arXiv subjects

Ziwei Yang

Publications and source records attributed to Ziwei Yang.

At least 19 recordsLinked to original sources

arXiv2026

Engineering of Dual Wavelength, Polarization Selective Metalenses in Silicon Carbide

Spin defects in silicon carbide (SiC) are promising candidates for integrated quantum photonics, offering long-lived spin states and near-infrared emission suitable for low-loss photonic integration and fibre-based quantum communication. However, light extraction from these defects remains challenging due the relatively high refractive index of SiC. Metalenses offer a compact approach to enhance light collection by engineering the wavefront directly at the material interface. Here, we design and fabricate monolithic metalenses from SiC bulk material that simultaneously operate at 860 and 1240 nm, matching with emission from the nitrogen vacancy and silicon vacancy colour centers. By independently engineering the phase response at both wavelengths, the metalens enables collection and polarization manipulation of the emitted light. We further employ the metalenses to demonstrate optically detected magnetic resonance of both defects simultaneously. These multifunctional metalenses provide a compact optical interface for scalable integrated SiC photonic devices.

quant-ph↗

arXiv2026

All-optical control of nonlinear emission from resonant metasurfaces

Nonlinear optics underpins a broad range of photonic technologies, from classical and quantum light sources to emerging nonlinear photonic neural networks. Yet, conventional nonlinear optical devices exhibit static functionality: their transfer characteristics and emission profiles are dictated by the intrinsic nonlinear process and locked by fabrication, limiting adaptability. Here, we introduce an ultra-thin metasurface platform that enables dynamic reconfiguration of nonlinear functionality in a contact-less fashion. By leveraging all-optical control of the optical torque exerted on liquid crystal molecules infiltrating a resonant metasurface, we achieve tunable polynomial nonlinear transfer functions based on third-harmonic generation process. This mechanism further allows real-time modulation of nonlinear weighting across different diffraction orders, revealing a previously unexplored interplay between mode structure and nonlinear emission. Our approach opens up a pathway toward field-programmable nonlinear photonic systems, offering unprecedented flexibility for reconfigurable nonlinear signal processing and adaptive photonic computing.

physics.optics↗

arXiv2025

DeepEvidence: Empowering Biomedical Discovery with Deep Knowledge Graph Research

Biomedical knowledge graphs (KGs) encode vast, heterogeneous information spanning literature, genes, pathways, drugs, diseases, and clinical trials, but leveraging them collectively for scientific discovery remains difficult. Their structural differences, continual evolution, and limited cross-resource alignment require substantial manual integration, limiting the depth and scale of knowledge exploration. We introduce DeepEvidence, an AI-agent framework designed to perform Deep Research across various heterogeneous biomedical KGs. Unlike generic Deep Research systems that rely primarily on internet-scale text, DeepEvidence incorporates specialized knowledge-graph tooling and coordinated exploration strategies to systematically bridge heterogeneous resources. At its core is an orchestrator that directs two complementary agents: Breadth-First ReSearch (BFRS) for broad, multi-graph entity search, and Depth-First ReSearch (DFRS) for multi-hop, evidence-focused reasoning. An internal, incrementally built evidence graph provides a structured record of retrieved entities, relations, and supporting evidence. To operate at scale, DeepEvidence includes unified interfaces for querying diverse biomedical APIs and an execution sandbox that enables programmatic data retrieval, extraction, and analysis. Across established deep-reasoning benchmarks and four key stages of the biomedical discovery lifecycle: drug discovery, pre-clinical experimentation, clinical trial development, and evidence-based medicine, DeepEvidence demonstrates substantial gains in systematic exploration and evidence synthesis. These results highlight the potential of knowledge-graph-driven Deep Research to accelerate biomedical discovery.

