arXiv subjects

Jiayi Xin

Publications and source records attributed to Jiayi Xin.

13 recordsLinked to original sources

arXiv2026

M2G-LLM: Enhancing Clinical Prediction via Multimodal Graph Reasoning and LLM Context Injection

Integrating diverse data modalities --- such as clinical notes, laboratory results, and medical imaging --- is essential for advancing clinical decision-making. While Large Language Models (LLMs) have shown remarkable performance in processing unstructured clinical text, their limited capacity to incorporate non-text modalities hinders their broader utility in healthcare applications. Here, we introduce M2G-LLM (Multimodal MedGraph-LLM), a novel framework that enhances LLMs with multimodal integration and alignment via Graph Neural Networks (GNNs). Our approach models temporal relationships between patient visits, propagates information across clinically similar patients, and aligns heterogeneous data sources to construct enriched multimodal context vectors. These vectors are injected into the intermediate layers of the LLM, enabling joint reasoning over textual and non-textual modalities. We evaluate M2G-LLM on the MIMIC-IV and MIMIC-CXR datasets, demonstrating improvements in clinical prediction tasks over strong baseline models. Our results highlight the promise of combining the language understanding of LLMs with the relational reasoning capabilities of GNNs for comprehensive, multimodal healthcare analysis.

cs.LG↗

arXiv2026

CurveRL: Principled Distribution-Aware Context Reweighting for LLM Reasoning

Context or prompt-level reweighting has emerged as a central algorithmic lever in Reinforcement Learning with Verified Rewards (RLVR) for improving the reasoning capability of large language models, yet the principle determining what constitutes an optimal weighting remains poorly understood. We address this gap by formulating prompt reweighting as a functional derivative of a utility functional defined in the pass-rate function space, yielding a unified optimality framework that accommodates existing schemes, including REINFORCE and GRPO. Building on this optimality framework, we propose a distribution-aware prompt reweighting approach, called CurveRL, based on a quantile coordinate transform, in which the weight assigned to each prompt depends not on the absolute value of pass rates but on its rank and density to reflect the distributional structure of the pass rates in the learning dynamics. Extensive experiments across multiple benchmarks demonstrate that our proposed CurveRL consistently outperforms GRPO and other RLVR baselines. Our study identifies context-distribution control as a principled axis for analyzing and designing prompt-reweighted RLVR algorithms. The code is released in https://github.com/zhyzmath/CurveRL.

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arXiv2026

UCS: Estimating Unseen Coverage for Improved In-Context Learning

In-context learning (ICL) performance depends critically on which demonstrations are placed in the prompt, yet most existing selectors prioritize heuristic notions of relevance or diversity and provide limited insight into the coverage of a demonstration set. We propose Unseen Coverage Selection (UKS), a training-free, subset-level coverage prior motivated by the principle that a good demonstration set should expose the model to latent cluster unrevealed by the currently selected subset. UCS operationalizes this idea by (1) inducing discrete latent clusters from model-consistent embeddings and (2) estimating the number of unrevealed clusters within a candidate subset via a Smoothed Good--Turing estimator from its empirical frequency spectrum. Unlike previous selection methods, UCS is coverage-based and training-free, and can be seamlessly combined with both query-dependent and query-independent selection baselines via a simple regularized objective. Experiments on multiple intent-classification and reasoning benchmarks with frontier Large Language Models show that augmenting strong baselines with UCS consistently improves ICL accuracy by up to 2-6% under the same selection budget, while also yielding insights into task- and model-level latent cluster distributions. Code is available at https://github.com/Raina-Xin/UCS.

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arXiv2026

CAMEL: An ECG Language Model for Forecasting Cardiac Events

Electrocardiograms (ECG) are electrical recordings of the heart that are critical for diagnosing cardiovascular conditions. ECG language models (ELMs) have recently emerged as a promising framework for ECG classification accompanied by report generation. However, current models cannot forecast future cardiac events despite the immense clinical value for planning earlier intervention. To address this gap, we propose CAMEL, the first ELM that is capable of inference over longer signal durations which enables its forecasting capability. Our key insight is a specialized ECG encoder which enables cross-understanding of ECG signals with text. We train CAMEL using established LLM training procedures, combining LoRA adaptation with a curriculum learning pipeline. Our curriculum includes ECG classification, metrics calculations, and multi-turn conversations to elicit reasoning. CAMEL demonstrates strong zero-shot performance across 6 tasks and 9 datasets, including ECGForecastBench, a new benchmark that we introduce for forecasting arrhythmias. CAMEL is on par with or surpasses ELMs and fully supervised baselines both in- and out-of-distribution, achieving SOTA results on ECGBench (+7.0% absolute average gain) as well as ECGForecastBench (+12.4% over fully supervised models and +21.1% over zero-shot ELMs).

