arXiv subjects

Di He

Publications and source records attributed to Di He.

At least 55 records · Page 3Linked to original sources

arXiv2025

End-to-End Crystal Structure Prediction from Powder X-Ray Diffraction

Powder X-ray diffraction (PXRD) is a prevalent technique in materials characterization. While the analysis of PXRD often requires extensive human manual intervention, and most automated method only achieved at coarse-grained level. The more difficult and important task of fine-grained crystal structure prediction from PXRD remains unaddressed. This study introduces XtalNet, the first equivariant deep generative model for end-to-end crystal structure prediction from PXRD. Unlike previous crystal structure prediction methods that rely solely on composition, XtalNet leverages PXRD as an additional condition, eliminating ambiguity and enabling the generation of complex organic structures with up to 400 atoms in the unit cell. XtalNet comprises two modules: a Contrastive PXRD-Crystal Pretraining (CPCP) module that aligns PXRD space with crystal structure space, and a Conditional Crystal Structure Generation (CCSG) module that generates candidate crystal structures conditioned on PXRD patterns. Evaluation on two MOF datasets (hMOF-100 and hMOF-400) demonstrates XtalNet's effectiveness. XtalNet achieves a top-10 Match Rate of 90.2% and 79% for hMOF-100 and hMOF-400 in conditional crystal structure prediction task, respectively. XtalNet enables the direct prediction of crystal structures from experimental measurements, eliminating the need for manual intervention and external databases. This opens up new possibilities for automated crystal structure determination and the accelerated discovery of novel materials.

physics.chem-ph↗

arXiv2025

LarvSeg: Exploring Image Classification Data For Large Vocabulary Semantic Segmentation via Category-wise Attentive Classifier

Scaling up the vocabulary of semantic segmentation models is extremely challenging because annotating large-scale mask labels is labour-intensive and time-consuming. Recently, language-guided segmentation models have been proposed to address this challenge. However, their performance drops significantly when applied to out-of-distribution categories. In this paper, we propose a new large vocabulary semantic segmentation framework, called LarvSeg. Different from previous works, LarvSeg leverages image classification data to scale the vocabulary of semantic segmentation models as large-vocabulary classification datasets usually contain balanced categories and are much easier to obtain. However, for classification tasks, the category is image-level, while for segmentation we need to predict the label at pixel level. To address this issue, we first propose a general baseline framework to incorporate image-level supervision into the training process of a pixel-level segmentation model, making the trained network perform semantic segmentation on newly introduced categories in the classification data. We then observe that a model trained on segmentation data can group pixel features of categories beyond the training vocabulary. Inspired by this finding, we design a category-wise attentive classifier to apply supervision to the precise regions of corresponding categories to improve the model performance. Extensive experiments demonstrate that LarvSeg significantly improves the large vocabulary semantic segmentation performance, especially in the categories without mask labels. For the first time, we provide a 21K-category semantic segmentation model with the help of ImageNet21K. The code is available at https://github.com/HaojunYu1998/large_voc_seg.

cs.CV↗

arXiv2025

A Foundational Generative Model for Breast Ultrasound Image Analysis

Foundational models have emerged as powerful tools for addressing various tasks in clinical settings. However, their potential development to breast ultrasound analysis remains untapped. In this paper, we present BUSGen, the first foundational generative model specifically designed for breast ultrasound image analysis. Pretrained on over 3.5 million breast ultrasound images, BUSGen has acquired extensive knowledge of breast structures, pathological features, and clinical variations. With few-shot adaptation, BUSGen can generate repositories of realistic and informative task-specific data, facilitating the development of models for a wide range of downstream tasks. Extensive experiments highlight BUSGen's exceptional adaptability, significantly exceeding real-data-trained foundational models in breast cancer screening, diagnosis, and prognosis. In breast cancer early diagnosis, our approach outperformed all board-certified radiologists (n=9), achieving an average sensitivity improvement of 16.5% (P-value<0.0001). Additionally, we characterized the scaling effect of using generated data which was as effective as the collected real-world data for training diagnostic models. Moreover, extensive experiments demonstrated that our approach improved the generalization ability of downstream models. Importantly, BUSGen protected patient privacy by enabling fully de-identified data sharing, making progress forward in secure medical data utilization. An online demo of BUSGen is available at https://aibus.bio.

cs.AI↗

arXiv2024

Do Efficient Transformers Really Save Computation?