cs.IR↗

arXiv2025

FinGAIA: A Chinese Benchmark for AI Agents in Real-World Financial Domain

The booming development of AI agents presents unprecedented opportunities for automating complex tasks across various domains. However, their multi-step, multi-tool collaboration capabilities in the financial sector remain underexplored. This paper introduces FinGAIA, an end-to-end benchmark designed to evaluate the practical abilities of AI agents in the financial domain. FinGAIA comprises 407 meticulously crafted tasks, spanning seven major financial sub-domains: securities, funds, banking, insurance, futures, trusts, and asset management. These tasks are organized into three hierarchical levels of scenario depth: basic business analysis, asset decision support, and strategic risk management. We evaluated 10 mainstream AI agents in a zero-shot setting. The best-performing agent, ChatGPT, achieved an overall accuracy of 48.9\%, which, while superior to non-professionals, still lags financial experts by over 35 percentage points. Error analysis has revealed five recurring failure patterns: Cross-modal Alignment Deficiency, Financial Terminological Bias, Operational Process Awareness Barrier, among others. These patterns point to crucial directions for future research. Our work provides the first agent benchmark closely related to the financial domain, aiming to objectively assess and promote the development of agents in this crucial field. Partial data is available at https://github.com/SUFE-AIFLM-Lab/FinGAIA.

cs.CL↗

arXiv2025

Enhanced Multimodal Aspect-Based Sentiment Analysis by LLM-Generated Rationales

There has been growing interest in Multimodal Aspect-Based Sentiment Analysis (MABSA) in recent years. Existing methods predominantly rely on pre-trained small language models (SLMs) to collect information related to aspects and sentiments from both image and text, with an aim to align these two modalities. However, small SLMs possess limited capacity and knowledge, often resulting in inaccurate identification of meaning, aspects, sentiments, and their interconnections in textual and visual data. On the other hand, Large language models (LLMs) have shown exceptional capabilities in various tasks by effectively exploring fine-grained information in multimodal data. However, some studies indicate that LLMs still fall short compared to fine-tuned small models in the field of ABSA. Based on these findings, we propose a novel framework, termed LRSA, which combines the decision-making capabilities of SLMs with additional information provided by LLMs for MABSA. Specifically, we inject explanations generated by LLMs as rationales into SLMs and employ a dual cross-attention mechanism for enhancing feature interaction and fusion, thereby augmenting the SLMs' ability to identify aspects and sentiments. We evaluated our method using two baseline models, numerous experiments highlight the superiority of our approach on three widely-used benchmarks, indicating its generalizability and applicability to most pre-trained models for MABSA.

cs.CL↗

arXiv2025

GraphGDel: Constructing and Learning Graph Representations of Genome-Scale Metabolic Models for Growth-Coupled Gene Deletion Prediction

In genome-scale constraint-based metabolic models, gene deletion strategies are essential for achieving growth-coupled production, where cell growth and target metabolite synthesis occur simultaneously. Despite the inherently networked nature of genome-scale metabolic models, existing computational approaches rely primarily on sequential data and lack graph representations that capture their complex relationships, as both well-defined graph constructions and learning frameworks capable of exploiting them remain largely unexplored. To address this gap, we present a twofold solution. First, we introduce a systematic pipeline for constructing graph representations from constraint-based metabolic models. Second, we develop a deep learning framework that integrates these graph representations with gene and metabolite sequence data to predict growth-coupled gene deletion strategies. Across three metabolic models, our approach consistently outperforms established baselines, with improvements in overall accuracy of 14.04%, 16.26%, and 13.18% over a deep feedforward neural network baseline, 6.17%, 4.96%, and 5.31% over a sequence-learning baseline, and 5.10%, 4.36%, and 4.70% over a topology-aware graph aggregation baseline on the same metabolite graph, respectively. The source code and example datasets are available at: https://github.com/MetNetComp/GraphGDel.

q-bio.QM↗

arXiv2025

ExPath: Targeted Pathway Inference for Biological Knowledge Bases via Graph Learning and Explanation

Retrieving targeted pathways in biological knowledge bases, particularly when incorporating wet-lab experimental data, remains a challenging task and often requires downstream analyses and specialized expertise. In this paper, we frame this challenge as a solvable graph learning and explaining task and propose a novel subgraph inference framework, ExPAth, that explicitly integrates experimental data to classify various graphs (bio-networks) in biological databases. The links (representing pathways) that contribute more to classification can be considered as targeted pathways. Our framework can seamlessly integrate biological foundation models to encode the experimental molecular data. We propose ML-oriented biological evaluations and a new metric. The experiments involving 301 bio-networks evaluations demonstrate that pathways inferred by ExPath are biologically meaningful, achieving up to 4.5x higher Fidelity+ (necessity) and 14x lower Fidelity- (sufficiency) than explainer baselines, while preserving signaling chains up to 4x longer.

