spectroscopic survey

The upcoming Chinese Space Station Telescope (CSST) slitless spectroscopic survey poses a challenge of flux calibration, which requires a large number of flux-standard stars. In this work, we design an uncertainty-aware residual attention network, the UaRA-net, to derive the CSST SEDs with a resolution of R = 200 over the wavelength range of 2500-10000 Åusing LAMOST normalized spectra with a resolution of R = 2000 over the wavelength range of 4000-7000 Å. With the special structure and training strategy, the proposed model can not only provide accurate predictions of SEDs but also their corresponding errors. The precision of the predicted SEDs depends on effective temperature (Teff), wavelength, and the LAMOST spectral signal-to-noise ratios (SNRs), particularly in the GU band. For stars with Teff = 6000 K, the typical SED precisions in the GU band are 4.2%, 2.1%, and 1.5% at SNR values of 20, 40, and 80, respectively. As Teff increases to 8000 K, the precision increases to 1.2%, 0.6%, and 0.5%, respectively. The precision is higher at redder wavelengths. In the GI band, the typical SED precisions for stars with Teff = 6000 K increase to 0.3%, 0.1%, and 0.1% at SNR values of 20, 40, and 80, respectively. We further verify our model using the empirical spectra of the MILES and find good performance. The proposed method will open up new possibilities for optimal utilization of slitless spectra of the CSST and other surveys.

astro-ph.IM↗

arXiv2024

A comprehensive correction of the Gaia DR3 XP spectra

By combining spectra from the CALSPEC and NGSL, as well as spectroscopic data from the LAMOST Data Release 7 (DR7), we have analyzed and corrected the systematic errors of the Gaia DR3 BP/RP (XP) spectra. The errors depend on the normalized spectral energy distribution (simplified by two independent ``colors'') and $G$ magnitude. Our corrections are applicable in the range of approximately $-0.5<BP-RP<2$, $3<G<17.5$ and $E(B-V)<0.8$. To validate our correction, we conduct independent tests by comparing with the MILES and LEMONY spectra. The results demonstrate that the systematic errors of $BP-RP$ and $G$ have been effectively corrected, especially in the near ultraviolet. The consistency between the corrected Gaia XP spectra and the MILES and LEMONY is better than 2 per cent in the wavelength range of $336-400$\,nm and 1 per cent in redder wavelengths. A global absolute calibration is also carried out by comparing the synthetic Gaia photometry from the corrected XP spectra with the corrected Gaia DR3 photometry. Our study opens up new possibilities for using XP spectra in many fields. A Python package is publicly available to do the corrections (https://doi.org/10.12149/101375 or https://github.com/HiromonGON/GaiaXPcorrection).

astro-ph.IM↗

arXiv2024

On the Model-Misspecification in Reinforcement Learning

The success of reinforcement learning (RL) crucially depends on effective function approximation when dealing with complex ground-truth models. Existing sample-efficient RL algorithms primarily employ three approaches to function approximation: policy-based, value-based, and model-based methods. However, in the face of model misspecification (a disparity between the ground-truth and optimal function approximators), it is shown that policy-based approaches can be robust even when the policy function approximation is under a large locally-bounded misspecification error, with which the function class may exhibit a $Ω(1)$ approximation error in specific states and actions, but remains small on average within a policy-induced state distribution. Yet it remains an open question whether similar robustness can be achieved with value-based and model-based approaches, especially with general function approximation. To bridge this gap, in this paper we present a unified theoretical framework for addressing model misspecification in RL. We demonstrate that, through meticulous algorithm design and sophisticated analysis, value-based and model-based methods employing general function approximation can achieve robustness under local misspecification error bounds. In particular, they can attain a regret bound of $\widetilde{O}\left(\text{poly}(d H)(\sqrt{K} + Kζ) \right)$, where $d$ represents the complexity of the function class, $H$ is the episode length, $K$ is the total number of episodes, and $ζ$ denotes the local bound for misspecification error. Furthermore, we propose an algorithmic framework that can achieve the same order of regret bound without prior knowledge of $ζ$, thereby enhancing its practical applicability.

cs.LG↗

arXiv2024

Multi-modal Learning with Missing Modality in Predicting Axillary Lymph Node Metastasis

Multi-modal Learning has attracted widespread attention in medical image analysis. Using multi-modal data, whole slide images (WSIs) and clinical information, can improve the performance of deep learning models in the diagnosis of axillary lymph node metastasis. However, clinical information is not easy to collect in clinical practice due to privacy concerns, limited resources, lack of interoperability, etc. Although patient selection can ensure the training set to have multi-modal data for model development, missing modality of clinical information can appear during test. This normally leads to performance degradation, which limits the use of multi-modal models in the clinic. To alleviate this problem, we propose a bidirectional distillation framework consisting of a multi-modal branch and a single-modal branch. The single-modal branch acquires the complete multi-modal knowledge from the multi-modal branch, while the multi-modal learns the robust features of WSI from the single-modal. We conduct experiments on a public dataset of Lymph Node Metastasis in Early Breast Cancer to validate the method. Our approach not only achieves state-of-the-art performance with an AUC of 0.861 on the test set without missing data, but also yields an AUC of 0.842 when the rate of missing modality is 80\%. This shows the effectiveness of the approach in dealing with multi-modal data and missing modality. Such a model has the potential to improve treatment decision-making for early breast cancer patients who have axillary lymph node metastatic status.

