arXiv subjects

Yu Shi

Publications and source records attributed to Yu Shi.

At least 109 records · Page 6Linked to original sources

arXiv2024

MatterSim: A Deep Learning Atomistic Model Across Elements, Temperatures and Pressures

Accurate and fast prediction of materials properties is central to the digital transformation of materials design. However, the vast design space and diverse operating conditions pose significant challenges for accurately modeling arbitrary material candidates and forecasting their properties. We present MatterSim, a deep learning model actively learned from large-scale first-principles computations, for efficient atomistic simulations at first-principles level and accurate prediction of broad material properties across the periodic table, spanning temperatures from 0 to 5000 K and pressures up to 1000 GPa. Out-of-the-box, the model serves as a machine learning force field, and shows remarkable capabilities not only in predicting ground-state material structures and energetics, but also in simulating their behavior under realistic temperatures and pressures, signifying an up to ten-fold enhancement in precision compared to the prior best-in-class. This enables MatterSim to compute materials' lattice dynamics, mechanical and thermodynamic properties, and beyond, to an accuracy comparable with first-principles methods. Specifically, MatterSim predicts Gibbs free energies for a wide range of inorganic solids with near-first-principles accuracy and achieves a 15 meV/atom resolution for temperatures up to 1000K compared with experiments. This opens an opportunity to predict experimental phase diagrams of materials at minimal computational cost. Moreover, MatterSim also serves as a platform for continuous learning and customization by integrating domain-specific data. The model can be fine-tuned for atomistic simulations at a desired level of theory or for direct structure-to-property predictions, achieving high data efficiency with a reduction in data requirements by up to 97%.

cond-mat.mtrl-sci↗

arXiv2024

Actions Speak Louder than Words: Trillion-Parameter Sequential Transducers for Generative Recommendations

Large-scale recommendation systems are characterized by their reliance on high cardinality, heterogeneous features and the need to handle tens of billions of user actions on a daily basis. Despite being trained on huge volume of data with thousands of features, most Deep Learning Recommendation Models (DLRMs) in industry fail to scale with compute. Inspired by success achieved by Transformers in language and vision domains, we revisit fundamental design choices in recommendation systems. We reformulate recommendation problems as sequential transduction tasks within a generative modeling framework ("Generative Recommenders"), and propose a new architecture, HSTU, designed for high cardinality, non-stationary streaming recommendation data. HSTU outperforms baselines over synthetic and public datasets by up to 65.8% in NDCG, and is 5.3x to 15.2x faster than FlashAttention2-based Transformers on 8192 length sequences. HSTU-based Generative Recommenders, with 1.5 trillion parameters, improve metrics in online A/B tests by 12.4% and have been deployed on multiple surfaces of a large internet platform with billions of users. More importantly, the model quality of Generative Recommenders empirically scales as a power-law of training compute across three orders of magnitude, up to GPT-3/LLaMa-2 scale, which reduces carbon footprint needed for future model developments, and further paves the way for the first foundational models in recommendations.

cs.LG↗

arXiv2024

Test-Time Training on Graphs with Large Language Models (LLMs)

Graph Neural Networks have demonstrated great success in various fields of multimedia. However, the distribution shift between the training and test data challenges the effectiveness of GNNs. To mitigate this challenge, Test-Time Training (TTT) has been proposed as a promising approach. Traditional TTT methods require a demanding unsupervised training strategy to capture the information from test to benefit the main task. Inspired by the great annotation ability of Large Language Models (LLMs) on Text-Attributed Graphs (TAGs), we propose to enhance the test-time training on graphs with LLMs as annotators. In this paper, we design a novel Test-Time Training pipeline, LLMTTT, which conducts the test-time adaptation under the annotations by LLMs on a carefully-selected node set. Specifically, LLMTTT introduces a hybrid active node selection strategy that considers not only node diversity and representativeness, but also prediction signals from the pre-trained model. Given annotations from LLMs, a two-stage training strategy is designed to tailor the test-time model with the limited and noisy labels. A theoretical analysis ensures the validity of our method and extensive experiments demonstrate that the proposed LLMTTT can achieve a significant performance improvement compared to existing Out-of-Distribution (OOD) generalization methods.

