arXiv subjects

Yidan Shi

Publications and source records attributed to Yidan Shi.

7 recordsLinked to original sources

arXiv2026

RetroAgent: Harnessing LLMs to Search Over Structured Memory for Agentic Retrosynthesis Planning

Multi-step retrosynthesis planning seeks to decompose a target molecule into commercially available building blocks through a sequence of feasible reactions. The vast combinatorial search space makes this task challenging even for expert chemists. Traditional methods combine tree search with offline-trained value networks that score candidates in isolation, without reasoning about complete multi-step routes. Recent work leverages Large Language Models (LLMs) for this task, but relies on simple interfaces that limit exploration of the full search space. We introduce RetroAgent, an LLM agent that bridges symbolic search and neural reasoning through a harness with structured memory. Through memory and chemistry tools, the agent observes the full search state, including explored routes, available alternatives, and properties of intermediates, enabling informed decisions grounded in both global progress and domain knowledge. Experiments on in-distribution and out-of-distribution benchmarks demonstrate that RetroAgent delivers strong performance and generalization.

cs.AI↗

arXiv2026

ARLArena: A Unified Framework for Stable Agentic Reinforcement Learning

Agentic reinforcement learning (ARL) has rapidly gained attention as a promising paradigm for training agents to solve complex, multi-step interactive tasks. Despite encouraging early results, ARL remains highly unstable, often leading to training collapse. This instability limits scalability to larger environments and longer interaction horizons, and constrains systematic exploration of algorithmic design choices. In this paper, we first propose ARLArena, a stable training recipe and systematic analysis framework that examines training stability in a controlled and reproducible setting. ARLArena first constructs a clean and standardized testbed. Then, we decompose policy gradient into four core design dimensions and assess the performance and stability of each dimension. Through this fine-grained analysis, we distill a unified perspective on ARL and propose SAMPO, a stable agentic policy optimization method designed to mitigate the dominant sources of instability in ARL. Empirically, SAMPO achieves consistently stable training and strong performance across diverse agentic tasks. Overall, this study provides a unifying policy gradient perspective for ARL and offers practical guidance for building stable and reproducible LLM-based agent training pipelines.

cs.AI↗

arXiv2026

A Survey of Reasoning and Agentic Systems in Time Series with Large Language Models

Time series reasoning treats time as a first-class axis and incorporates intermediate evidence directly into the answer. This survey defines the problem and organizes the literature by reasoning topology with three families: direct reasoning in one step, linear chain reasoning with explicit intermediates, and branch-structured reasoning that explores, revises, and aggregates. The topology is crossed with the main objectives of the field, including traditional time series analysis, explanation and understanding, causal inference and decision making, and time series generation, while a compact tag set spans these axes and captures decomposition and verification, ensembling, tool use, knowledge access, multimodality, agent loops, and LLM alignment regimes. Methods and systems are reviewed across domains, showing what each topology enables and where it breaks down in faithfulness or robustness, along with curated datasets, benchmarks, and resources that support study and deployment (https://github.com/blacksnail789521/Time-Series-Reasoning-Survey). Evaluation practices that keep evidence visible and temporally aligned are highlighted, and guidance is distilled on matching topology to uncertainty, grounding with observable artifacts, planning for shift and streaming, and treating cost and latency as design budgets. We emphasize that reasoning structures must balance capacity for grounding and self-correction against computational cost and reproducibility, while future progress will likely depend on benchmarks that tie reasoning quality to utility and on closed-loop testbeds that trade off cost and risk under shift-aware, streaming, and long-horizon settings. Taken together, these directions mark a shift from narrow accuracy toward reliability at scale, enabling systems that not only analyze but also understand, explain, and act on dynamic worlds with traceable evidence and credible outcomes.

cs.AI↗

arXiv2026

PG-LRF: Physiology-Guided Latent Rectified Flow for Electro-Hemodynamic PPG-to-ECG Generation