cs.LG↗

arXiv2024

DBgDel: Database-Enhanced Gene Deletion Framework for Growth-Coupled Production in Genome-Scale Metabolic Models

When simulating metabolite productions with genome-scale constraint-based metabolic models, gene deletion strategies are necessary to achieve growth-coupled production, which means cell growth and target metabolite production occur simultaneously. Since obtaining gene deletion strategies for large genome-scale models suffers from significant computational time, it is necessary to develop methods to mitigate this computational burden. In this study, we introduce a novel framework for computing gene deletion strategies. The proposed framework first mines related databases to extract prior information about gene deletions for growth-coupled production. It then integrates the extracted information with downstream algorithms to narrow down the algorithmic search space, resulting in highly efficient calculations on genome-scale models. Computational experiment results demonstrated that our framework can compute stoichiometrically feasible gene deletion strategies for numerous target metabolites, showcasing a noteworthy improvement in computational efficiency. Specifically, our framework achieves an average 6.1-fold acceleration in computational speed compared to existing methods while maintaining a respectable success rate. The source code of DBgDel with examples are available on https://github.com/MetNetComp/DBgDel.

q-bio.QM↗

arXiv2024

Can Large Language Models Replace Data Scientists in Biomedical Research?

Data science plays a critical role in biomedical research, but it requires professionals with expertise in coding and medical data analysis. Large language models (LLMs) have shown great potential in supporting medical tasks and performing well in general coding tests. However, existing evaluations fail to assess their capability in biomedical data science, particularly in handling diverse data types such as genomics and clinical datasets. To address this gap, we developed a benchmark of data science coding tasks derived from the analyses of 39 published studies. This benchmark comprises 293 coding tasks (128 in Python and 165 in R) performed on real-world TCGA-type genomics and clinical data. Our findings reveal that the vanilla prompting of LLMs yields suboptimal performances due to drawbacks in following input instructions, understanding target data, and adhering to standard analysis practices. Next, we benchmarked six cutting-edge LLMs and advanced adaptation methods, finding two methods to be particularly effective: chain-of-thought prompting, which provides a step-by-step plan for data analysis, which led to a 21% code accuracy improvement (56.6% versus 35.3%); and self-reflection, enabling LLMs to refine the buggy code iteratively, yielding an 11% code accuracy improvement (45.5% versus 34.3%). Building on these insights, we developed a platform that integrates LLMs into the data science workflow for medical professionals. In a user study with five medical professionals, we found that while LLMs cannot fully automate programming tasks, they significantly streamline the programming process. We found that 80% of their submitted code solutions were incorporated from LLM-generated code, with up to 96% reuse in some cases. Our analysis highlights the potential of LLMs to enhance data science efficiency in biomedical research when integrated into expert workflows.

cs.AI↗

arXiv2024

GeSubNet: Gene Interaction Inference for Disease Subtype Network Generation

Retrieving gene functional networks from knowledge databases presents a challenge due to the mismatch between disease networks and subtype-specific variations. Current solutions, including statistical and deep learning methods, often fail to effectively integrate gene interaction knowledge from databases or explicitly learn subtype-specific interactions. To address this mismatch, we propose GeSubNet, which learns a unified representation capable of predicting gene interactions while distinguishing between different disease subtypes. Graphs generated by such representations can be considered subtype-specific networks. GeSubNet is a multi-step representation learning framework with three modules: First, a deep generative model learns distinct disease subtypes from patient gene expression profiles. Second, a graph neural network captures representations of prior gene networks from knowledge databases, ensuring accurate physical gene interactions. Finally, we integrate these two representations using an inference loss that leverages graph generation capabilities, conditioned on the patient separation loss, to refine subtype-specific information in the learned representation. GeSubNet consistently outperforms traditional methods, with average improvements of 30.6%, 21.0%, 20.1%, and 56.6% across four graph evaluation metrics, averaged over four cancer datasets. Particularly, we conduct a biological simulation experiment to assess how the behavior of selected genes from over 11,000 candidates affects subtypes or patient distributions. The results show that the generated network has the potential to identify subtype-specific genes with an 83% likelihood of impacting patient distribution shifts.

