arXiv subjects

Haoxiang Xia

Publications and source records attributed to Haoxiang Xia.

12 recordsLinked to original sources

arXiv2026

GRIT: Graph-Regularized Logit Refinement for Zero-shot Cell Type Annotation

Cell type annotation is a fundamental step in the analysis of single-cell RNA sequencing (scRNA-seq) data. In practice, human experts often rely on the structure revealed by principal component analysis (PCA) followed by $k$-nearest neighbor ($k$-NN) graph construction to guide annotation. While effective, this process is labor-intensive and does not scale to large datasets. Recent advances in CLIP-style models offer a promising path toward automating cell type annotation. By aligning scRNA-seq profiles with natural language descriptions, models like LangCell enable zero-shot annotation. While LangCell demonstrates decent zero-shot performance, its predictions remain suboptimal. In this paper, we propose a principled inference-time paradigm for zero-shot cell type annotation (GRIT) which bridges the scalability of pre-trained foundation models with the structural robustness relied upon in human expert annotation workflows. Specifically, we enforce local consistency of the zero-shot CLIP logits over the task-specific PCA-based $k$-NN graph. We evaluate our approach on 14 annotated human scRNA-seq datasets from 4 distinct studies, spanning 11 organs and over 200,000 single cells. Our method consistently improves zero-shot annotation accuracy, achieving accuracy gains of up to 10\%. Further analysis showcase the mechanism by which GRIT effectively propagates correct signals through the graph, pulling back mislabeled cells toward more accurate predictions. The method is training-free, model-agnostic, and serves as a simple yet effective plug-in for enhancing zero-shot cell type annotation.

q-bio.GN↗

arXiv2025

Beyond N-grams: A Hierarchical Reward Learning Framework for Clinically-Aware Medical Report Generation

Automatic medical report generation can greatly reduce the workload of doctors, but it is often unreliable for real-world deployment. Current methods can write formally fluent sentences but may be factually flawed, introducing serious medical errors known as clinical hallucinations, which make them untrustworthy for diagnosis. To bridge this gap, we introduce HiMed-RL, a Hierarchical Medical Reward Learning Framework designed to explicitly prioritize clinical quality. HiMed-RL moves beyond simple text matching by deconstructing reward learning into three synergistic levels: it first ensures linguistic fluency at the token-level, then enforces factual grounding at the concept-level by aligning key medical terms with expert knowledge, and finally assesses high-level diagnostic consistency at the semantic-level using a specialized LLM verifier. This hierarchical reward is implemented via a Human-inspired Dynamic Reward Adjustment, a strategy which first teaches the model to learn basic facts before progressing to more complex diagnostic reasoning. Experimentally, HiMed-3B achieves state-of-the-art performance on both in-domain and out-of-domain benchmarks, particularly on the latter, with an improvement of 12.1% over the second-best baseline. Our work provides a robust paradigm for generating reports that not only improve fluency but clinical fine-grained quality.

cs.CE↗

arXiv2025

Co-evolution of cooperation and resource allocation in the advantageous environment-based spatial multi-game using adaptive control

In real-life complex systems, individuals often encounter multiple social dilemmas that cannot be effectively captured using a single-game model. Furthermore, the environment and limited resources both play a crucial role in shaping individuals' decision-making behaviors. In this study, we employ an adaptive control mechanism by which agents may benefit from their environment, thus redefining their individual fitness. Under this setting, a detailed examination of the co-evolution of individual strategies and resource allocation is carried. Through extensive simulations, we find that the advantageous environment mechanism not only significantly increases the proportion of cooperators in the system but also influences the resource distribution among individuals. Additionally, limited resources reinforce cooperative behaviors within the system while shaping the evolutionary dynamics and strategic interactions across different dilemmas. Once the system reaches equilibrium, resource distribution becomes highly imbalanced. To promote fairer resource allocation, we introduce a minimum resource guarantee mechanism. Our results show that this mechanism not only reduces disparities in resource distribution across the entire system and among individuals in different dilemmas but also significantly enhances cooperative behavior in higher resource intervals. Finally, to assess the robustness of our model, we further examine the influence of the advantageous environment on system-wide cooperation in small-world and random graph network models.

