Ziwei Yang

Longrong Yang, Xianpan Zhou, Xuewei Li et al.

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.

Jinghui Lu, Haiyang Yu, Yanjie Wang et al.

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.

Zheng Chen, Ziwei Yang, Lingwei Zhu et al.

This paper proposes a novel framework for automatically capturing the time-frequency nature of electroencephalogram (EEG) signals of human sleep based on the authoritative sleep medicine guidance. The framework consists of two parts: the first part extracts informative features by partitioning the input EEG spectrograms into a sequence of time-frequency patches. The second part is constituted by an attention-based architecture to efficiently search for the correlation between partitioned time-frequency patches and defining factors of sleep stages in parallel. The proposed pipeline is validated on the Sleep Heart Health Study dataset with new state-of-the-art results for the stages wake, N2, and N3, obtaining respective F1 scores of 0.93, 0.88, and 0.87, with only EEG signals used. The proposed method also has a high inter-rater reliability of 0.80 kappa. We also visualize the correspondence between sleep staging decisions and features extracted by the proposed method, providing strong interpretability for our model.

Huiqi Deng, Na Zou, Mengnan Du et al.

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.

Ziwei Yang, Lingwei Zhu, Zheng Chen et al.

Cancer is one of the deadliest diseases worldwide. Accurate diagnosis and classification of cancer subtypes are indispensable for effective clinical treatment. Promising results on automatic cancer subtyping systems have been published recently with the emergence of various deep learning methods. However, such automatic systems often overfit the data due to the high dimensionality and scarcity. In this paper, we propose to investigate automatic subtyping from an unsupervised learning perspective by directly constructing the underlying data distribution itself, hence sufficient data can be generated to alleviate the issue of overfitting. Specifically, we bypass the strong Gaussianity assumption that typically exists but fails in the unsupervised learning subtyping literature due to small-sized samples by vector quantization. Our proposed method better captures the latent space features and models the cancer subtype manifestation on a molecular basis, as demonstrated by the extensive experimental results.

Zheng Chen, Ziwei Yang, Lingwei Zhu et al.

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.

Ziwei Yang, Rikuto Kotoge, Xihao Piao et al.

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.

Zheng Chen, Lingwei Zhu, Ziwei Yang et al.

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.

Zheng Chen, Lingwei Zhu, Ziwei Yang et al.

An end-to-end platform assembling multiple tiers is built for precisely cognizing brain activities. Being fed massive electroencephalogram (EEG) data, the time-frequency spectrograms are conventionally projected into the episode-wise feature matrices (seen as tier-1). A spiking neural network (SNN) based tier is designed to distill the principle information in terms of spike-streams from the rare features, which maintains the temporal implication in the nature of EEGs. The proposed tier-3 transposes time- and space-domain of spike patterns from the SNN; and feeds the transposed pattern-matrices into an artificial neural network (ANN, Transformer specifically) known as tier-4, where a special spanning topology is proposed to match the two-dimensional input form. In this manner, cognition such as classification is conducted with high accuracy. For proof-of-concept, the sleep stage scoring problem is demonstrated by introducing multiple EEG datasets with the largest comprising 42,560 hours recorded from 5,793 subjects. From experiment results, our platform achieves the general cognition overall accuracy of 87% by leveraging sole EEG, which is 2% superior to the state-of-the-art. Moreover, our developed multi-tier methodology offers visible and graphical interpretations of the temporal characteristics of EEG by identifying the critical episodes, which is demanded in neurodynamics but hardly appears in conventional cognition scenarios.

Ziwei Yang, Zheng Chen, Yasuko Matsubara et al.

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.

Zhaowei Liu, Xin Guo, Fangqi Lou et al.

Reasoning large language models are rapidly evolving across various domains. However, their capabilities in handling complex financial tasks still require in-depth exploration. In this paper, we introduce Fin-R1, a reasoning large language model specifically designed for the financial sector. Fin-R1 is built using a two-stage architecture, leveraging a financial reasoning dataset distilled and processed based on DeepSeek-R1. Through supervised fine-tuning (SFT) and reinforcement learning (RL) training, it demonstrates performance close to DeepSeek-R1 with a parameter size of 7 billion across a range of financial reasoning tasks. It achieves the state-of-the-art (SOTA) in the FinQA and ConvFinQA tasks between those LLMs in our evaluation, surpassing larger models in other tasks as well. Fin-R1 showcases strong reasoning and decision-making capabilities, providing solutions to various problems encountered in the financial domain. Our code is available at https://github.com/SUFE-AIFLM-Lab/Fin-R1.

Lingwei Zhu, Koki Odani, Ziwei Yang et al.

Recently there has seen promising results on automatic stage scoring by extracting spatio-temporal features from electroencephalogram (EEG). Such methods entail laborious manual feature engineering and domain knowledge. In this study, we propose an adaptive scheme to probabilistically encode, filter and accumulate the input signals and weight the resultant features by the half-Gaussian probabilities of signal intensities. The adaptive representations are subsequently fed into a transformer model to automatically mine the relevance between features and corresponding stages. Extensive experiments on the largest public dataset against state-of-the-art methods validate the effectiveness of our proposed method and reveal promising future directions.

Ziwei Yang, Takeyuki Tamura

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.

Lingfeng Zeng, Fangqi Lou, Zixuan Wang et al.

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.

Ziwei Yang, Takeyuki Tamura

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 of varying scale, our approach consistently outperforms established baselines, achieves improvements of 14.04%, 16.26%, and 13.18% in overall accuracy. The source code and example datasets are available at: https://github.com/MetNetComp/GraphGDel.

Ruyi Zhang, Ziwei Yang, Zhi Yang et al.

Accuracy predictor is trained to predict the validation accuracy of an network from its architecture encoding. It can effectively assist in designing networks and improving Neural Architecture Search(NAS) efficiency. However, a high-performance predictor depends on adequate trainning samples, which requires unaffordable computation overhead. To alleviate this problem, we propose a novel framework to train an accuracy predictor under few training samples. The framework consists ofdata augmentation methods and an ensemble learning algorithm. The data augmentation methods calibrate weak labels and inject noise to feature space. The ensemble learning algorithm, termed cascade bagging, trains two-level models by sampling data and features. In the end, the advantages of above methods are proved in the Performance Prediciton Track of CVPR2021 1st Lightweight NAS Challenge. Our code is made public at: https://github.com/dlongry/Solutionto-CVPR2021-NAS-Track2.

Jinghui Lu, Ziwei Yang, Yanjie Wang et al.

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.

Jun Cao, Jiyi Li, Ziwei Yang et al.

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.

Ziwei Yang, Zheng Chen, Xin Liu et al.

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.

Rikuto Kotoge, Ziwei Yang, Zheng Chen et al.

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.

Zifeng Wang, Benjamin Danek, Ziwei Yang et al.

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.

Ziwei Yang, Ruyi Zhang, Zhi Yang et al.

One-shot neural architecture search (NAS) applies weight-sharing supernet to reduce the unaffordable computation overhead of automated architecture designing. However, the weight-sharing technique worsens the ranking consistency of performance due to the interferences between different candidate networks. To address this issue, we propose a candidates enhancement method and progressive training pipeline to improve the ranking correlation of supernet. Specifically, we carefully redesign the sub-networks in the supernet and map the original supernet to a new one of high capacity. In addition, we gradually add narrow branches of supernet to reduce the degree of weight sharing which effectively alleviates the mutual interference between sub-networks. Finally, our method ranks the 1st place in the Supernet Track of CVPR2021 1st Lightweight NAS Challenge.