As transformer-based language models are trained on increasingly large datasets and with vast numbers of parameters, finding more efficient alternatives to the standard Transformer has become very valuable. While many efficient Transformers and Transformer alternatives have been proposed, none provide theoretical guarantees that they are a suitable replacement for the standard Transformer. This makes it challenging to identify when to use a specific model and what directions to prioritize for further investigation. In this paper, we aim to understand the capabilities and limitations of efficient Transformers, specifically the Sparse Transformer and the Linear Transformer. We focus on their reasoning capability as exhibited by Chain-of-Thought (CoT) prompts and follow previous works to model them as Dynamic Programming (DP) problems. Our results show that while these models are expressive enough to solve general DP tasks, contrary to expectations, they require a model size that scales with the problem size. Nonetheless, we identify a class of DP problems for which these models can be more efficient than the standard Transformer. We confirm our theoretical results through experiments on representative DP tasks, adding to the understanding of efficient Transformers' practical strengths and weaknesses.

cs.LG↗

arXiv2024

Static Microlensing: Concept, Method and Candidates

We propose a novel microlensing event search method that differs from either the traditional time domain method, astrometric microlensing, or the parallax microlensing method. Our method assumes that stars with nearly identical "genes" - normalized Spectral Energy Distributions (SED) bear the same luminosity within the intrinsic scatter due to stellar properties. Given a sample of stars with similar normalized SEDs, the outliers in luminosity distribution can be considered microlensing events by excluding other possible variations. In this case, we can select microlensing events from archive data rather than time domain monitoring the sky, which we describe as static microlensing. Following this concept, we collect the data from Gaia DR3 and SDSS DR16 from the northern galactic cap at high galactic latitudes. This area is not preferable for normal microlensing search due to the low stellar density and, therefore, low discovery rate. By applying a similarity search algorithm, we find 5 microlensing candidates in the Galactic halo.

astro-ph.GA↗

arXiv2024

Bridging Geometric States via Geometric Diffusion Bridge

The accurate prediction of geometric state evolution in complex systems is critical for advancing scientific domains such as quantum chemistry and material modeling. Traditional experimental and computational methods face challenges in terms of environmental constraints and computational demands, while current deep learning approaches still fall short in terms of precision and generality. In this work, we introduce the Geometric Diffusion Bridge (GDB), a novel generative modeling framework that accurately bridges initial and target geometric states. GDB leverages a probabilistic approach to evolve geometric state distributions, employing an equivariant diffusion bridge derived by a modified version of Doob's $h$-transform for connecting geometric states. This tailored diffusion process is anchored by initial and target geometric states as fixed endpoints and governed by equivariant transition kernels. Moreover, trajectory data can be seamlessly leveraged in our GDB framework by using a chain of equivariant diffusion bridges, providing a more detailed and accurate characterization of evolution dynamics. Theoretically, we conduct a thorough examination to confirm our framework's ability to preserve joint distributions of geometric states and capability to completely model the underlying dynamics inducing trajectory distributions with negligible error. Experimental evaluations across various real-world scenarios show that GDB surpasses existing state-of-the-art approaches, opening up a new pathway for accurately bridging geometric states and tackling crucial scientific challenges with improved accuracy and applicability.

cs.LG↗

arXiv2024

Knowledge-driven AI-generated data for accurate and interpretable breast ultrasound diagnoses

Data-driven deep learning models have shown great capabilities to assist radiologists in breast ultrasound (US) diagnoses. However, their effectiveness is limited by the long-tail distribution of training data, which leads to inaccuracies in rare cases. In this study, we address a long-standing challenge of improving the diagnostic model performance on rare cases using long-tailed data. Specifically, we introduce a pipeline, TAILOR, that builds a knowledge-driven generative model to produce tailored synthetic data. The generative model, using 3,749 lesions as source data, can generate millions of breast-US images, especially for error-prone rare cases. The generated data can be further used to build a diagnostic model for accurate and interpretable diagnoses. In the prospective external evaluation, our diagnostic model outperforms the average performance of nine radiologists by 33.5% in specificity with the same sensitivity, improving their performance by providing predictions with an interpretable decision-making process. Moreover, on ductal carcinoma in situ (DCIS), our diagnostic model outperforms all radiologists by a large margin, with only 34 DCIS lesions in the source data. We believe that TAILOR can potentially be extended to various diseases and imaging modalities.