cs.LG↗

arXiv2024

MLOmics: Cancer Multi-Omics Database for Machine Learning

Framing the investigation of diverse cancers as a machine learning problem has recently shown significant potential in multi-omics analysis and cancer research. Empowering these successful machine learning models are the high-quality training datasets with sufficient data volume and adequate preprocessing. However, while there exist several public data portals, including The Cancer Genome Atlas (TCGA) multi-omics initiative or open-bases such as the LinkedOmics, these databases are not off-the-shelf for existing machine learning models. In this paper, we introduce MLOmics, an open cancer multi-omics database aiming at serving better the development and evaluation of bioinformatics and machine learning models. MLOmics contains 8,314 patient samples covering all 32 cancer types with four omics types, stratified features, and extensive baselines. Complementary support for downstream analysis and bio-knowledge linking are also included to support interdisciplinary analysis.

q-bio.GN↗

arXiv2024

A Bounding Box is Worth One Token: Interleaving Layout and Text in a Large Language Model for Document Understanding

Recently, many studies have demonstrated that exclusively incorporating OCR-derived text and spatial layouts with large language models (LLMs) can be highly effective for document understanding tasks. However, existing methods that integrate spatial layouts with text have limitations, such as producing overly long text sequences or failing to fully leverage the autoregressive traits of LLMs. In this work, we introduce Interleaving Layout and Text in a Large Language Model (LayTextLLM)} for document understanding. LayTextLLM projects each bounding box to a single embedding and interleaves it with text, efficiently avoiding long sequence issues while leveraging autoregressive traits of LLMs. LayTextLLM not only streamlines the interaction of layout and textual data but also shows enhanced performance in KIE and VQA. Comprehensive benchmark evaluations reveal significant improvements of LayTextLLM, with a 15.2% increase on KIE tasks and 10.7% on VQA tasks compared to previous SOTA OCR-based LLMs. All resources are available at https://github.com/LayTextLLM/LayTextLLM.

cs.CL↗

arXiv2024

PaDeLLM-NER: Parallel Decoding in Large Language Models for Named Entity Recognition

In this study, we aim to reduce generation latency for Named Entity Recognition (NER) with Large Language Models (LLMs). The main cause of high latency in LLMs is the sequential decoding process, which autoregressively generates all labels and mentions for NER, significantly increase the sequence length. To this end, we introduce Parallel Decoding in LLM for NE} (PaDeLLM-NER), a approach that integrates seamlessly into existing generative model frameworks without necessitating additional modules or architectural modifications. PaDeLLM-NER allows for the simultaneous decoding of all mentions, thereby reducing generation latency. Experiments reveal that PaDeLLM-NER significantly increases inference speed that is 1.76 to 10.22 times faster than the autoregressive approach for both English and Chinese. Simultaneously it maintains the quality of predictions as evidenced by the performance that is on par with the state-of-the-art across various datasets.

cs.CL↗

arXiv2023

Bridging Cross-task Protocol Inconsistency for Distillation in Dense Object Detection

Knowledge distillation (KD) has shown potential for learning compact models in dense object detection. However, the commonly used softmax-based distillation ignores the absolute classification scores for individual categories. Thus, the optimum of the distillation loss does not necessarily lead to the optimal student classification scores for dense object detectors. This cross-task protocol inconsistency is critical, especially for dense object detectors, since the foreground categories are extremely imbalanced. To address the issue of protocol differences between distillation and classification, we propose a novel distillation method with cross-task consistent protocols, tailored for the dense object detection. For classification distillation, we address the cross-task protocol inconsistency problem by formulating the classification logit maps in both teacher and student models as multiple binary-classification maps and applying a binary-classification distillation loss to each map. For localization distillation, we design an IoU-based Localization Distillation Loss that is free from specific network structures and can be compared with existing localization distillation losses. Our proposed method is simple but effective, and experimental results demonstrate its superiority over existing methods. Code is available at https://github.com/TinyTigerPan/BCKD.

cs.CV↗

arXiv2023

MoCLIM: Towards Accurate Cancer Subtyping via Multi-Omics Contrastive Learning with Omics-Inference Modeling