physics.soc-ph↗

arXiv2024

Initial Burst of Disruptive Efforts Ensuring Scientific Career Viability

Despite persistent efforts to understand the dynamics of creativity of scientists over careers in terms of productivity, impact, and prize, little is known about the dynamics of scientists' disruptive efforts that affect individual academic careers and drive scientific advance. Drawing on millions of data over six decades and across nineteen disciplines, associating the publication records of individual scientists with the disruption index, we systematically quantify the temporal pattern of disruptive ideas over individual scientific careers, providing a detailed understanding of the macro phenomenon of scientific stagnation from the individual perspective. We start by checking the relationship between disruption-based and citation-based publication profiles. Next, we observe the finite inequality in the disruptive productivity of scientists, diminishing gradually as the level of disruption increases. We then identify the initial burst phenomenon in disruption dynamics. It is further revealed that while early engagement in high disruption frictions away initial productivity, compared to initial advantage in productivity or impact, initial high disruption ensures more subsequent academic viability evidenced by a longer career span and relatively final higher productivity, but does not necessarily guarantee academic success throughout careers. Further analysis shows that increasing disruptive work is uncorrelated to overall productivity but negatively correlated with the overall impact. However, increasing disruptive work in the early career is associated with higher overall productivity, yet lower overall productivity in the later career. Our research underscores the urgent need for a policy shift that encourages a balance between the pursuit of disruptive efforts and the achievement of impactful outcomes.

physics.soc-ph↗

arXiv2023

Science as Exploration in a Knowledge Landscape: Tracing Hotspots or Seeking Opportunity?

The selection of research topics by scientists can be viewed as an exploration process conducted by individuals with cognitive limitations traversing a complex cognitive landscape influenced by both individual and social factors. While existing theoretical investigations have provided valuable insights, the intricate and multifaceted nature of modern science hinders the implementation of empirical experiments. This study leverages advancements in deep learning techniques to investigate the patterns and dynamic mechanisms of topic-transition among scientists. By constructing the knowledge space across 6 large-scale disciplines, we depict the trajectories of scientists' topic transitions within this space, measuring the flow and distance of research regions across different sub-spaces. Our findings reveal a predominantly conservative pattern of topic transition at the individual level, with scientists primarily exploring local knowledge spaces. Furthermore, simulation modeling analysis identifies research intensity, driven by the concentration of scientists within a specific region, as the key facilitator of topic transition. Conversely, the knowledge distance between fields serves as a significant barrier to exploration. Notably, despite potential opportunities for breakthrough discoveries at the intersection of subfields, empirical evidence suggests that these opportunities do not exert a strong pull on scientists, leading them to favor familiar research areas. Our study provides valuable insights into the exploration dynamics of scientific knowledge production, highlighting the influence of individual cognition, social factors, and the intrinsic structure of the knowledge landscape itself. These findings offer a framework for understanding and potentially shaping the course of scientific progress.

physics.soc-ph↗

arXiv2023

Scientists' bounded mobility on the epistemic landscape

Despite persistent efforts in revealing the temporal patterns in scientific careers, little attention has been paid to the spatial patterns of scientific activities in the knowledge space. Here, drawing on millions of papers in six disciplines, we consider scientists' publication sequence as "walks" on the quantifiable epistemic landscape constructed from large-scale bibliometric corpora by combining embedding and manifold learning algorithms, aiming to reveal the individual research topic dynamics and association between research radius with academic performance, along their careers. Intuitively, the visualization shows the localized and bounded nature of mobile trajectories. We further find that the distributions of scientists' transition radius and transition pace are both left-skewed compared with the results of controlled experiments. Then, we observe the mixed exploration and exploitation pattern and the corresponding strategic trade-off in the research transition, where scientists both deepen their previous research with frequency bias and explore new research with knowledge proximity bias. We further develop a bounded exploration-exploitation (BEE) model to reproduce the observed patterns. Moreover, the association between scientists' research radius and academic performance shows that extensive exploration will not lead to a sustained increase in academic output but a decrease in impact. In addition, we also note that disruptive findings are more derived from an extensive transition, whereas there is a saturation in this association. Our study contributes to the comprehension of the mobility patterns of scientists in the knowledge space, thereby providing significant implications for the development of scientific policy-making.

physics.soc-ph↗

arXiv2020

Estimating international trade status of countries from global liner shipping networks

Maritime shipping is a backbone of international trade and, thus, the world economy. Cargo-loaded vessels travel from one country's port to another via an underlying port-to-port transport network, contributing to international trade values of countries en route. We hypothesize that ports that involve trans-shipment activities serve as a third-party broker to mediate trade between two foreign countries and contribute to the corresponding country's status in international trade. We test this hypothesis using a port-level dataset of global liner shipping services. We propose two indices that quantify the importance of countries in the global liner shipping network and show that they explain a large amount of variation in individual countries' international trade values and related measures. These results support a long-standing view in maritime economics, which has yet to be directly tested, that countries that are strongly integrated into the global maritime transportation network have enhanced access to global markets and trade opportunities.

cs.SI↗

arXiv2020

Consensus, Bi-polarization and Multiformity in Opinion Dynamics with Bidirectional Thresholds