eess.IV↗

arXiv2024

Online Pseudo-Zeroth-Order Training of Neuromorphic Spiking Neural Networks

Brain-inspired neuromorphic computing with spiking neural networks (SNNs) is a promising energy-efficient computational approach. However, successfully training SNNs in a more biologically plausible and neuromorphic-hardware-friendly way is still challenging. Most recent methods leverage spatial and temporal backpropagation (BP), not adhering to neuromorphic properties. Despite the efforts of some online training methods, tackling spatial credit assignments by alternatives with comparable performance as spatial BP remains a significant problem. In this work, we propose a novel method, online pseudo-zeroth-order (OPZO) training. Our method only requires a single forward propagation with noise injection and direct top-down signals for spatial credit assignment, avoiding spatial BP's problem of symmetric weights and separate phases for layer-by-layer forward-backward propagation. OPZO solves the large variance problem of zeroth-order methods by the pseudo-zeroth-order formulation and momentum feedback connections, while having more guarantees than random feedback. Combining online training, OPZO can pave paths to on-chip SNN training. Experiments on neuromorphic and static datasets with fully connected and convolutional networks demonstrate the effectiveness of OPZO with similar performance compared with spatial BP, as well as estimated low training costs.

cs.NE↗

arXiv2024

GeoMFormer: A General Architecture for Geometric Molecular Representation Learning

Molecular modeling, a central topic in quantum mechanics, aims to accurately calculate the properties and simulate the behaviors of molecular systems. The molecular model is governed by physical laws, which impose geometric constraints such as invariance and equivariance to coordinate rotation and translation. While numerous deep learning approaches have been developed to learn molecular representations under these constraints, most of them are built upon heuristic and costly modules. We argue that there is a strong need for a general and flexible framework for learning both invariant and equivariant features. In this work, we introduce a novel Transformer-based molecular model called GeoMFormer to achieve this goal. Using the standard Transformer modules, two separate streams are developed to maintain and learn invariant and equivariant representations. Carefully designed cross-attention modules bridge the two streams, allowing information fusion and enhancing geometric modeling in each stream. As a general and flexible architecture, we show that many previous architectures can be viewed as special instantiations of GeoMFormer. Extensive experiments are conducted to demonstrate the power of GeoMFormer. All empirical results show that GeoMFormer achieves strong performance on both invariant and equivariant tasks of different types and scales. Code and models will be made publicly available at https://github.com/c-tl/GeoMFormer.

cs.LG↗

arXiv2024

Two Stones Hit One Bird: Bilevel Positional Encoding for Better Length Extrapolation

In this work, we leverage the intrinsic segmentation of language sequences and design a new positional encoding method called Bilevel Positional Encoding (BiPE). For each position, our BiPE blends an intra-segment encoding and an inter-segment encoding. The intra-segment encoding identifies the locations within a segment and helps the model capture the semantic information therein via absolute positional encoding. The inter-segment encoding specifies the segment index, models the relationships between segments, and aims to improve extrapolation capabilities via relative positional encoding. Theoretical analysis shows this disentanglement of positional information makes learning more effective. The empirical results also show that our BiPE has superior length extrapolation capabilities across a wide range of tasks in diverse text modalities.

cs.LG↗

arXiv2024

Block Coordinate Descent Methods for Optimization under J-Orthogonality Constraints with Applications