Precision medicine fundamentally aims to establish causality between dysregulated biochemical mechanisms and cancer subtypes. Omics-based cancer subtyping has emerged as a revolutionary approach, as different level of omics records the biochemical products of multistep processes in cancers. This paper focuses on fully exploiting the potential of multi-omics data to improve cancer subtyping outcomes, and hence developed MoCLIM, a representation learning framework. MoCLIM independently extracts the informative features from distinct omics modalities. Using a unified representation informed by contrastive learning of different omics modalities, we can well-cluster the subtypes, given cancer, into a lower latent space. This contrast can be interpreted as a projection of inter-omics inference observed in biological networks. Experimental results on six cancer datasets demonstrate that our approach significantly improves data fit and subtyping performance in fewer high-dimensional cancer instances. Moreover, our framework incorporates various medical evaluations as the final component, providing high interpretability in medical analysis.

q-bio.GN↗

arXiv2023

Understanding and Unifying Fourteen Attribution Methods with Taylor Interactions

Various attribution methods have been developed to explain deep neural networks (DNNs) by inferring the attribution/importance/contribution score of each input variable to the final output. However, existing attribution methods are often built upon different heuristics. There remains a lack of a unified theoretical understanding of why these methods are effective and how they are related. To this end, for the first time, we formulate core mechanisms of fourteen attribution methods, which were designed on different heuristics, into the same mathematical system, i.e., the system of Taylor interactions. Specifically, we prove that attribution scores estimated by fourteen attribution methods can all be reformulated as the weighted sum of two types of effects, i.e., independent effects of each individual input variable and interaction effects between input variables. The essential difference among the fourteen attribution methods mainly lies in the weights of allocating different effects. Based on the above findings, we propose three principles for a fair allocation of effects to evaluate the faithfulness of the fourteen attribution methods.

cs.LG↗

arXiv2022

Cancer Subtyping by Improved Transcriptomic Features Using Vector Quantized Variational Autoencoder

Defining and separating cancer subtypes is essential for facilitating personalized therapy modality and prognosis of patients. The definition of subtypes has been constantly recalibrated as a result of our deepened understanding. During this recalibration, researchers often rely on clustering of cancer data to provide an intuitive visual reference that could reveal the intrinsic characteristics of subtypes. The data being clustered are often omics data such as transcriptomics that have strong correlations to the underlying biological mechanism. However, while existing studies have shown promising results, they suffer from issues associated with omics data: sample scarcity and high dimensionality. As such, existing methods often impose unrealistic assumptions to extract useful features from the data while avoiding overfitting to spurious correlations. In this paper, we propose to leverage a recent strong generative model, Vector Quantized Variational AutoEncoder (VQ-VAE), to tackle the data issues and extract informative latent features that are crucial to the quality of subsequent clustering by retaining only information relevant to reconstructing the input. VQ-VAE does not impose strict assumptions and hence its latent features are better representations of the input, capable of yielding superior clustering performance with any mainstream clustering method. Extensive experiments and medical analysis on multiple datasets comprising 10 distinct cancers demonstrate the VQ-VAE clustering results can significantly and robustly improve prognosis over prevalent subtyping systems.

cs.LG↗

arXiv2022

Automated Cancer Subtyping via Vector Quantization Mutual Information Maximization

Cancer subtyping is crucial for understanding the nature of tumors and providing suitable therapy. However, existing labelling methods are medically controversial, and have driven the process of subtyping away from teaching signals. Moreover, cancer genetic expression profiles are high-dimensional, scarce, and have complicated dependence, thereby posing a serious challenge to existing subtyping models for outputting sensible clustering. In this study, we propose a novel clustering method for exploiting genetic expression profiles and distinguishing subtypes in an unsupervised manner. The proposed method adaptively learns categorical correspondence from latent representations of expression profiles to the subtypes output by the model. By maximizing the problem -- agnostic mutual information between input expression profiles and output subtypes, our method can automatically decide a suitable number of subtypes. Through experiments, we demonstrate that our proposed method can refine existing controversial labels, and, by further medical analysis, this refinement is proven to have a high correlation with cancer survival rates.

cs.LG↗