cs.LG↗

arXiv2024

Modality-Agnostic Structural Image Representation Learning for Deformable Multi-Modality Medical Image Registration

Establishing dense anatomical correspondence across distinct imaging modalities is a foundational yet challenging procedure for numerous medical image analysis studies and image-guided radiotherapy. Existing multi-modality image registration algorithms rely on statistical-based similarity measures or local structural image representations. However, the former is sensitive to locally varying noise, while the latter is not discriminative enough to cope with complex anatomical structures in multimodal scans, causing ambiguity in determining the anatomical correspondence across scans with different modalities. In this paper, we propose a modality-agnostic structural representation learning method, which leverages Deep Neighbourhood Self-similarity (DNS) and anatomy-aware contrastive learning to learn discriminative and contrast-invariance deep structural image representations (DSIR) without the need for anatomical delineations or pre-aligned training images. We evaluate our method on multiphase CT, abdomen MR-CT, and brain MR T1w-T2w registration. Comprehensive results demonstrate that our method is superior to the conventional local structural representation and statistical-based similarity measures in terms of discriminability and accuracy.

cs.CV↗

arXiv2024

Revisiting azimuthal angular asymmetries in diffractive di-jet production

We explore the impact of initial state soft gluon radiations on the azimuthal angle asymmetries in photo-production of hard di-jet via coherent diffraction in ultraperipheral heavy ion collisions, as well as in electron-proton ($ep$) and electron-nucleus ($eA$) collisions. The primary production mechanism is identified as the diffractive production of two hard jets, accompanied by a collinear gluon emission along the beam direction. In contrast, the diffractive exclusive di-jet production, where the initial state radiation is absent, is suppressed due to color transparency. Our analysis shows that azimuthal asymmetries, traditionally attributed to final state gluon emissions, are reduced by the presence of initial state radiations. The sensitivity of azimuthal asymmetries to both initial and final state radiations suggests that they could provide novel insights into the mechanisms of di-jet production in diffractive processes.

hep-ph↗

arXiv2023

3DGAUnet: 3D generative adversarial networks with a 3D U-Net based generator to achieve the accurate and effective synthesis of clinical tumor image data for pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) presents a critical global health challenge, and early detection is crucial for improving the 5-year survival rate. Recent medical imaging and computational algorithm advances offer potential solutions for early diagnosis. Deep learning, particularly in the form of convolutional neural networks (CNNs), has demonstrated success in medical image analysis tasks, including classification and segmentation. However, the limited availability of clinical data for training purposes continues to provide a significant obstacle. Data augmentation, generative adversarial networks (GANs), and cross-validation are potential techniques to address this limitation and improve model performance, but effective solutions are still rare for 3D PDAC, where contrast is especially poor owing to the high heterogeneity in both tumor and background tissues. In this study, we developed a new GAN-based model, named 3DGAUnet, for generating realistic 3D CT images of PDAC tumors and pancreatic tissue, which can generate the interslice connection data that the existing 2D CT image synthesis models lack. Our innovation is to develop a 3D U-Net architecture for the generator to improve shape and texture learning for PDAC tumors and pancreatic tissue. Our approach offers a promising path to tackle the urgent requirement for creative and synergistic methods to combat PDAC. The development of this GAN-based model has the potential to alleviate data scarcity issues, elevate the quality of synthesized data, and thereby facilitate the progression of deep learning models to enhance the accuracy and early detection of PDAC tumors, which could profoundly impact patient outcomes. Furthermore, this model has the potential to be adapted to other types of solid tumors, hence making significant contributions to the field of medical imaging in terms of image processing models.

