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Chenwei Zhang

Chenwei Zhang contributes to research discovery and scholarly infrastructure.

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Computation and Language Artificial Intelligence Machine Learning Biomolecules cond-mat.mtrl-sci Information Retrieval physics.soc-ph Quantitative Methods Social and Information Networks

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preprint2026arXiv

Enhancing Cryo-EM Density Map Segmentation in Phenix for Improved Atomic Model Building

We introduce PhenixCraft, a fully automated pipeline for building atomic models from cryo-EM density maps. By integrating AlphaFold predictions, we enhance the map-segmentation step in Phenix during model building, addressing challenges posed by noise and artifacts that traditionally hinder this step. Our results demonstrate PhenixCraft's superior performance in TM-scores and sequence accuracy, significantly improving upon the limitations and inefficiencies of traditional model building using Phenix.

preprint2026arXiv

T$^2$PO: Uncertainty-Guided Exploration Control for Stable Multi-Turn Agentic Reinforcement Learning

Recent progress in multi-turn reinforcement learning (RL) has significantly improved reasoning LLMs' performances on complex interactive tasks. Despite advances in stabilization techniques such as fine-grained credit assignment and trajectory filtering, instability remains pervasive and often leads to training collapse. We argue that this instability stems from inefficient exploration in multi-turn settings, where policies continue to generate low-information actions that neither reduce uncertainty nor advance task progress. To address this issue, we propose Token- and Turn-level Policy Optimization (T$^2$PO), an uncertainty-aware framework that explicitly controls exploration at fine-grained levels. At the token level, T$^2$PO monitors uncertainty dynamics and triggers a thinking intervention once the marginal uncertainty change falls below a threshold. At the turn level, T$^2$PO identifies interactions with negligible exploration progress and dynamically resamples such turns to avoid wasted rollouts. We evaluate T$^2$PO in diverse environments, including WebShop, ALFWorld, and Search QA, demonstrating substantial gains in training stability and performance improvements with better exploration efficiency. Code is available at: https://github.com/WillDreamer/T2PO.

preprint2026arXiv

Unintended Negative Impacts of Promotional Language in Patent Evaluation

Promotional language has been increasingly used to aid the communication of innovative ideas in science. Yet, less is known about its role in the context of technological innovation. Here, we use a validated and domain-diagnosed lexicon of 135 promotional words to study the association between promotional language and patent evaluation outcomes among 2.7 million USPTO patent applications. Our large-scale study reveals three unexpected findings. First, in contrast to scientific evaluation, we find that a higher frequency of promotional words is negatively associated with the probability of an application being (i) granted a patent, (ii) transferred ownership, and (iii) successfully appealed. This promotional penalty holds even after accounting for a range of confounding factors and is largely robust across different technological areas. Among matched samples, the difference in the success rate between the lowest and highest promotional density quintile is 5.5, 5.9, and 5.3 percentage points for patentability, transferability, and rejection reversal. Second, contrary to institutional skepticism, we show that promotional language is not a mask of weak technology, but objectively reflects the degree of combinatorial novelty and future citation impact. Third, digging into the mechanisms, we find that the tolerance to promotional framing is strongly moderated by human factors, with men and experienced examiners showing a higher acceptance of promotional narratives than women and novice examiners. By revealing an emerging paradox in the patent system, our study offers theoretical and practical implications for improving patent evaluation through more objective scrutiny of linguistic patterns in patent filings.

preprint2022arXiv

OA-Mine: Open-World Attribute Mining for E-Commerce Products with Weak Supervision

Automatic extraction of product attributes from their textual descriptions is essential for online shopper experience. One inherent challenge of this task is the emerging nature of e-commerce products -- we see new types of products with their unique set of new attributes constantly. Most prior works on this matter mine new values for a set of known attributes but cannot handle new attributes that arose from constantly changing data. In this work, we study the attribute mining problem in an open-world setting to extract novel attributes and their values. Instead of providing comprehensive training data, the user only needs to provide a few examples for a few known attribute types as weak supervision. We propose a principled framework that first generates attribute value candidates and then groups them into clusters of attributes. The candidate generation step probes a pre-trained language model to extract phrases from product titles. Then, an attribute-aware fine-tuning method optimizes a multitask objective and shapes the language model representation to be attribute-discriminative. Finally, we discover new attributes and values through the self-ensemble of our framework, which handles the open-world challenge. We run extensive experiments on a large distantly annotated development set and a gold standard human-annotated test set that we collected. Our model significantly outperforms strong baselines and can generalize to unseen attributes and product types.

preprint2022arXiv

Team Power Dynamics and Team Impact: New Perspectives on Scientific Collaboration using Career Age as a Proxy for Team Power

