arXiv subjects

Yonggui Huang

Publications and source records attributed to Yonggui Huang.

3 recordsLinked to original sources

arXiv2026

CIR-DDG: backbone-agnostic residual correction of antibody-antigen affinity changes with explicit cross-chain geometry

Motivation: Accurate prediction of mutation-induced protein--protein binding free-energy changes is important for antibody affinity maturation, yet scarce labels and complex interface geometry limit generalization. Heterogeneous predictors may process three-dimensional complexes without preserving the cross-chain signals most relevant to a mutation in their final scalar output. Results: We introduce CIR-DDG, a lightweight residual adapter that combines a fixed base prediction with 22 interpretable descriptors of cross-chain distance, contact density and site--partner context. In complex-level five-fold evaluation on SKEMPI 2.0 measurements from 343 complexes, CIR-DDG improved all six tested backbones on antibody--antigen interface mutations: Spearman correlation increased by 0.0346--0.1296, while RMSE decreased by 0.0074--0.0408\kcalmol. Cross-validated probing, equal-capacity controls and feature ablations support the complementarity of explicit geometry. On an independent SARS-CoV-2 RBD--ACE2 deep-mutational-scan benchmark of 3669 substitutions, the fold-specific adapters transferred without any retraining: the absolute interface Spearman correlation increased by 0.026--0.081 for all four evaluable backbones, showing that the learned geometric correction generalizes beyond SKEMPI thermodynamic measurements. Availability and implementation: CIR-DDG is available at https://github.com/ecnuabmlab/CIR-ddG.

q-bio.QM↗

arXiv2026

MEMTS: Internalizing Domain Knowledge via Parameterized Memory for Retrieval-Free Domain Adaptation of Time Series Foundation Models

While Time Series Foundation Models (TSFMs) have demonstrated exceptional performance in generalized forecasting, their performance often degrades significantly when deployed in real-world vertical domains characterized by temporal distribution shifts and domain-specific periodic structures. Current solutions are primarily constrained by two paradigms: Domain-Adaptive Pretraining (DAPT), which improves short-term domain fitting but frequently disrupts previously learned global temporal patterns due to catastrophic forgetting; and Retrieval-Augmented Generation (RAG), which incorporates external knowledge but introduces substantial retrieval overhead. This creates a severe scalability bottleneck that fails to meet the high-efficiency requirements of real-time stream processing. To break this impasse, we propose Memory for Time Series (MEMTS), a lightweight and plug-and-play method for retrieval-free domain adaptation in time series forecasting. The key component of MEMTS is a Knowledge Persistence Module (KPM), which internalizes domain-specific temporal dynamics, such as recurring seasonal patterns and trends into a compact set of learnable latent prototypes. In doing so, it transforms fragmented historical observations into continuous, parameterized knowledge representations. This paradigm shift enables MEMTS to achieve accurate domain adaptation with constant-time inference and near-zero latency, while effectively mitigating catastrophic forgetting of general temporal patterns, all without requiring any architectural modifications to the frozen TSFM backbone. Extensive experiments on multiple datasets demonstrate the SOTA performance of MEMTS.

cs.LG↗

arXiv2025

Dynamic Knowledge Exchange and Dual-diversity Review: Concisely Unleashing the Potential of a Multi-Agent Research Team

Scientific progress increasingly relies on effective collaboration among researchers, a dynamic that large language models (LLMs) have only begun to emulate. While recent LLM-based scientist agents show promise in autonomous scientific discovery, they often lack the interactive reasoning and evaluation mechanisms essential to real-world research. We propose IDVSCI (Internal Discussion and Vote SCIentists), a multi-agent framework built on LLMs that incorporates two key innovations: a Dynamic Knowledge Exchange mechanism enabling iterative feedback among agents, and a Dual-Diversity Review paradigm that simulates heterogeneous expert evaluation. These components jointly promote deeper reasoning and the generation of more creative and impactful scientific ideas. To evaluate the effectiveness and generalizability of our approach, we conduct experiments on two datasets: a widely used benchmark in computer science and a new dataset we introduce in the health sciences domain. Results show that IDVSCI consistently achieves the best performance across both datasets, outperforming existing systems such as AI Scientist and VIRSCI. These findings highlight the value of modeling interaction and peer review dynamics in LLM-based autonomous research.

cs.AI↗