arXiv subjects

Liwei Wang

Publications and source records attributed to Liwei Wang.

At least 73 records · Page 4Linked 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

The discrete Painlevé XXXIV hierarchy arising from the gap probability distributions of Freud random matrix ensembles

We consider the symmetric gap probability distributions of certain Freud unitary ensembles. This problem is related to the Hankel determinants generated by the Freud weights supported on the complement of a symmetric interval. By using Chen and Ismail's ladder operator approach, we obtain the difference equations satisfied by the recurrence coefficients for the orthogonal polynomials with the discontinuous Freud weights. We find that these equations, with a minor change of variables, are the discrete Painlevé XXXIV hierarchy proposed by Cresswell and Joshi [{\em J. Phys. A: Math. Gen.} {\bf 32} ({1999}) {655--669}]. This is the first time that the discrete Painlevé XXXIV hierarchy appears in the study of Random Matrix Theory. We also derive the differential-difference equations for the recurrence coefficients and show the relationship between the logarithmic derivative of the gap probabilities, the nontrivial leading coefficients of the monic orthogonal polynomials and the recurrence coefficients.

nlin.SI↗

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↗

arXiv2025

Explainable Diagnosis Prediction through Neuro-Symbolic Integration

Diagnosis prediction is a critical task in healthcare, where timely and accurate identification of medical conditions can significantly impact patient outcomes. Traditional machine learning and deep learning models have achieved notable success in this domain but often lack interpretability which is a crucial requirement in clinical settings. In this study, we explore the use of neuro-symbolic methods, specifically Logical Neural Networks (LNNs), to develop explainable models for diagnosis prediction. Essentially, we design and implement LNN-based models that integrate domain-specific knowledge through logical rules with learnable thresholds. Our models, particularly $M_{\text{multi-pathway}}$ and $M_{\text{comprehensive}}$, demonstrate superior performance over traditional models such as Logistic Regression, SVM, and Random Forest, achieving higher accuracy (up to 80.52\%) and AUROC scores (up to 0.8457) in the case study of diabetes prediction. The learned weights and thresholds within the LNN models provide direct insights into feature contributions, enhancing interpretability without compromising predictive power. These findings highlight the potential of neuro-symbolic approaches in bridging the gap between accuracy and explainability in healthcare AI applications. By offering transparent and adaptable diagnostic models, our work contributes to the advancement of precision medicine and supports the development of equitable healthcare solutions. Future research will focus on extending these methods to larger and more diverse datasets to further validate their applicability across different medical conditions and populations.

cs.LG↗

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

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

Enhancing Temporal Modeling of Video LLMs via Time Gating

Video Large Language Models (Video LLMs) have achieved impressive performance on video-and-language tasks, such as video question answering. However, most existing Video LLMs neglect temporal information in video data, leading to struggles with temporal-aware video understanding. To address this gap, we propose a Time Gating Video LLM (TG-Vid) designed to enhance temporal modeling through a novel Time Gating module (TG). The TG module employs a time gating mechanism on its sub-modules, comprising gating spatial attention, gating temporal attention, and gating MLP. This architecture enables our model to achieve a robust understanding of temporal information within videos. Extensive evaluation of temporal-sensitive video benchmarks (i.e., MVBench, TempCompass, and NExT-QA) demonstrates that our TG-Vid model significantly outperforms the existing Video LLMs. Further, comprehensive ablation studies validate that the performance gains are attributed to the designs of our TG module. Our code is available at https://github.com/LaVi-Lab/TG-Vid.

