Author name cluster

Ziwei Yang

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

3 papers

1 author row

AAAI Conference 2026 Conference Paper

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

Rikuto Kotoge
Ziwei Yang
Zheng Chen
Yushun Dong
Yasuko Matsubara
Jimeng Sun
Yasushi Sakurai

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 4.5× higher Fidelity+ (necessity) and 14× lower Fidelity- (sufficiency) than explainer baselines, while preserving signaling chains up to 4× longer.

PDF Details DOI

NeurIPS Conference 2024 Conference Paper

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

Jinghui Lu
Ziwei Yang
Yanjie Wang
Xuejing Liu
Brian Mac Namee
Can Huang

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. All resources are available at https: //github. com/GeorgeLuImmortal/PaDeLLM_NER.

PDF Details DOI

IJCAI Conference 2022 Conference Paper

Multi-Tier Platform for Cognizing Massive Electroencephalogram

Zheng Chen
Lingwei Zhu
Ziwei Yang
Renyuan Zhang

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.

PDF Details DOI