Many empirical networks are intrinsically pluralistic, with interactions occurring within groups of arbitrary agents. Then the agent in the network can be influenced by types of neighbors, common examples include similarity, opposition, and negligibility. Although the influence of neighbors can be described as an amicable and antagonistic relationship in complex real-world systems accurately, and the research on the dynamic process of public opinion evolution with different types of influence is valuable, few studies have mentioned that issue. In this paper, we develop a novel model on networks of agents with the bi-directional bounded thresholds for studying the evolution of opinion dynamics. We define the scope of individual assimilation and exclusion to identify different types of neighbors and calculate the impact of the corresponding neighbors on the individuals by converting the opinion difference. The simulation results show that the proposed mechanism can effectively explain the formation of bi-polarization during opinion evolution and the settings of the bi-directional bounded thresholds significantly influence the eventual distribution of opinions. Furthermore, we explore the impacts of the initial conditions and the structure of the small-world network on the evolution of opinions.

physics.soc-ph↗

arXiv2020

Modular gateway-ness connectivity and structural core organization in maritime network science

Around 80% of global trade by volume is transported by sea, and thus the maritime transportation system is fundamental to the world economy. To better exploit new international shipping routes, we need to understand the current ones and their complex systems association with international trade. We investigate the structure of the global liner shipping network (GLSN), finding it is an economic small-world network with a trade-off between high transportation efficiency and low wiring cost. To enhance understanding of this trade-off, we examine the modular segregation of the GLSN; we study provincial-, connector-hub ports and propose the definition of gateway-hub ports, using three respective structural measures. The gateway-hub structural-core organization seems a salient property of the GLSN, which proves importantly associated to network integration and function in realizing the cargo transportation of international trade. This finding offers new insights into the GLSN's structural organization complexity and its relevance to international trade.

physics.soc-ph↗

arXiv2019

Multiscale core-periphery structure in a global liner shipping network

Maritime transport accounts for a majority of trades in volume, of which 70% in value is carried by container ships that transit regular routes on fixed schedules in the ocean. In the present paper, we analyse a data set of global liner shipping as a network of ports. In particular, we construct the network of the ports as the one-mode projection of a bipartite network composed of ports and ship routes. Like other transportation networks, global liner shipping networks may have core-periphery structure, where a core and a periphery are groups of densely and sparsely interconnected nodes, respectively. Core-periphery structure may have practical implications for understanding the robustness, efficiency and uneven development of international transportation systems. We develop an algorithm to detect core-periphery pairs in a network, which allows one to find core and peripheral nodes on different scales and uses a configuration model that accounts for the fact that the network is obtained by the one-mode projection of a bipartite network. We also found that most ports are core (as opposed to peripheral) ports and that ports in some countries in Europe, America and Asia belong to a global core-periphery pair across different scales, whereas ports in other countries do not.

physics.soc-ph↗

arXiv2016

An Investigation of Intra-Urban Mobility Pattern of Taxi Passengers

The study of human mobility patterns is of both theoretical and practical values in many aspects. For long-distance travels, a few research endeavors have shown that the displacements of human travels follow the power-law distribution. However, controversies remain in the issue of the scaling law of human mobility in intra-urban areas. In this work we focus on the mobility pattern of taxi passengers by examining five datasets of the three metropolitans of New York, Dalian and Nanjing. Through statistical analysis, we find that the lognormal distribution with a power-law tail can best approximate both the displacement and the duration time of taxi trips, as well as the vacant time of taxicabs, in all the examined cities. The universality of scaling law of human mobility is subsequently discussed, in accordance with the data analytics.

physics.soc-ph↗

arXiv2015

Evolution of Scientific Collaboration Network Driven by Homophily and Heterophily

Many scientific collaboration networks exhibit clear community and small world structures. However, the studies on the underlying mechanisms for the formation and evolution of community and small world structures are still insufficient. The mechanisms of homophily and heterophily based on scholars' traits are two important factors for the formation of community and inter-communal links, which may deserve further exploration. In this paper, a multi-agent model, which is based on combinatorial effects of homophily and heterophily, is developed to investigate the evolution of scientific collaboration networks. The simulation results indicate that agents with similar traits aggregate to form community by homophily, while heterophily plays a major role in the formation of inter-communal links. The pattern of network evolution revealed in simulations is essentially consistent with what is observed in empirical analyses, as in both cases the giant component evolves from a small cluster to a structure of chained-communities, and then to a small world network with community structure. This work may provides an alternative view on the underlying mechanisms for the formation of community and small world structures, complementary to the mainstream view that the small-world is generated from the combination of the structural embeddedness and structural holes mechanisms.

physics.soc-ph↗