The J-orthogonal matrix, also referred to as the hyperbolic orthogonal matrix, is a class of special orthogonal matrix in hyperbolic space, notable for its advantageous properties. These matrices are integral to optimization under J-orthogonal constraints, which have widespread applications in statistical learning and data science. However, addressing these problems is generally challenging due to their non-convex nature and the computational intensity of the constraints. Currently, algorithms for tackling these challenges are limited. This paper introduces JOBCD, a novel Block Coordinate Descent method designed to address optimizations with J-orthogonality constraints. We explore two specific variants of JOBCD: one based on a Gauss-Seidel strategy (GS-JOBCD), the other on a variance-reduced and Jacobi strategy (VR-J-JOBCD). Notably, leveraging the parallel framework of a Jacobi strategy, VR-J-JOBCD integrates variance reduction techniques to decrease oracle complexity in the minimization of finite-sum functions. For both GS-JOBCD and VR-J-JOBCD, we establish the oracle complexity under mild conditions and strong limit-point convergence results under the Kurdyka-Lojasiewicz inequality. To demonstrate the effectiveness of our method, we conduct experiments on hyperbolic eigenvalue problems, hyperbolic structural probe problems, and the ultrahyperbolic knowledge graph embedding problem. Extensive experiments using both real-world and synthetic data demonstrate that JOBCD consistently outperforms state-of-the-art solutions, by large margins.

cs.DS↗

arXiv2024

Temporal Spiking Neural Networks with Synaptic Delay for Graph Reasoning

Spiking neural networks (SNNs) are investigated as biologically inspired models of neural computation, distinguished by their computational capability and energy efficiency due to precise spiking times and sparse spikes with event-driven computation. A significant question is how SNNs can emulate human-like graph-based reasoning of concepts and relations, especially leveraging the temporal domain optimally. This paper reveals that SNNs, when amalgamated with synaptic delay and temporal coding, are proficient in executing (knowledge) graph reasoning. It is elucidated that spiking time can function as an additional dimension to encode relation properties via a neural-generalized path formulation. Empirical results highlight the efficacy of temporal delay in relation processing and showcase exemplary performance in diverse graph reasoning tasks. The spiking model is theoretically estimated to achieve $20\times$ energy savings compared to non-spiking counterparts, deepening insights into the capabilities and potential of biologically inspired SNNs for efficient reasoning. The code is available at https://github.com/pkuxmq/GRSNN.

cs.NE↗

arXiv2024

REST: Retrieval-Based Speculative Decoding

We introduce Retrieval-Based Speculative Decoding (REST), a novel algorithm designed to speed up language model generation. The key insight driving the development of REST is the observation that the process of text generation often includes certain common phases and patterns. Unlike previous methods that rely on a draft language model for speculative decoding, REST harnesses the power of retrieval to generate draft tokens. This method draws from the reservoir of existing knowledge, retrieving and employing relevant tokens based on the current context. Its plug-and-play nature allows for seamless integration and acceleration of any language models, all without necessitating additional training. When benchmarked on 7B and 13B language models in a single-batch setting, REST achieves a significant speedup of 1.62X to 2.36X on code or text generation. The code of REST is available at https://github.com/FasterDecoding/REST.

cs.CL↗

arXiv2024

Learning a Fourier Transform for Linear Relative Positional Encodings in Transformers

We propose a new class of linear Transformers called FourierLearner-Transformers (FLTs), which incorporate a wide range of relative positional encoding mechanisms (RPEs). These include regular RPE techniques applied for sequential data, as well as novel RPEs operating on geometric data embedded in higher-dimensional Euclidean spaces. FLTs construct the optimal RPE mechanism implicitly by learning its spectral representation. As opposed to other architectures combining efficient low-rank linear attention with RPEs, FLTs remain practical in terms of their memory usage and do not require additional assumptions about the structure of the RPE mask. Besides, FLTs allow for applying certain structural inductive bias techniques to specify masking strategies, e.g. they provide a way to learn the so-called local RPEs introduced in this paper and give accuracy gains as compared with several other linear Transformers for language modeling. We also thoroughly test FLTs on other data modalities and tasks, such as image classification, 3D molecular modeling, and learnable optimizers. To the best of our knowledge, for 3D molecular data, FLTs are the first Transformer architectures providing linear attention and incorporating RPE masking.

