Paper List
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STAR-GO: Improving Protein Function Prediction by Learning to Hierarchically Integrate Ontology-Informed Semantic Embeddings
This paper addresses the core challenge of generalizing protein function prediction to unseen or newly introduced Gene Ontology (GO) terms by overcomi...
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Incorporating indel channels into average-case analysis of seed-chain-extend
This paper addresses the core pain point of bridging the theoretical gap for the widely used seed-chain-extend heuristic by providing the first rigoro...
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Competition, stability, and functionality in excitatory-inhibitory neural circuits
This paper addresses the core challenge of extending interpretable energy-based frameworks to biologically realistic asymmetric neural networks, where...
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Enhancing Clinical Note Generation with ICD-10, Clinical Ontology Knowledge Graphs, and Chain-of-Thought Prompting Using GPT-4
This paper addresses the core challenge of generating accurate and clinically relevant patient notes from sparse inputs (ICD codes and basic demograph...
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Hypothesis-Based Particle Detection for Accurate Nanoparticle Counting and Digital Diagnostics
This paper addresses the core challenge of achieving accurate, interpretable, and training-free nanoparticle counting in digital diagnostic assays, wh...
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MCP-AI: Protocol-Driven Intelligence Framework for Autonomous Reasoning in Healthcare
This paper addresses the critical gap in healthcare AI systems that lack contextual reasoning, long-term state management, and verifiable workflows by...
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Model Gateway: Model Management Platform for Model-Driven Drug Discovery
This paper addresses the critical bottleneck of fragmented, ad-hoc model management in pharmaceutical research by providing a centralized, scalable ML...
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Tree Thinking in the Genomic Era: Unifying Models Across Cells, Populations, and Species
This paper addresses the fragmentation of tree-based inference methods across biological scales by identifying shared algorithmic principles and stati...
A Theoretical Framework for the Formation of Large Animal Groups: Topological Coordination, Subgroup Merging, and Velocity Inheritance
Department of Computer Science and Technology, Capital University of Economics and Business, Beijing 100070, China.
The 30-Second View
IN SHORT: This paper addresses the core problem of how large, coordinated animal groups form in nature, challenging the classical view of gradual aggregation by proposing a mechanism of rapid subgroup merging driven by topological network dynamics.
Innovation (TL;DR)
- Theory Introduces a topological coordination theory based on time-varying directed interaction networks, identifying a single dominant Strongly Connected Component (SCC) as the driver of group velocity.
- Methodology Proposes the 'velocity inheritance' mechanism, where a trailing subgroup aligns with and inherits the velocity of the leading subgroup's dominant SCC during merging events.
- Biology Provides a unified, mechanistic explanation for multiple empirical features of animal groups, including broad neighbor-distance distributions, directional asymmetry, and narrow-front/wide-rear geometry.
Key conclusions
- Large moving groups form not by slow accumulation but through rapid merging of pre-existing subgroups under high-density conditions, driven by topological network structure.
- The long-term interaction network of any coordinated group contains a single dominant SCC that dictates the collective velocity (speed and direction) for the entire group.
- Repeated subgroup merging, governed by velocity inheritance, predicts that larger groups move more slowly than the mean speed of the original constituent subgroups—a testable hypothesis for existing 3D tracking datasets.
Abstract: Large animal groups—bird flocks, fish schools, insect swarms—are often assumed to form by gradual aggregation of sparsely distributed individuals. Using a mathematically precise framework based on time-varying directed interaction networks, we show that this widely held view is incomplete. The theory demonstrates that large moving groups do not arise by slow accumulation; instead, they emerge through the rapid merging of multiple pre-existing subgroups that are simultaneously activated under high-density conditions. The key mechanism is topological: the long-term interaction structure of any moving group contains a single dominant strongly connected component (SCC). This dominant SCC determines the collective velocity—both speed and direction—of the entire group. When two subgroups encounter one another, the trailing subgroup aligns with—and ultimately inherits—the velocity of the dominant SCC of the leading subgroup. Repeated merging events naturally generate large groups whose speed is predicted to be lower than the mean speed of the original subgroups. The same dynamics explain several universal empirical features: broad neighbour-distance distributions, directional asymmetry in neighbour selection, and the characteristic narrow-front, wide-rear geometry of real flocks. The framework yields testable predictions for STARFLAG-style 3D datasets, offering a unified explanation for the formation, maintenance, and geometry of coordinated animal groups.