most citedAssemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

742 citations · 742 across the 21 of their papers we have counts for

collaborators

21 papers

cs.DC2026

SAGA: Workflow-Atomic Scheduling for AI Agent Inference on GPU Clusters

Dongxin Guo, Jikun Wu, Siu Ming Yiu

AI agents execute tens to hundreds of chained LLM calls per task, yet GPU schedulers treat each call as independent, discarding gigabytes of intermediate state between steps and in…

cs.NE2026

Parameter-Efficient Neuroevolution for Diverse LLM Generation: Quality-Diversity Optimization via Prompt Embedding Evolution

Dongxin Guo, Jikun Wu, Siu Ming Yiu

Large Language Models exhibit mode collapse, producing homogeneous outputs that fail to explore valid solution spaces. We present QD-LLM, a framework for parameter-efficient neuroe…

cs.NE2026

EvoPref: Multi-Objective Evolutionary Optimization Discovers Diverse LLM Alignments Beyond Gradient Descent

Dongxin Guo, Jikun Wu, Siu Ming Yiu

Gradient-based preference optimization methods for large language model (LLM) alignment suffer from preference collapse, converging to narrow behavioral modes while neglecting pref…

cs.AI2026

The Deterministic Horizon: When Extended Reasoning Fails and Tool Delegation Becomes Necessary

Dongxin Guo, Jikun Wu, Siu Ming Yiu

Extended chain-of-thought reasoning can degrade performance on deterministic state-tracking tasks, not solely because of preference biases but, on the evidence we present, because…

cs.CL2026

Model Collapse as Cultural Evolution

Dongxin Guo, Jikun Wu, Siu Ming Yiu

Model collapse, the progressive degradation of LLMs trained on their own outputs, has been characterized statistically but lacks a linguistic explanation for which structures degra…

cs.CL2026

Do Language Models Know What Not to Say? Causal Evidence for Statistical Preemption in LLMs

Dongxin Guo, Jikun Wu, Siu Ming Yiu

How do learners acquire knowledge of what is unacceptable without negative evidence? Construction Grammar proposes statistical preemption: exposure to a conventional form (e.g., "d…

cs.CL2026

Sparse Autoencoders Map Brain-LLM Alignment onto Cortical Semantic Topography

Dongxin Guo, Jikun Wu, Siu Ming Yiu

Intermediate layers of large language models (LLMs) best predict human brain responses to language, one of the most robust findings in computational neurolinguistics, yet why remai…

cs.CL2026

Brain-LLM Alignment Tracks Training Data, Not Typology

Dongxin Guo, Jikun Wu, Siu Ming Yiu

Brain-LLM alignment is well established in English, yet the brain's language network is neuroanatomically universal across languages. Does alignment also generalize cross-linguisti…

cs.IR2026

When to Retrieve During Reasoning: Adaptive Retrieval for Large Reasoning Models

Dongxin Guo, Jikun Wu, Siu Ming Yiu

Large reasoning models such as DeepSeek-R1 and OpenAI o1 generate extended chains of thought spanning thousands of tokens, yet their integration with retrieval-augmented generation…

cs.AI2026

FinGround: Detecting and Grounding Financial Hallucinations via Atomic Claim Verification

Dongxin Guo, Jikun Wu, Siu Ming Yiu

Financial AI systems must produce answers grounded in specific regulatory filings, yet current LLMs fabricate metrics, invent citations, and miscalculate derived quantities. These…

cs.CL2026

ComplianceNLP: Knowledge-Graph-Augmented RAG for Multi-Framework Regulatory Gap Detection

Dongxin Guo, Jikun Wu, Siu Ming Yiu

Financial institutions must track over 60,000 regulatory events annually, overwhelming manual compliance teams; the industry has paid over USD 300 billion in fines and settlements…

cs.SE2026

AgentEval: DAG-Structured Step-Level Evaluation for Agentic Workflows with Error Propagation Tracking

Dongxin Guo, Jikun Wu, Siu Ming Yiu

Agentic systems that chain reasoning, tool use, and synthesis into multi-step workflows are entering production, yet prevailing evaluation practices like end-to-end outcome checks…

cs.CL2026

RouteNLP: Closed-Loop LLM Routing with Conformal Cascading and Distillation Co-Optimization

Dongxin Guo, Jikun Wu, Siu Ming Yiu

Serving diverse NLP workloads with large language models is costly: at one enterprise partner, inference costs exceeded $200K/month despite over 70% of queries being routine tasks…

cs.LG2026

GeoCert: Certified Geometric AI for Reliable Forecasting

Regina Zhang, Zongru Li, Honggang Wen +4

Forecasting systems in science must be accurate, physically consistent, and certifiably reliable. Most existing models address prediction, constraint enforcement, and verification…

cs.LG2026

SafeAnchor: Preventing Cumulative Safety Erosion in Continual Domain Adaptation of Large Language Models

Dongxin Guo, Jikun Wu, Siu Ming Yiu

Safety alignment in large language models is remarkably shallow: it is concentrated in the first few output tokens and reversible by fine-tuning on as few as 100 adversarial exampl…

cs.LG2026

Closing the Theory-Practice Gap in Spiking Transformers via Effective Dimension

Dongxin Guo, Jikun Wu, Siu Ming Yiu

Spiking transformers achieve competitive accuracy with conventional transformers while offering - energy efficiency on neuromorphic hardware, yet no theoretical frame…

cs.LG2026

When Do Early-Exit Networks Generalize? A PAC-Bayesian Theory of Adaptive Depth

Dongxin Guo, Jikun Wu, Siu Ming Yiu

Early-exit neural networks enable adaptive computation by allowing confident predictions to exit at intermediate layers, achieving 2-8 inference speedup. Despite widespread…

cs.AI2026

Geometric Metrics for MoE Specialization: From Fisher Information to Early Failure Detection

Dongxin Guo, Jikun Wu, Siu Ming Yiu

Expert specialization is fundamental to Mixture-of-Experts (MoE) model success, yet existing metrics (cosine similarity, routing entropy) lack theoretical grounding and yield incon…

cs.GT2026

Coalition Formation in LLM Agent Networks: Stability Analysis and Convergence Guarantees

Dongxin Guo, Jikun Wu, Siu-Ming Yiu

Large Language Model (LLM) agents are increasingly deployed in multi-agent systems requiring strategic coordination. While recent work has analyzed LLM behavior in two-player games…

cs.LG2026

Capacity-Controlled Global Attention for Graph Transformers

Yang Liu, Dongxin Guo, Tom Zheng +3

Global self-attention drives modern graph transformers, yet the softmax at its core imposes a structural constraint rarely examined directly: every attention row is non-negative an…

q-bio.GN2013★ 742 cited

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov +88

Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished g…