eess.IV↗

arXiv2023

Liver Tumor Screening and Diagnosis in CT with Pixel-Lesion-Patient Network

Liver tumor segmentation and classification are important tasks in computer aided diagnosis. We aim to address three problems: liver tumor screening and preliminary diagnosis in non-contrast computed tomography (CT), and differential diagnosis in dynamic contrast-enhanced CT. A novel framework named Pixel-Lesion-pAtient Network (PLAN) is proposed. It uses a mask transformer to jointly segment and classify each lesion with improved anchor queries and a foreground-enhanced sampling loss. It also has an image-wise classifier to effectively aggregate global information and predict patient-level diagnosis. A large-scale multi-phase dataset is collected containing 939 tumor patients and 810 normal subjects. 4010 tumor instances of eight types are extensively annotated. On the non-contrast tumor screening task, PLAN achieves 95% and 96% in patient-level sensitivity and specificity. On contrast-enhanced CT, our lesion-level detection precision, recall, and classification accuracy are 92%, 89%, and 86%, outperforming widely used CNN and transformers for lesion segmentation. We also conduct a reader study on a holdout set of 250 cases. PLAN is on par with a senior human radiologist, showing the clinical significance of our results.

eess.IV↗

arXiv2023

Error metric for non-trace-preserving quantum operations

We study the problem of measuring errors in non-trace-preserving quantum operations, with a focus on their impact on quantum computing. We propose an error metric that efficiently provides an upper bound on the trace distance between the normalized output states from imperfect and ideal operations, while remaining compatible with the diamond distance. As a demonstration of its application, we apply our metric in the analysis of a lossy beam splitter and a nondeterministic conditional sign-flip gate, two primary non-trace-preserving operations in the Knill-Laflamme-Milburn protocol. We then turn to the leakage errors of neutral-atom quantum computers, finding that these errors scale worse than previously anticipated, implying a more stringent fault-tolerant threshold. We also assess the quantum Zeno gate's error using our metric. In a broader context, we discuss the potential of our metric to analyze general postselected protocols, where it can be employed to study error propagation and estimate thresholds in fault-tolerant quantum computing. The results highlight the critical role of our proposed error metric in understanding and addressing challenges in practical quantum information processing.

quant-ph↗

arXiv2023

CancerUniT: Towards a Single Unified Model for Effective Detection, Segmentation, and Diagnosis of Eight Major Cancers Using a Large Collection of CT Scans

Human readers or radiologists routinely perform full-body multi-organ multi-disease detection and diagnosis in clinical practice, while most medical AI systems are built to focus on single organs with a narrow list of a few diseases. This might severely limit AI's clinical adoption. A certain number of AI models need to be assembled non-trivially to match the diagnostic process of a human reading a CT scan. In this paper, we construct a Unified Tumor Transformer (CancerUniT) model to jointly detect tumor existence & location and diagnose tumor characteristics for eight major cancers in CT scans. CancerUniT is a query-based Mask Transformer model with the output of multi-tumor prediction. We decouple the object queries into organ queries, tumor detection queries and tumor diagnosis queries, and further establish hierarchical relationships among the three groups. This clinically-inspired architecture effectively assists inter- and intra-organ representation learning of tumors and facilitates the resolution of these complex, anatomically related multi-organ cancer image reading tasks. CancerUniT is trained end-to-end using a curated large-scale CT images of 10,042 patients including eight major types of cancers and occurring non-cancer tumors (all are pathology-confirmed with 3D tumor masks annotated by radiologists). On the test set of 631 patients, CancerUniT has demonstrated strong performance under a set of clinically relevant evaluation metrics, substantially outperforming both multi-disease methods and an assembly of eight single-organ expert models in tumor detection, segmentation, and diagnosis. This moves one step closer towards a universal high performance cancer screening tool.

eess.IV↗

arXiv2023

Improved Prognostic Prediction of Pancreatic Cancer Using Multi-Phase CT by Integrating Neural Distance and Texture-Aware Transformer

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer in which the tumor-vascular involvement greatly affects the resectability and, thus, overall survival of patients. However, current prognostic prediction methods fail to explicitly and accurately investigate relationships between the tumor and nearby important vessels. This paper proposes a novel learnable neural distance that describes the precise relationship between the tumor and vessels in CT images of different patients, adopting it as a major feature for prognosis prediction. Besides, different from existing models that used CNNs or LSTMs to exploit tumor enhancement patterns on dynamic contrast-enhanced CT imaging, we improved the extraction of dynamic tumor-related texture features in multi-phase contrast-enhanced CT by fusing local and global features using CNN and transformer modules, further enhancing the features extracted across multi-phase CT images. We extensively evaluated and compared the proposed method with existing methods in the multi-center (n=4) dataset with 1,070 patients with PDAC, and statistical analysis confirmed its clinical effectiveness in the external test set consisting of three centers. The developed risk marker was the strongest predictor of overall survival among preoperative factors and it has the potential to be combined with established clinical factors to select patients at higher risk who might benefit from neoadjuvant therapy.