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arXiv2025

The Impact of Language Mixing on Bilingual LLM Reasoning

Proficient multilingual speakers often intentionally switch languages in the middle of a conversation. Similarly, recent reasoning-focused bilingual large language models (LLMs) with strong capabilities in both languages exhibit language mixing-alternating languages within their chain of thought. Discouraging this behavior in DeepSeek-R1 was found to degrade accuracy, suggesting that language mixing may benefit reasoning. In this work, we study language switching in Chinese-English bilingual reasoning models. We identify reinforcement learning with verifiable rewards (RLVR) as the critical training stage that leads to language mixing. We show that language mixing can enhance reasoning: enforcing monolingual decoding reduces accuracy by 5.6 percentage points on MATH500. Additionally, a lightweight probe can be trained to predict whether a potential language switch would benefit or harm reasoning, and when used to guide decoding, increases accuracy by 2.92 percentage points. Our findings suggest that language mixing is not merely a byproduct of multilingual training, but is a strategic reasoning behavior.

cs.CL↗

arXiv2025

Improved Therapeutic Antibody Reformatting through Multimodal Machine Learning

Modern therapeutic antibody design often involves composing multi-part assemblages of individual functional domains, each of which may be derived from a different source or engineered independently. While these complex formats can expand disease applicability and improve safety, they present a significant engineering challenge: the function and stability of individual domains are not guaranteed in the novel format, and the entire molecule may no longer be synthesizable. To address these challenges, we develop a machine learning framework to predict "reformatting success" -- whether converting an antibody from one format to another will succeed or not. Our framework incorporates both antibody sequence and structural context, incorporating an evaluation protocol that reflects realistic deployment scenarios. In experiments on a real-world antibody reformatting dataset, we find the surprising result that large pretrained protein language models (PLMs) fail to outperform simple, domain-tailored, multimodal representations. This is particularly evident in the most difficult evaluation setting, where we test model generalization to a new starting antibody. In this challenging "new antibody, no data" scenario, our best multimodal model achieves high predictive accuracy, enabling prioritization of promising candidates and reducing wasted experimental effort.

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arXiv2025

Evaluating the Unseen Capabilities: How Many Theorems Do LLMs Know?

Accurate evaluation of large language models (LLMs) is crucial for understanding their capabilities and guiding their development. However, current evaluations often inconsistently reflect the actual capacities of these models. In this paper, we demonstrate that one of many contributing factors to this \textit{evaluation crisis} is the oversight of unseen knowledge -- information encoded by LLMs but not directly observed or not yet observed during evaluations. We introduce KnowSum, a statistical framework designed to provide a more comprehensive assessment by quantifying the unseen knowledge for a class of evaluation tasks. KnowSum estimates the unobserved portion by extrapolating from the appearance frequencies of observed knowledge instances. We demonstrate the effectiveness and utility of KnowSum across three critical applications: estimating total knowledge, evaluating information retrieval effectiveness, and measuring output diversity. Our experiments reveal that a substantial volume of knowledge is omitted when relying solely on observed LLM performance. Importantly, KnowSum yields significantly different comparative rankings for several common LLMs based on their internal knowledge.

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arXiv2025

I2MoE: Interpretable Multimodal Interaction-aware Mixture-of-Experts

Modality fusion is a cornerstone of multimodal learning, enabling information integration from diverse data sources. However, vanilla fusion methods are limited by (1) inability to account for heterogeneous interactions between modalities and (2) lack of interpretability in uncovering the multimodal interactions inherent in the data. To this end, we propose I2MoE (Interpretable Multimodal Interaction-aware Mixture of Experts), an end-to-end MoE framework designed to enhance modality fusion by explicitly modeling diverse multimodal interactions, as well as providing interpretation on a local and global level. First, I2MoE utilizes different interaction experts with weakly supervised interaction losses to learn multimodal interactions in a data-driven way. Second, I2MoE deploys a reweighting model that assigns importance scores for the output of each interaction expert, which offers sample-level and dataset-level interpretation. Extensive evaluation of medical and general multimodal datasets shows that I2MoE is flexible enough to be combined with different fusion techniques, consistently improves task performance, and provides interpretation across various real-world scenarios. Code is available at https://github.com/Raina-Xin/I2MoE.

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arXiv2024

Flex-MoE: Modeling Arbitrary Modality Combination via the Flexible Mixture-of-Experts

Multimodal learning has gained increasing importance across various fields, offering the ability to integrate data from diverse sources such as images, text, and personalized records, which are frequently observed in medical domains. However, in scenarios where some modalities are missing, many existing frameworks struggle to accommodate arbitrary modality combinations, often relying heavily on a single modality or complete data. This oversight of potential modality combinations limits their applicability in real-world situations. To address this challenge, we propose Flex-MoE (Flexible Mixture-of-Experts), a new framework designed to flexibly incorporate arbitrary modality combinations while maintaining robustness to missing data. The core idea of Flex-MoE is to first address missing modalities using a new missing modality bank that integrates observed modality combinations with the corresponding missing ones. This is followed by a uniquely designed Sparse MoE framework. Specifically, Flex-MoE first trains experts using samples with all modalities to inject generalized knowledge through the generalized router ($\mathcal{G}$-Router). The $\mathcal{S}$-Router then specializes in handling fewer modality combinations by assigning the top-1 gate to the expert corresponding to the observed modality combination. We evaluate Flex-MoE on the ADNI dataset, which encompasses four modalities in the Alzheimer's Disease domain, as well as on the MIMIC-IV dataset. The results demonstrate the effectiveness of Flex-MoE highlighting its ability to model arbitrary modality combinations in diverse missing modality scenarios. Code is available at https://github.com/UNITES-Lab/flex-moe.