Electrocardiography (ECG) is the clinical standard for cardiac assessment but requires dedicated hardware that does not scale to daily-life monitoring. Photoplethysmography (PPG) is ubiquitous in wearables but lacks ECG-specific diagnostic morphology and is corrupted by motion and sensor noise. PPG-to-ECG generation aims to bridge this gap by recovering electrical morphology and timing from peripheral pulse signals. However, existing methods largely rely on statistical alignment and data-driven generation. They fail to explicitly structure the latent space around physiology-aware electro-hemodynamic factors and lack constraints from forward physiological dynamics. To address these challenges, we propose PG-LRF, a physiology-guided latent rectified flow framework. PG-LRF introduces an electro-hemodynamic simulator that co-models ECG and PPG through shared cardiac phase dynamics. Guided by this simulator, a Physiology-Aware AutoEncoder learns a structured electro-hemodynamic latent space. Then we integrate this simulator guidance into a PPG-conditioned latent rectified flow, enforcing ECG-side morphology consistency and ECG-to-PPG forward hemodynamic consistency during generative transport. Experiments on the large-scale MC-MED dataset demonstrate that PG-LRF significantly improves PPG-to-ECG generation and downstream cardiovascular disease classification, proving its ability to generate ECGs that are both signal-faithful and physiologically plausible under the ECG-to-PPG hemodynamic pathway

eess.SP↗

arXiv2026

Utilizing the Score of Data Distribution for Hyperspectral Anomaly Detection

Hyperspectral images (HSIs) are a type of image that contains abundant spectral information. As a type of real-world data, the high-dimensional spectra in hyperspectral images are actually determined by only a few factors, such as chemical composition and illumination. Thus, spectra in hyperspectral images are highly likely to satisfy the manifold hypothesis. Based on the hyperspectral manifold hypothesis, we propose a novel hyperspectral anomaly detection method (named ScoreAD) that leverages the time-dependent gradient field of the data distribution (i.e., the score), as learned by a score-based generative model (SGM). Our method first trains the SGM on the entire set of spectra from the hyperspectral image. At test time, each spectrum is passed through a perturbation kernel, and the resulting perturbed spectrum is fed into the trained SGM to obtain the estimated score. The manifold hypothesis of HSIs posits that background spectra reside on one or more low-dimensional manifolds. Conversely, anomalous spectra, owing to their unique spectral signatures, are considered outliers that do not conform to the background manifold. Based on this fundamental discrepancy in their manifold distributions, we leverage a generative SGM to achieve hyperspectral anomaly detection. Experiments on the four hyperspectral datasets demonstrate the effectiveness of the proposed method. The code is available at https://github.com/jiahuisheng/ScoreAD.

cs.CV↗

arXiv2025

Time-IMM: A Dataset and Benchmark for Irregular Multimodal Multivariate Time Series

Time series data in real-world applications such as healthcare, climate modeling, and finance are often irregular, multimodal, and messy, with varying sampling rates, asynchronous modalities, and pervasive missingness. However, existing benchmarks typically assume clean, regularly sampled, unimodal data, creating a significant gap between research and real-world deployment. We introduce Time-IMM, a dataset specifically designed to capture cause-driven irregularity in multimodal multivariate time series. Time-IMM represents nine distinct types of time series irregularity, categorized into trigger-based, constraint-based, and artifact-based mechanisms. Complementing the dataset, we introduce IMM-TSF, a benchmark library for forecasting on irregular multimodal time series, enabling asynchronous integration and realistic evaluation. IMM-TSF includes specialized fusion modules, including a timestamp-to-text fusion module and a multimodality fusion module, which support both recency-aware averaging and attention-based integration strategies. Empirical results demonstrate that explicitly modeling multimodality on irregular time series data leads to substantial gains in forecasting performance. Time-IMM and IMM-TSF provide a foundation for advancing time series analysis under real-world conditions. The dataset is publicly available at https://github.com/blacksnail789521/Time-IMM, and the benchmark library can be accessed at https://github.com/blacksnail789521/IMM-TSF. Project page: https://blacksnail789521.github.io/time-imm-project-page/

cs.LG↗

arXiv2024

A Finite Mixture Hidden Markov Model for Intermittently Observed Disease Process with Heterogeneity and Partially Known Disease Type

Continuous-time multistate models are widely used for analyzing interval-censored data on disease progression over time. Sometimes, diseases manifest differently and what appears to be a coherent collection of symptoms is the expression of multiple distinct disease subtypes. To address this complexity, we propose a mixture hidden Markov model, where the observation process encompasses states representing common symptomatic stages across these diseases, and each underlying process corresponds to a distinct disease subtype. Our method models both the overall and the type-specific disease incidence/prevalence accounting for sampling conditions and exactly observed death times. Additionally, it can utilize partially available disease-type information, which offers insights into the pathway through specific hidden states in the disease process, to aid in the estimation. We present both a frequentist and a Bayesian way to obtain the estimates. The finite sample performance is evaluated through simulation studies. We demonstrate our method using the Nun Study and model the development and progression of dementia, encompassing both Alzheimer's disease (AD) and non-AD dementia.

stat.ME↗