cs.CV↗

arXiv2024

Large Language Models Struggle in Token-Level Clinical Named Entity Recognition

Large Language Models (LLMs) have revolutionized various sectors, including healthcare where they are employed in diverse applications. Their utility is particularly significant in the context of rare diseases, where data scarcity, complexity, and specificity pose considerable challenges. In the clinical domain, Named Entity Recognition (NER) stands out as an essential task and it plays a crucial role in extracting relevant information from clinical texts. Despite the promise of LLMs, current research mostly concentrates on document-level NER, identifying entities in a more general context across entire documents, without extracting their precise location. Additionally, efforts have been directed towards adapting ChatGPT for token-level NER. However, there is a significant research gap when it comes to employing token-level NER for clinical texts, especially with the use of local open-source LLMs. This study aims to bridge this gap by investigating the effectiveness of both proprietary and local LLMs in token-level clinical NER. Essentially, we delve into the capabilities of these models through a series of experiments involving zero-shot prompting, few-shot prompting, retrieval-augmented generation (RAG), and instruction-fine-tuning. Our exploration reveals the inherent challenges LLMs face in token-level NER, particularly in the context of rare diseases, and suggests possible improvements for their application in healthcare. This research contributes to narrowing a significant gap in healthcare informatics and offers insights that could lead to a more refined application of LLMs in the healthcare sector.

cs.CL↗

arXiv2024

Making Long-Context Language Models Better Multi-Hop Reasoners

Recent advancements in long-context modeling have enhanced language models (LMs) for complex tasks across multiple NLP applications. Despite this progress, we find that these models struggle with multi-hop reasoning and exhibit decreased performance in the presence of noisy contexts. In this paper, we introduce Reasoning with Attributions, a novel approach that prompts LMs to supply attributions for each assertion during their reasoning. We validate our approach through experiments on three multi-hop datasets, employing both proprietary and open-source models, and demonstrate its efficacy and resilience. Furthermore, we explore methods to augment reasoning capabilities via fine-tuning and offer an attribution-annotated dataset and a specialized training strategy. Our fine-tuned model achieves competitive performance on multi-hop reasoning benchmarks, closely paralleling proprietary LMs such as ChatGPT and Claude-instant.

cs.CL↗

arXiv2024

Laplace approximation for Bayesian variable selection via Le Cam's one-step procedure

Variable selection in high-dimensional spaces is a pervasive challenge in contemporary scientific exploration and decision-making. However, existing approaches that are known to enjoy strong statistical guarantees often struggle to cope with the computational demands arising from the high dimensionality. To address this issue, we propose a novel Laplace approximation method based on Le Cam's one-step procedure (\textsf{OLAP}), designed to effectively tackles the computational burden. Under some classical high-dimensional assumptions we show that \textsf{OLAP} is a statistically consistent variable selection procedure. Furthermore, we show that the approach produces a posterior distribution that can be explored in polynomial time using a simple Gibbs sampling algorithm. Toward that polynomial complexity result, we also made some general, noteworthy contributions to the mixing time analysis of Markov chains. We illustrate the method using logistic and Poisson regression models applied to simulated and real data examples.

stat.ME↗

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

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

Beyond Embeddings: The Promise of Visual Table in Visual Reasoning

Visual representation learning has been a cornerstone in computer vision, involving typical forms such as visual embeddings, structural symbols, and text-based representations. Despite the success of CLIP-type visual embeddings, they often lack access to world knowledge critical for visual reasoning. In this work, we propose Visual Table, a novel form of visual representation tailored for visual reasoning. Visual tables are constructed as hierarchical descriptions of visual scenes, featuring a scene description and multiple object-centric descriptions covering categories, attributes, and knowledge. Thanks to the structural and textual formats, visual tables offer unique advantages over mere visual embeddings, such as interpretability and controllable editing. Furthermore, they deliver instance-level world knowledge and detailed attributes that are essential for visual reasoning. To create visual tables, we develop a generator trained on the dataset with collected, small-scale annotations. Extensive results on 11 visual reasoning benchmarks demonstrate that the generated visual tables significantly outperform previous structural and text-based representations. Moreover, they consistently enhance state-of-the-art multimodal large language models across diverse benchmarks, showcasing their potential for advancing visual reasoning tasks. Our code is available at https://github.com/LaVi-Lab/Visual-Table.

cs.CV↗

arXiv2024

Provably Efficient Exploration in Quantum Reinforcement Learning with Logarithmic Worst-Case Regret