eess.IV↗

arXiv2023

Ultra-broadband and compact 2$\times$2 3-dB silicon adiabatic coupler based on supermode-injected adjoint shape optimization

The 2$\times$2 3-dB couplers are one of the most widely used and important components in silicon photonics. We propose an ultra-broadband and compact 2$\times$2 3-dB adiabatic coupler defined by b-splines and optimized with an efficient supermode-injected adjoint shape optimization. By employing mode adiabatic evolution and mode coupling at two different wavelength ranges, respectively, we achieve an ultra-broad bandwidth of 530 nm from 1150nm to1680nm with a power imbalance below $\pm$0.76 dB in a compact coupling length of 30 $μm$ according to our simulation results. The supermode-injected adjoint shape optimization can also be applied to the design of other photonic devices based on supermode manipulation.

physics.optics↗

arXiv2023

Long-MIL: Scaling Long Contextual Multiple Instance Learning for Histopathology Whole Slide Image Analysis

Histopathology image analysis is the golden standard of clinical diagnosis for Cancers. In doctors daily routine and computer-aided diagnosis, the Whole Slide Image (WSI) of histopathology tissue is used for analysis. Because of the extremely large scale of resolution, previous methods generally divide the WSI into a large number of patches, then aggregate all patches within a WSI by Multi-Instance Learning (MIL) to make the slide-level prediction when developing computer-aided diagnosis tools. However, most previous WSI-MIL models using global-attention without pairwise interaction and any positional information, or self-attention with absolute position embedding can not well handle shape varying large WSIs, e.g. testing WSIs after model deployment may be larger than training WSIs, since the model development set is always limited due to the difficulty of histopathology WSIs collection. To deal with the problem, in this paper, we propose to amend position embedding for shape varying long-contextual WSI by introducing Linear Bias into Attention, and adapt it from 1-d long sequence into 2-d long-contextual WSI which helps model extrapolate position embedding to unseen or under-fitted positions. We further utilize Flash-Attention module to tackle the computational complexity of Transformer, which also keep full self-attention performance compared to previous attention approximation work. Our method, Long-contextual MIL (Long-MIL) are evaluated on extensive experiments including 4 dataset including WSI classification and survival prediction tasks to validate the superiority on shape varying WSIs. The source code will be open-accessed soon.

cs.CV↗

arXiv2023

Test-Time Training for Semantic Segmentation with Output Contrastive Loss

Although deep learning-based segmentation models have achieved impressive performance on public benchmarks, generalizing well to unseen environments remains a major challenge. To improve the model's generalization ability to the new domain during evaluation, the test-time training (TTT) is a challenging paradigm that adapts the source-pretrained model in an online fashion. Early efforts on TTT mainly focus on the image classification task. Directly extending these methods to semantic segmentation easily experiences unstable adaption due to segmentation's inherent characteristics, such as extreme class imbalance and complex decision spaces. To stabilize the adaptation process, we introduce contrastive loss (CL), known for its capability to learn robust and generalized representations. Nevertheless, the traditional CL operates in the representation space and cannot directly enhance predictions. In this paper, we resolve this limitation by adapting the CL to the output space, employing a high temperature, and simplifying the formulation, resulting in a straightforward yet effective loss function called Output Contrastive Loss (OCL). Our comprehensive experiments validate the efficacy of our approach across diverse evaluation scenarios. Notably, our method excels even when applied to models initially pre-trained using domain adaptation methods on test domain data, showcasing its resilience and adaptability.\footnote{Code and more information could be found at~ \url{https://github.com/dazhangyu123/OCL}}

cs.CV↗

arXiv2023

Efficient Robust Bayesian Optimization for Arbitrary Uncertain Inputs

Bayesian Optimization (BO) is a sample-efficient optimization algorithm widely employed across various applications. In some challenging BO tasks, input uncertainty arises due to the inevitable randomness in the optimization process, such as machining errors, execution noise, or contextual variability. This uncertainty deviates the input from the intended value before evaluation, resulting in significant performance fluctuations in the final result. In this paper, we introduce a novel robust Bayesian Optimization algorithm, AIRBO, which can effectively identify a robust optimum that performs consistently well under arbitrary input uncertainty. Our method directly models the uncertain inputs of arbitrary distributions by empowering the Gaussian Process with the Maximum Mean Discrepancy (MMD) and further accelerates the posterior inference via Nystrom approximation. Rigorous theoretical regret bound is established under MMD estimation error and extensive experiments on synthetic functions and real problems demonstrate that our approach can handle various input uncertainties and achieve state-of-the-art performance.