eess.IV↗

arXiv2023

Robust Representation Learning for Unreliable Partial Label Learning

Partial Label Learning (PLL) is a type of weakly supervised learning where each training instance is assigned a set of candidate labels, but only one label is the ground-truth. However, this idealistic assumption may not always hold due to potential annotation inaccuracies, meaning the ground-truth may not be present in the candidate label set. This is known as Unreliable Partial Label Learning (UPLL) that introduces an additional complexity due to the inherent unreliability and ambiguity of partial labels, often resulting in a sub-optimal performance with existing methods. To address this challenge, we propose the Unreliability-Robust Representation Learning framework (URRL) that leverages unreliability-robust contrastive learning to help the model fortify against unreliable partial labels effectively. Concurrently, we propose a dual strategy that combines KNN-based candidate label set correction and consistency-regularization-based label disambiguation to refine label quality and enhance the ability of representation learning within the URRL framework. Extensive experiments demonstrate that the proposed method outperforms state-of-the-art PLL methods on various datasets with diverse degrees of unreliability and ambiguity. Furthermore, we provide a theoretical analysis of our approach from the perspective of the expectation maximization (EM) algorithm. Upon acceptance, we pledge to make the code publicly accessible.

cs.LG↗

arXiv2023

Unreliable Partial Label Learning with Recursive Separation

Partial label learning (PLL) is a typical weakly supervised learning problem in which each instance is associated with a candidate label set, and among which only one is true. However, the assumption that the ground-truth label is always among the candidate label set would be unrealistic, as the reliability of the candidate label sets in real-world applications cannot be guaranteed by annotators. Therefore, a generalized PLL named Unreliable Partial Label Learning (UPLL) is proposed, in which the true label may not be in the candidate label set. Due to the challenges posed by unreliable labeling, previous PLL methods will experience a marked decline in performance when applied to UPLL. To address the issue, we propose a two-stage framework named Unreliable Partial Label Learning with Recursive Separation (UPLLRS). In the first stage, the self-adaptive recursive separation strategy is proposed to separate the training set into a reliable subset and an unreliable subset. In the second stage, a disambiguation strategy is employed to progressively identify the ground-truth labels in the reliable subset. Simultaneously, semi-supervised learning methods are adopted to extract valuable information from the unreliable subset. Our method demonstrates state-of-the-art performance as evidenced by experimental results, particularly in situations of high unreliability. Code and supplementary materials are available at https://github.com/dhiyu/UPLLRS.

cs.AI↗

arXiv2023

SLPT: Selective Labeling Meets Prompt Tuning on Label-Limited Lesion Segmentation

Medical image analysis using deep learning is often challenged by limited labeled data and high annotation costs. Fine-tuning the entire network in label-limited scenarios can lead to overfitting and suboptimal performance. Recently, prompt tuning has emerged as a more promising technique that introduces a few additional tunable parameters as prompts to a task-agnostic pre-trained model, and updates only these parameters using supervision from limited labeled data while keeping the pre-trained model unchanged. However, previous work has overlooked the importance of selective labeling in downstream tasks, which aims to select the most valuable downstream samples for annotation to achieve the best performance with minimum annotation cost. To address this, we propose a framework that combines selective labeling with prompt tuning (SLPT) to boost performance in limited labels. Specifically, we introduce a feature-aware prompt updater to guide prompt tuning and a TandEm Selective LAbeling (TESLA) strategy. TESLA includes unsupervised diversity selection and supervised selection using prompt-based uncertainty. In addition, we propose a diversified visual prompt tuning strategy to provide multi-prompt-based discrepant predictions for TESLA. We evaluate our method on liver tumor segmentation and achieve state-of-the-art performance, outperforming traditional fine-tuning with only 6% of tunable parameters, also achieving 94% of full-data performance by labeling only 5% of the data.