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arXiv2023

Prefix-Tree Decoding for Predicting Mass Spectra from Molecules

Computational predictions of mass spectra from molecules have enabled the discovery of clinically relevant metabolites. However, such predictive tools are still limited as they occupy one of two extremes, either operating (a) by fragmenting molecules combinatorially with overly rigid constraints on potential rearrangements and poor time complexity or (b) by decoding lossy and nonphysical discretized spectra vectors. In this work, we use a new intermediate strategy for predicting mass spectra from molecules by treating mass spectra as sets of molecular formulae, which are themselves multisets of atoms. After first encoding an input molecular graph, we decode a set of molecular subformulae, each of which specify a predicted peak in the mass spectrum, the intensities of which are predicted by a second model. Our key insight is to overcome the combinatorial possibilities for molecular subformulae by decoding the formula set using a prefix tree structure, atom-type by atom-type, representing a general method for ordered multiset decoding. We show promising empirical results on mass spectra prediction tasks.

q-bio.QM↗

arXiv2023

MIST-CF: Chemical formula inference from tandem mass spectra

Chemical formula annotation for tandem mass spectrometry (MS/MS) data is the first step toward structurally elucidating unknown metabolites. While great strides have been made toward solving this problem, the current state-of-the-art method depends on time-intensive, proprietary, and expert-parameterized fragmentation tree construction and scoring. In this work we extend our previous spectrum Transformer methodology into an energy based modeling framework, MIST-CF, for learning to rank chemical formula and adduct assignments given an unannotated MS/MS spectrum. Importantly, MIST-CF learns in a data dependent fashion using a Formula Transformer neural network architecture and circumvents the need for fragmentation tree construction. We train and evaluate our model on a large open-access database, showing an absolute improvement of 10% top 1 accuracy over other neural network architectures. We further validate our approach on the CASMI2022 challenge dataset, achieving nearly equivalent performance to the winning entry within the positive mode category without any manual curation or post-processing of our results. These results demonstrate an exciting strategy to more powerfully leverage MS2 fragment peaks for predicting MS1 precursor chemical formula with data driven learning.

q-bio.QM↗

arXiv2023

Retrieved Sequence Augmentation for Protein Representation Learning

Protein language models have excelled in a variety of tasks, ranging from structure prediction to protein engineering. However, proteins are highly diverse in functions and structures, and current state-of-the-art models including the latest version of AlphaFold rely on Multiple Sequence Alignments (MSA) to feed in the evolutionary knowledge. Despite their success, heavy computational overheads, as well as the de novo and orphan proteins remain great challenges in protein representation learning. In this work, we show that MSAaugmented models inherently belong to retrievalaugmented methods. Motivated by this finding, we introduce Retrieved Sequence Augmentation(RSA) for protein representation learning without additional alignment or pre-processing. RSA links query protein sequences to a set of sequences with similar structures or properties in the database and combines these sequences for downstream prediction. We show that protein language models benefit from the retrieval enhancement on both structure prediction and property prediction tasks, with a 5% improvement on MSA Transformer on average while being 373 times faster. In addition, we show that our model can transfer to new protein domains better and outperforms MSA Transformer on de novo protein prediction. Our study fills a much-encountered gap in protein prediction and brings us a step closer to demystifying the domain knowledge needed to understand protein sequences. Code is available on https://github.com/HKUNLP/RSA.

q-bio.BM↗

arXiv2022

Selective Annotation Makes Language Models Better Few-Shot Learners

Many recent approaches to natural language tasks are built on the remarkable abilities of large language models. Large language models can perform in-context learning, where they learn a new task from a few task demonstrations, without any parameter updates. This work examines the implications of in-context learning for the creation of datasets for new natural language tasks. Departing from recent in-context learning methods, we formulate an annotation-efficient, two-step framework: selective annotation that chooses a pool of examples to annotate from unlabeled data in advance, followed by prompt retrieval that retrieves task examples from the annotated pool at test time. Based on this framework, we propose an unsupervised, graph-based selective annotation method, voke-k, to select diverse, representative examples to annotate. Extensive experiments on 10 datasets (covering classification, commonsense reasoning, dialogue, and text/code generation) demonstrate that our selective annotation method improves the task performance by a large margin. On average, vote-k achieves a 12.9%/11.4% relative gain under an annotation budget of 18/100, as compared to randomly selecting examples to annotate. Compared to state-of-the-art supervised finetuning approaches, it yields similar performance with 10-100x less annotation cost across 10 tasks. We further analyze the effectiveness of our framework in various scenarios: language models with varying sizes, alternative selective annotation methods, and cases where there is a test data domain shift. We hope that our studies will serve as a basis for data annotations as large language models are increasingly applied to new tasks. Our code is available at https://github.com/HKUNLP/icl-selective-annotation.

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