While quantum reinforcement learning (RL) has attracted a surge of attention recently, its theoretical understanding is limited. In particular, it remains elusive how to design provably efficient quantum RL algorithms that can address the exploration-exploitation trade-off. To this end, we propose a novel UCRL-style algorithm that takes advantage of quantum computing for tabular Markov decision processes (MDPs) with $S$ states, $A$ actions, and horizon $H$, and establish an $\mathcal{O}(\mathrm{poly}(S, A, H, \log T))$ worst-case regret for it, where $T$ is the number of episodes. Furthermore, we extend our results to quantum RL with linear function approximation, which is capable of handling problems with large state spaces. Specifically, we develop a quantum algorithm based on value target regression (VTR) for linear mixture MDPs with $d$-dimensional linear representation and prove that it enjoys $\mathcal{O}(\mathrm{poly}(d, H, \log T))$ regret. Our algorithms are variants of UCRL/UCRL-VTR algorithms in classical RL, which also leverage a novel combination of lazy updating mechanisms and quantum estimation subroutines. This is the key to breaking the $Ω(\sqrt{T})$-regret barrier in classical RL. To the best of our knowledge, this is the first work studying the online exploration in quantum RL with provable logarithmic worst-case regret.

quant-ph↗

arXiv2024

Visual Autoregressive Modeling: Scalable Image Generation via Next-Scale Prediction

We present Visual AutoRegressive modeling (VAR), a new generation paradigm that redefines the autoregressive learning on images as coarse-to-fine "next-scale prediction" or "next-resolution prediction", diverging from the standard raster-scan "next-token prediction". This simple, intuitive methodology allows autoregressive (AR) transformers to learn visual distributions fast and generalize well: VAR, for the first time, makes GPT-like AR models surpass diffusion transformers in image generation. On ImageNet 256x256 benchmark, VAR significantly improve AR baseline by improving Frechet inception distance (FID) from 18.65 to 1.73, inception score (IS) from 80.4 to 350.2, with around 20x faster inference speed. It is also empirically verified that VAR outperforms the Diffusion Transformer (DiT) in multiple dimensions including image quality, inference speed, data efficiency, and scalability. Scaling up VAR models exhibits clear power-law scaling laws similar to those observed in LLMs, with linear correlation coefficients near -0.998 as solid evidence. VAR further showcases zero-shot generalization ability in downstream tasks including image in-painting, out-painting, and editing. These results suggest VAR has initially emulated the two important properties of LLMs: Scaling Laws and zero-shot task generalization. We have released all models and codes to promote the exploration of AR/VAR models for visual generation and unified learning.

cs.CV↗

arXiv2024

Quantum Algorithms and Lower Bounds for Finite-Sum Optimization

Finite-sum optimization has wide applications in machine learning, covering important problems such as support vector machines, regression, etc. In this paper, we initiate the study of solving finite-sum optimization problems by quantum computing. Specifically, let $f_1,\ldots,f_n\colon\mathbb{R}^d\to\mathbb{R}$ be $\ell$-smooth convex functions and $ψ\colon\mathbb{R}^d\to\mathbb{R}$ be a $μ$-strongly convex proximal function. The goal is to find an $ε$-optimal point for $F(\mathbf{x})=\frac{1}{n}\sum_{i=1}^n f_i(\mathbf{x})+ψ(\mathbf{x})$. We give a quantum algorithm with complexity $\tilde{O}\big(n+\sqrt{d}+\sqrt{\ell/μ}\big(n^{1/3}d^{1/3}+n^{-2/3}d^{5/6}\big)\big)$, improving the classical tight bound $\tildeΘ\big(n+\sqrt{n\ell/μ}\big)$. We also prove a quantum lower bound $\tildeΩ(n+n^{3/4}(\ell/μ)^{1/4})$ when $d$ is large enough. Both our quantum upper and lower bounds can extend to the cases where $ψ$ is not necessarily strongly convex, or each $f_i$ is Lipschitz but not necessarily smooth. In addition, when $F$ is nonconvex, our quantum algorithm can find an $ε$-critial point using $\tilde{O}(n+\ell(d^{1/3}n^{1/3}+\sqrt{d})/ε^2)$ queries.

quant-ph↗