cs.CV↗

arXiv2023

Parton shower algorithm with saturation effect

We extend the previously developed small $x$ parton shower algorithm to include the kinematic constraint effect and $k_t$ resummation effect. This work enables the Monte Carlo generator to simultaneously resum large $k_t$ and small $x$ logarithms in the saturation regime for the first time. It is an important step towards simulating processes involving multiple well separated hard scales, such as di-jet production in eA collisions at EIC.

hep-ph↗

arXiv2023

Rotating BTZ-like black hole and central charges in Einstein-bumblebee gravity

We obtain an exact rotating BTZ-like black hole solution by solving the corresponding gravitational field equations and the bumblebee motion equations in Einstein-bumblebee gravity theory. Result is presented for the purely radial Lorentz symmetry violating and can only exist with a linear functional potential of the bumblebee field. This black hole has two horizons and an ergosphere which are dependent on the bumblebee coupling constant $\ell$. The concepts of the area and volume of the horizon should be renewed in this LV spacetime due to the nontrivial contribution of coupling between the bumblebee field and the Ricci tensor. Only in this way, the entropy-area relation, first law of thermodynamics and the Smarr formula can still be constructed. We also study the AdS/CFT correspondence of this black hole, find that the entropy product of its inner and outer horizons is universal. So the central charges of the dual CFT on the boundary can be obtained via the thermodynamic method, and they can reappear black hole mass and angular momentum in the bulk.

gr-qc↗

arXiv2023

Towards Predicting Equilibrium Distributions for Molecular Systems with Deep Learning

Advances in deep learning have greatly improved structure prediction of molecules. However, many macroscopic observations that are important for real-world applications are not functions of a single molecular structure, but rather determined from the equilibrium distribution of structures. Traditional methods for obtaining these distributions, such as molecular dynamics simulation, are computationally expensive and often intractable. In this paper, we introduce a novel deep learning framework, called Distributional Graphormer (DiG), in an attempt to predict the equilibrium distribution of molecular systems. Inspired by the annealing process in thermodynamics, DiG employs deep neural networks to transform a simple distribution towards the equilibrium distribution, conditioned on a descriptor of a molecular system, such as a chemical graph or a protein sequence. This framework enables efficient generation of diverse conformations and provides estimations of state densities. We demonstrate the performance of DiG on several molecular tasks, including protein conformation sampling, ligand structure sampling, catalyst-adsorbate sampling, and property-guided structure generation. DiG presents a significant advancement in methodology for statistically understanding molecular systems, opening up new research opportunities in molecular science.

physics.chem-ph↗

arXiv2023

Z-Code++: A Pre-trained Language Model Optimized for Abstractive Summarization

This paper presents Z-Code++, a new pre-trained language model optimized for abstractive text summarization. The model extends the state of the art encoder-decoder model using three techniques. First, we use a two-phase pre-training process to improve model's performance on low-resource summarization tasks. The model is first pre-trained using text corpora for language understanding, and then is continually pre-trained on summarization corpora for grounded text generation. Second, we replace self-attention layers in the encoder with disentangled attention layers, where each word is represented using two vectors that encode its content and position, respectively. Third, we use fusion-in-encoder, a simple yet effective method of encoding long sequences in a hierarchical manner. Z-Code++ creates new state of the art on 9 out of 13 text summarization tasks across 5 languages. Our model is parameter-efficient in that it outperforms the 600x larger PaLM-540B on XSum, and the finetuned 200x larger GPT3-175B on SAMSum. In zero-shot and few-shot settings, our model substantially outperforms the competing models.

cs.CL↗

arXiv2023

Handling Trade-Offs in Speech Separation with Sparsely-Gated Mixture of Experts

Employing a monaural speech separation (SS) model as a front-end for automatic speech recognition (ASR) involves balancing two kinds of trade-offs. First, while a larger model improves the SS performance, it also requires a higher computational cost. Second, an SS model that is more optimized for handling overlapped speech is likely to introduce more processing artifacts in non-overlapped-speech regions. In this paper, we address these trade-offs with a sparsely-gated mixture-of-experts (MoE) architecture. Comprehensive evaluation results obtained using both simulated and real meeting recordings show that our proposed sparsely-gated MoE SS model achieves superior separation capabilities with less speech distortion, while involving only a marginal run-time cost increase.

eess.AS↗