cs.LG↗

arXiv2023

J-PLUS: Photometric Re-calibration with the Stellar Color Regression Method and an Improved Gaia XP Synthetic Photometry Method

We employ the corrected Gaia Early Data Release 3 (EDR3) photometric data and spectroscopic data from the Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) DR7 to assemble a sample of approximately 0.25 million FGK dwarf photometric standard stars for the 12 J-PLUS filters using the Stellar Color Regression (SCR) method. We then independently validated the J-PLUS DR3 photometry, and uncovered significant systematic errors: up to 15 mmag in the results of Stellar Locus (SL) method, and up to 10 mmag mainly caused by magnitude-, color-, and extinction-dependent errors of the Gaia XP spectra with the Gaia BP/RP (XP) Synthetic Photometry (XPSP) method. We have also further developed the XPSP method using the corrected Gaia XP spectra by Huang et al. (2023) and applied it to the J-PLUS DR3 photometry. This resulted in an agreement of 1-5 mmag with the SCR method, and a two-fold improvement in the J-PLUS zero-point precision. Finally, the zero-point calibration for around 91% of the tiles within the LAMOST observation footprint is determined through the SCR method, with the remaining approximately 9% of tiles outside this footprint relying on the improved XPSP method. The re-calibrated J-PLUS DR3 photometric data establishes a solid data foundation for conducting research that depends on high-precision photometric calibration.

astro-ph.SR↗

arXiv2023

Review on Decarbonizing the Transportation Sector in China: Overview, Analysis, and Perspectives

This review identifies challenges and effective strategies to decarbonize China's rapidly growing transportation sector, currently the third largest carbon emitter, considering China's commitment to peak carbon emissions by 2030 and achieve carbon neutrality by 2060. Key challenges include rising travel demand, unreached peak car ownership, declining bus ridership, gaps between energy technology research and practical application, and limited institutional capacity for decarbonization. This review categorizes current decarbonization measures, strategies, and policies in China's transportation sector using the "Avoid, Shift, Improve" framework, complemented by a novel strategic vector of "Institutional Capacity & Technology Development" to capture broader development perspectives. This comprehensive analysis aims to facilitate informed decision-making and promote collaborative strategies for China's transition to a sustainable transportation future.

econ.GN↗

arXiv2023

S-PLUS: Photometric Re-calibration with the Stellar Color Regression Method and an Improved Gaia XP Synthetic Photometry Method

We present a comprehensive re-calibration of medium- and broad-band photometry from the Southern Photometric Local Universe Survey (S-PLUS) by leveraging two approaches: an improved Gaia XP Synthetic Photometry (XPSP) method with corrected Gaia XP spectra, the Stellar Color Regression (SCR) method with corrected Gaia EDR3 photometric data and spectroscopic data from LAMOST DR7. Through the use of millions of stars as standards per band, we demonstrate the existence of position-dependent systematic errors, up to 23 mmag for the Main Survey region, in the S-PLUS DR4 photometric data. A comparison between the XPSP and SCR methods reveals minor differences in zero-point offsets, typically within the range of 1 to 6 mmag, indicating the accuracy of the re-calibration, and a two- to three-fold improvement in the zero-point precision. During this process, we also verified and corrected for the systematic errors related to CCD position. The corrected S-PLUS DR4 photometric data will provide a solid data foundation for conducting scientific research that relies on high-calibration precision. Our results underscore the power of the XPSP method in combination with the SCR method, showcasing their effectiveness in enhancing calibration precision for wide-field surveys when combined with Gaia photometry and XP spectra, to be applied for other S-PLUS sub-surveys.

astro-ph.IM↗

arXiv2023

ELIXR: Towards a general purpose X-ray artificial intelligence system through alignment of large language models and radiology vision encoders

In this work, we present an approach, which we call Embeddings for Language/Image-aligned X-Rays, or ELIXR, that leverages a language-aligned image encoder combined or grafted onto a fixed LLM, PaLM 2, to perform a broad range of chest X-ray tasks. We train this lightweight adapter architecture using images paired with corresponding free-text radiology reports from the MIMIC-CXR dataset. ELIXR achieved state-of-the-art performance on zero-shot chest X-ray (CXR) classification (mean AUC of 0.850 across 13 findings), data-efficient CXR classification (mean AUCs of 0.893 and 0.898 across five findings (atelectasis, cardiomegaly, consolidation, pleural effusion, and pulmonary edema) for 1% (~2,200 images) and 10% (~22,000 images) training data), and semantic search (0.76 normalized discounted cumulative gain (NDCG) across nineteen queries, including perfect retrieval on twelve of them). Compared to existing data-efficient methods including supervised contrastive learning (SupCon), ELIXR required two orders of magnitude less data to reach similar performance. ELIXR also showed promise on CXR vision-language tasks, demonstrating overall accuracies of 58.7% and 62.5% on visual question answering and report quality assurance tasks, respectively. These results suggest that ELIXR is a robust and versatile approach to CXR AI.

cs.CV↗