arXiv subjects

Hanlin Xiao

Publications and source records attributed to Hanlin Xiao.

8 recordsLinked to original sources

arXiv2026

Data-Scarce, Multi-Granular, Multimodal: Benchmark Design for Biosynthetic Gene Clusters

Biosynthetic gene clusters (BGCs) are co-located genes that encode the biosynthesis of specialized metabolites, an important source of antibiotics, anticancer agents, immunosuppressants, and agricultural bioactives. Deep learning, particularly self-supervised foundation models, has spurred interest in BGC sequence modeling, but evaluation has lagged behind: existing benchmarks often rely on coarse classification over small curated datasets, providing limited discrimination among models and insight into downstream utility. We propose a benchmark-design framework in which an informative benchmark should be discriminative, separating models with statistical confidence, and applicable, spanning scientifically meaningful tasks under different levels of generalization. We instantiate this framework as BGC-Bench, which derives five tasks from MIBiG, ranging from A-domain substrate prediction to BGC-molecule retrieval, evaluates them under genotype- and phenotype-shift splits, includes an active-learning setting for label-scarce discovery, and is easily extensible to new tasks and encoders. BGCs further provide a shared testbed across granularities and modalities: BGC-Bench compares twelve encoders on nucleotide, amino-acid, or Pfam-domain sequences, including compositional baselines for each input type, and combines BGC and chemical encoders for cross-modal retrieval. No single representation dominates: the best granularity depends on the biological scale of the task, and pretrained encoders do not consistently outperform other representations across tasks and splits. Active-learning experiments show that most tasks remain data-limited, encoder rankings change with labeling budget, and acquisition strategies yield modest gains. These results show that BGC model evaluation requires task-diverse, shift-aware benchmarks, and the framework can be generalized to benchmark design beyond BGCs.

cs.AI↗

arXiv2026

Calibrated Typed Decisions for Entity, Relation, and Event Extraction

Information extraction models often perform well on the datasets they are trained on, but transferring to new domains and annotation guidelines remains challenging. Supporting user-specified types alone does not resolve this problem. We present CalOn, a unified 0.6B-parameter encoder for entity, relation, and event extraction across datasets and schemas. The model jointly encodes text and type definitions, then directly identifies entity spans, relations between spans, and event triggers and arguments. Its extraction decisions consider the requested types together, using their combined evidence to identify relevant candidates before assigning a type. This gives all three tasks a common probabilistic formulation while keeping every extracted mention anchored to the input text. We train on diverse sources, and supplement supervised learning with a reward that encourages correct extractions and penalises incorrect ones. Across 40 benchmarks, CalOn outperforms the evaluated baselines on most benchmarks. It leads all reported relation extraction benchmarks and achieves the highest average F1 for event triggers and arguments with gold triggers. The same model also performs strongly on aspect sentiment triplet extraction and pronoun resolution through its span-pair formulation. A correction for the probability bias introduced during training improves confidence estimates for entities, relations, and event arguments after calibration, with little change in F1.

cs.CL↗

arXiv2026

Why Large Language Models and Humans Converge and Diverge in Evaluating Creativity

Despite the growing use of large language models (LLMs) as creativity evaluators, evidence of their alignment with human evaluations remains mixed, raising the question of when and why their judgments converge with or diverge from those of humans. Across three studies and six widely used LLMs, we addressed this gap by identifying the standards underlying LLM creativity evaluation and examining their downstream implications. Study 1 showed that LLMs generally relied on a narrower subset of human creativity evaluation standards. Convergence with human standards was strongest in the novelty dimension, whereas divergence was clearest in the contextual dimension, which captures social, market, and reputational information. Moreover, each LLM exhibited distinct, model-specific standards that varied substantially in breadth. These differences in evaluation standards were reflected in actual creativity judgments. Study 2 (N = 1,103 ideas) showed that LLM evaluations were moderately correlated with human evaluations, and individual LLMs with broader standards better distinguished ideas humans judged as more versus less creative. Study 3 (N = 1,195 participants) showed that LLMs were less sensitive to contextual information: such information significantly altered human creativity ratings but left LLM ratings largely unchanged. Together, our findings help explain the mixed evidence on LLM-human alignment, showing that alignment depends on the evidence a judgment demands and the standards each model applies. Selecting an LLM evaluator is therefore a consequential decision: different models, applying different standards, recognise different ideas as creative.

cs.CL↗

arXiv2026

Disentangling Similarity and Relatedness in Topic Models

The recent success of large pre-trained language models (PLMs) has motivated their integration into topic modeling. However, PLM-augmented topic models differ from classical co-occurrence models such as Latent Dirichlet Allocation (LDA) not only in performance, but also in the type of semantic structure they capture. We formalize this distinction along two psycholinguistic axes: thematic relatedness (dog/bone) and taxonomic similarity (dog/wolf). To measure both axes over topic words, we construct a large synthetic benchmark of word pairs using LLM-based annotation and train a neural scorer on it. Across multiple corpora and model families, the scorer places different topic-model families at distinct positions within the joint similarity-relatedness space. The two scores further predict downstream task performance: tasks requiring similarity benefit from similarity-rich topics, whereas tasks requiring relatedness benefit from the converse, and excessive emphasis on either axis degrades performance on tasks aligned with the opposing semantic structure. Neither axis is uniformly beneficial. Measuring both therefore provides a practical, model-agnostic diagnostic for evaluating the semantic structure captured by topic models.