Power dynamics influence every aspect of scientific collaboration. Team power dynamics can be measured by team power level and team power hierarchy. Team power level is conceptualized as the average level of the possession of resources, expertise, or decision-making authorities of a team. Team power hierarchy represents the vertical differences of the possessions of resources in a team. In Science of Science, few studies have looked at scientific collaboration from the perspective of team power dynamics. This research examines how team power dynamics affect team impact to fill the research gap. In this research, all co-authors of one publication are treated as one team. Team power level and team power hierarchy of one team are measured by the mean and Gini index of career age of co-authors in this team. Team impact is quantified by citations of a paper authored by this team. By analyzing over 7.7 million teams from Science (e.g., Computer Science, Physics), Social Sciences (e.g., Sociology, Library & Information Science), and Arts & Humanities (e.g., Art), we find that flat team structure is associated with higher team impact, especially when teams have high team power level. These findings have been repeated in all five disciplines except Art, and are consistent in various types of teams from Computer Science including teams from industry or academia, teams with different gender groups, teams with geographical contrast, and teams with distinct size.

preprint2021arXiv

Minimally-Supervised Structure-Rich Text Categorization via Learning on Text-Rich Networks

Text categorization is an essential task in Web content analysis. Considering the ever-evolving Web data and new emerging categories, instead of the laborious supervised setting, in this paper, we focus on the minimally-supervised setting that aims to categorize documents effectively, with a couple of seed documents annotated per category. We recognize that texts collected from the Web are often structure-rich, i.e., accompanied by various metadata. One can easily organize the corpus into a text-rich network, joining raw text documents with document attributes, high-quality phrases, label surface names as nodes, and their associations as edges. Such a network provides a holistic view of the corpus' heterogeneous data sources and enables a joint optimization for network-based analysis and deep textual model training. We therefore propose a novel framework for minimally supervised categorization by learning from the text-rich network. Specifically, we jointly train two modules with different inductive biases -- a text analysis module for text understanding and a network learning module for class-discriminative, scalable network learning. Each module generates pseudo training labels from the unlabeled document set, and both modules mutually enhance each other by co-training using pooled pseudo labels. We test our model on two real-world datasets. On the challenging e-commerce product categorization dataset with 683 categories, our experiments show that given only three seed documents per category, our framework can achieve an accuracy of about 92%, significantly outperforming all compared methods; our accuracy is only less than 2% away from the supervised BERT model trained on about 50K labeled documents.

preprint2020arXiv

Attribute2vec: Deep Network Embedding Through Multi-Filtering GCN

We present a multi-filtering Graph Convolution Neural Network (GCN) framework for network embedding task. It uses multiple local GCN filters to do feature extraction in every propagation layer. We show this approach could capture different important aspects of node features against the existing attribute embedding based method. We also show that with multi-filtering GCN approach, we can achieve significant improvement against baseline methods when training data is limited. We also perform many empirical experiments and demonstrate the benefit of using multiple filters against single filter as well as most current existing network embedding methods for both the link prediction and node classification tasks.

preprint2020arXiv

AutoKnow: Self-Driving Knowledge Collection for Products of Thousands of Types

Can one build a knowledge graph (KG) for all products in the world? Knowledge graphs have firmly established themselves as valuable sources of information for search and question answering, and it is natural to wonder if a KG can contain information about products offered at online retail sites. There have been several successful examples of generic KGs, but organizing information about products poses many additional challenges, including sparsity and noise of structured data for products, complexity of the domain with millions of product types and thousands of attributes, heterogeneity across large number of categories, as well as large and constantly growing number of products. We describe AutoKnow, our automatic (self-driving) system that addresses these challenges. The system includes a suite of novel techniques for taxonomy construction, product property identification, knowledge extraction, anomaly detection, and synonym discovery. AutoKnow is (a) automatic, requiring little human intervention, (b) multi-scalable, scalable in multiple dimensions (many domains, many products, and many attributes), and (c) integrative, exploiting rich customer behavior logs. AutoKnow has been operational in collecting product knowledge for over 11K product types.

preprint2020arXiv

CG-BERT: Conditional Text Generation with BERT for Generalized Few-shot Intent Detection

In this paper, we formulate a more realistic and difficult problem setup for the intent detection task in natural language understanding, namely Generalized Few-Shot Intent Detection (GFSID). GFSID aims to discriminate a joint label space consisting of both existing intents which have enough labeled data and novel intents which only have a few examples for each class. To approach this problem, we propose a novel model, Conditional Text Generation with BERT (CG-BERT). CG-BERT effectively leverages a large pre-trained language model to generate text conditioned on the intent label. By modeling the utterance distribution with variational inference, CG-BERT can generate diverse utterances for the novel intents even with only a few utterances available. Experimental results show that CG-BERT achieves state-of-the-art performance on the GFSID task with 1-shot and 5-shot settings on two real-world datasets.