cs.LG↗

arXiv2024

Boosting Meta-Training with Base Class Information for Few-Shot Learning

Few-shot learning, a challenging task in machine learning, aims to learn a classifier adaptable to recognize new, unseen classes with limited labeled examples. Meta-learning has emerged as a prominent framework for few-shot learning. Its training framework is originally a task-level learning method, such as Model-Agnostic Meta-Learning (MAML) and Prototypical Networks. And a recently proposed training paradigm called Meta-Baseline, which consists of sequential pre-training and meta-training stages, gains state-of-the-art performance. However, as a non-end-to-end training method, indicating the meta-training stage can only begin after the completion of pre-training, Meta-Baseline suffers from higher training cost and suboptimal performance due to the inherent conflicts of the two training stages. To address these limitations, we propose an end-to-end training paradigm consisting of two alternative loops. In the outer loop, we calculate cross entropy loss on the entire training set while updating only the final linear layer. In the inner loop, we employ the original meta-learning training mode to calculate the loss and incorporate gradients from the outer loss to guide the parameter updates. This training paradigm not only converges quickly but also outperforms existing baselines, indicating that information from the overall training set and the meta-learning training paradigm could mutually reinforce one another. Moreover, being model-agnostic, our framework achieves significant performance gains, surpassing the baseline systems by approximate 1%.

cs.LG↗

arXiv2024

$\widetilde{O}(N^2)$ Representation of General Continuous Anti-symmetric Function

In quantum mechanics, the wave function of fermion systems such as many-body electron systems are anti-symmetric (AS) and continuous, and it is crucial yet challenging to find an ansatz to represent them. This paper addresses this challenge by presenting an ${\widetilde O}(N^2)$ ansatz based on permutation-equivariant functions. We prove that our ansatz can represent any AS continuous functions, and can accommodate the determinant-based structure proposed by Hutter [14], solving the proposed open problems that ${O}(N)$ Slater determinants are sufficient to provide universal representation of AS continuous functions. Together, we offer a generalizable and efficient approach to representing AS continuous functions, shedding light on designing neural networks to learn wave functions.

quant-ph↗

arXiv2024

Hebbian Learning based Orthogonal Projection for Continual Learning of Spiking Neural Networks

Neuromorphic computing with spiking neural networks is promising for energy-efficient artificial intelligence (AI) applications. However, different from humans who continually learn different tasks in a lifetime, neural network models suffer from catastrophic forgetting. How could neuronal operations solve this problem is an important question for AI and neuroscience. Many previous studies draw inspiration from observed neuroscience phenomena and propose episodic replay or synaptic metaplasticity, but they are not guaranteed to explicitly preserve knowledge for neuron populations. Other works focus on machine learning methods with more mathematical grounding, e.g., orthogonal projection on high dimensional spaces, but there is no neural correspondence for neuromorphic computing. In this work, we develop a new method with neuronal operations based on lateral connections and Hebbian learning, which can protect knowledge by projecting activity traces of neurons into an orthogonal subspace so that synaptic weight update will not interfere with old tasks. We show that Hebbian and anti-Hebbian learning on recurrent lateral connections can effectively extract the principal subspace of neural activities and enable orthogonal projection. This provides new insights into how neural circuits and Hebbian learning can help continual learning, and also how the concept of orthogonal projection can be realized in neuronal systems. Our method is also flexible to utilize arbitrary training methods based on presynaptic activities/traces. Experiments show that our method consistently solves forgetting for spiking neural networks with nearly zero forgetting under various supervised training methods with different error propagation approaches, and outperforms previous approaches under various settings. Our method can pave a solid path for building continual neuromorphic computing systems.

cs.NE↗

arXiv2024

DOF: Accelerating High-order Differential Operators with Forward Propagation

Solving partial differential equations (PDEs) efficiently is essential for analyzing complex physical systems. Recent advancements in leveraging deep learning for solving PDE have shown significant promise. However, machine learning methods, such as Physics-Informed Neural Networks (PINN), face challenges in handling high-order derivatives of neural network-parameterized functions. Inspired by Forward Laplacian, a recent method of accelerating Laplacian computation, we propose an efficient computational framework, Differential Operator with Forward-propagation (DOF), for calculating general second-order differential operators without losing any precision. We provide rigorous proof of the advantages of our method over existing methods, demonstrating two times improvement in efficiency and reduced memory consumption on any architectures. Empirical results illustrate that our method surpasses traditional automatic differentiation (AutoDiff) techniques, achieving 2x improvement on the MLP structure and nearly 20x improvement on the MLP with Jacobian sparsity.

cs.LG↗