cs.CL↗

arXiv2026

Cross-Granularity Representations for Biological Sequences: Insights from ESM and BiGCARP

Recent advances in general-purpose foundation models have stimulated the development of large biological sequence models. While natural language shows symbolic granularity (characters, words, sentences), biological sequences exhibit hierarchical granularity whose levels (nucleotides, amino acids, protein domains, genes) further encode biologically functional information. In this paper, we investigate the integration of cross-granularity knowledge from models through a case study of BiGCARP, a Pfam domain-level model for biosynthetic gene clusters, and ESM, an amino acid-level protein language model. Using representation analysis tools and a set of probe tasks, we first explain why a straightforward cross-model embedding initialization fails to improve downstream performance in BiGCARP, and show that deeper-layer embeddings capture a more contextual and faithful representation of the model's learned knowledge. Furthermore, we demonstrate that representations at different granularities encode complementary biological knowledge, and that combining them yields measurable performance gains in intermediate-level prediction tasks. Our findings highlight cross-granularity integration as a promising strategy for improving both the performance and interpretability of biological foundation models.

cs.LG↗

arXiv2025

Citrus: Leveraging Expert Cognitive Pathways in a Medical Language Model for Advanced Medical Decision Support

Large language models (LLMs), particularly those with reasoning capabilities, have rapidly advanced in recent years, demonstrating significant potential across a wide range of applications. However, their deployment in healthcare, especially in disease reasoning tasks, is hindered by the challenge of acquiring expert-level cognitive data. In this paper, we introduce Citrus, a medical language model that bridges the gap between clinical expertise and AI reasoning by emulating the cognitive processes of medical experts. The model is trained on a large corpus of simulated expert disease reasoning data, synthesized using a novel approach that accurately captures the decision-making pathways of clinicians. This approach enables Citrus to better simulate the complex reasoning processes involved in diagnosing and treating medical conditions. To further address the lack of publicly available datasets for medical reasoning tasks, we release the last-stage training data, including a custom-built medical diagnostic dialogue dataset. This open-source contribution aims to support further research and development in the field. Evaluations using authoritative benchmarks such as MedQA, covering tasks in medical reasoning and language understanding, show that Citrus achieves superior performance compared to other models of similar size. These results highlight Citrus potential to significantly enhance medical decision support systems, providing a more accurate and efficient tool for clinical decision-making.

cs.AI↗

arXiv2024

Beacon-enabled TDMA Ultraviolet Communication Network System Design and Realization

Nonline of sight (NLOS) ultraviolet (UV) scattering communication can serve as a good candidate for outdoor optical wireless communication (OWC) in the cases of non-perfect transmitter-receiver alignment and radio silence. We design and demonstrate a NLOS UV scattering communication network system in this paper, where a beacon-enabled time division multiple access (TDMA) scheme is adopted. In our system, LED and PMT are employed for transmitter and receiver devices, repectivey. Furthermore, we design algorithms for beacon transmission, beacon reception, time compensation, and time slot transition for hardware realization in field-programmable gate array (FPGA) board based on master-slave structure, where master node periodically transmits beacon signals to slave nodes. Experimental results are provided to evaluate the time synchronization error and specify the system key parameters for real-time implementation. We perform field tests for real-time communication network with the transmission range over 110 multiplied by 90 square meters, where the system throughput reaches 800kbps.

eess.SY↗

arXiv2023

What Really is `Molecule' in Molecular Communications? The Quest for Physics of Particle-based Information Carriers

Molecular communication, as implied by its name, uses molecules as information carriers for communication between objects. It has an advantage over traditional electromagnetic-wave-based communication in that molecule-based systems could be biocompatible, operable in challenging environments, and energetically undemanding. Consequently, they are envisioned to have a broad range of applications, such as in the Internet of Bio-nano Things, targeted drug delivery, and agricultural monitoring. Despite the rapid development of the field, with an increasing number of theoretical models and experimental testbeds established by researchers, a fundamental aspect of the field has often been sidelined, namely, the nature of the molecule in molecular communication. The potential information molecules could exhibit a wide range of properties, making them require drastically different treatments when being modeled and experimented upon. Therefore, in this paper, we delve into the intricacies of commonly used information molecules, examining their fundamental physical characteristics, associated communication systems, and potential applications in a more realistic manner, focusing on the influence of their own properties. Through this comprehensive survey, we aim to offer a novel yet essential perspective on molecular communication, thereby bridging the current gap between theoretical research and real-world applications.

eess.SP↗