preprint2020arXiv

Entity Synonym Discovery via Multipiece Bilateral Context Matching

Being able to automatically discover synonymous entities in an open-world setting benefits various tasks such as entity disambiguation or knowledge graph canonicalization. Existing works either only utilize entity features, or rely on structured annotations from a single piece of context where the entity is mentioned. To leverage diverse contexts where entities are mentioned, in this paper, we generalize the distributional hypothesis to a multi-context setting and propose a synonym discovery framework that detects entity synonyms from free-text corpora with considerations on effectiveness and robustness. As one of the key components in synonym discovery, we introduce a neural network model SYNONYMNET to determine whether or not two given entities are synonym with each other. Instead of using entities features, SYNONYMNET makes use of multiple pieces of contexts in which the entity is mentioned, and compares the context-level similarity via a bilateral matching schema. Experimental results demonstrate that the proposed model is able to detect synonym sets that are not observed during training on both generic and domain-specific datasets: Wiki+Freebase, PubMed+UMLS, and MedBook+MKG, with up to 4.16% improvement in terms of Area Under the Curve and 3.19% in terms of Mean Average Precision compared to the best baseline method.

preprint2020arXiv

Generative Temporal Link Prediction via Self-tokenized Sequence Modeling

We formalize networks with evolving structures as temporal networks and propose a generative link prediction model, Generative Link Sequence Modeling (GLSM), to predict future links for temporal networks. GLSM captures the temporal link formation patterns from the observed links with a sequence modeling framework and has the ability to generate the emerging links by inferring from the probability distribution on the potential future links. To avoid overfitting caused by treating each link as a unique token, we propose a self-tokenization mechanism to transform each raw link in the network to an abstract aggregation token automatically. The self-tokenization is seamlessly integrated into the sequence modeling framework, which allows the proposed GLSM model to have the generalization capability to discover link formation patterns beyond raw link sequences. We compare GLSM with the existing state-of-art methods on five real-world datasets. The experimental results demonstrate that GLSM obtains future positive links effectively in a generative fashion while achieving the best performance (2-10\% improvements on AUC) among other alternatives.

preprint2020arXiv

Med2Meta: Learning Representations of Medical Concepts with Meta-Embeddings

Distributed representations of medical concepts have been used to support downstream clinical tasks recently. Electronic Health Records (EHR) capture different aspects of patients' hospital encounters and serve as a rich source for augmenting clinical decision making by learning robust medical concept embeddings. However, the same medical concept can be recorded in different modalities (e.g., clinical notes, lab results)-with each capturing salient information unique to that modality-and a holistic representation calls for relevant feature ensemble from all information sources. We hypothesize that representations learned from heterogeneous data types would lead to performance enhancement on various clinical informatics and predictive modeling tasks. To this end, our proposed approach makes use of meta-embeddings, embeddings aggregated from learned embeddings. Firstly, modality-specific embeddings for each medical concept is learned with graph autoencoders. The ensemble of all the embeddings is then modeled as a meta-embedding learning problem to incorporate their correlating and complementary information through a joint reconstruction. Empirical results of our model on both quantitative and qualitative clinical evaluations have shown improvements over state-of-the-art embedding models, thus validating our hypothesis.

preprint2020arXiv

Octet: Online Catalog Taxonomy Enrichment with Self-Supervision

Taxonomies have found wide applications in various domains, especially online for item categorization, browsing, and search. Despite the prevalent use of online catalog taxonomies, most of them in practice are maintained by humans, which is labor-intensive and difficult to scale. While taxonomy construction from scratch is considerably studied in the literature, how to effectively enrich existing incomplete taxonomies remains an open yet important research question. Taxonomy enrichment not only requires the robustness to deal with emerging terms but also the consistency between existing taxonomy structure and new term attachment. In this paper, we present a self-supervised end-to-end framework, Octet, for Online Catalog Taxonomy EnrichmenT. Octet leverages heterogeneous information unique to online catalog taxonomies such as user queries, items, and their relations to the taxonomy nodes while requiring no other supervision than the existing taxonomies. We propose to distantly train a sequence labeling model for term extraction and employ graph neural networks (GNNs) to capture the taxonomy structure as well as the query-item-taxonomy interactions for term attachment. Extensive experiments in different online domains demonstrate the superiority of Octet over state-of-the-art methods via both automatic and human evaluations. Notably, Octet enriches an online catalog taxonomy in production to 2 times larger in the open-world evaluation.

preprint2019arXiv

Multi-Grained Named Entity Recognition

This paper presents a novel framework, MGNER, for Multi-Grained Named Entity Recognition where multiple entities or entity mentions in a sentence could be non-overlapping or totally nested. Different from traditional approaches regarding NER as a sequential labeling task and annotate entities consecutively, MGNER detects and recognizes entities on multiple granularities: it is able to recognize named entities without explicitly assuming non-overlapping or totally nested structures. MGNER consists of a Detector that examines all possible word segments and a Classifier that categorizes entities. In addition, contextual information and a self-attention mechanism are utilized throughout the framework to improve the NER performance. Experimental results show that MGNER outperforms current state-of-the-art baselines up to 4.4% in terms of the F1 score among nested/non-overlapping NER tasks.

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