arXiv subjects

Jimeng Shi

Publications and source records attributed to Jimeng Shi.

At least 19 recordsLinked to original sources

arXiv2026

Accurate, Efficient, and Explainable Deep Learning Approaches for Environmental Science Problems

Environmental science plays a pivotal role in safeguarding ecosystems, a domain driven by large-scale, heterogeneous data. In the big data era, artificial intelligence (AI) has emerged as a transformative tool for learning patterns and supporting decision-making. This dissertation develops AI-based approaches tailored to complex environmental science problems to achieve Environmental Intelligence, studying three specific challenges. First, we focus on flood prediction and management in coastal river systems. Conventional physics-based models are computationally intensive, limiting real-time application. To overcome this, we propose a deep learning (DL)-based model, WaLeF, for water level forecasting, and a forecast-informed DL model, FIDLAr, to manage water levels. Evaluated in a flood-prone coastal system in South Florida characterized by extreme rainfall and sea level fluctuations, FIDLAr outperforms baselines in accuracy and efficiency while providing interpretable outputs. Second, we target global weather prediction, which is challenged by massive data scale. Traditional physics methods are deterministic and computationally heavy. We propose CoDiCast, a conditional diffusion model tailored for probabilistic weather forecasting. Adapted from generative AI for predictive tasks, experiments show CoDiCast achieves accurate, efficient forecasts with explicit uncertainty quantification. Lastly, we address scientific question-answering in environmental science. When answering in-domain questions, large language models (LLMs) often suffer from hallucinations due to out-of-date or limited knowledge. While retrieval-augmented generation (RAG) retrieves domain-specific knowledge, existing methods trade off accuracy, efficiency, or explainability. We propose Hypercube-RAG, built on a structured text cube framework, which successfully exhibits all three properties simultaneously.

cs.LG↗

arXiv2026

Retrieval is Cheap, Show Me the Code: Executable Multi-Hop Reasoning for Retrieval-Augmented Generation

Retrieval-Augmented Generation (RAG) has become a standard approach for knowledge-intensive question answering, but existing systems remain brittle on multi-hop questions, where solving the task requires chaining multiple retrieval and reasoning steps. Key challenges are that current methods represent reasoning through free-form natural language, where intermediate states are implicit, retrieval queries can drift from intended entities, and errors are detected by the same model that produces them making self-reflection an unreliable, ungrounded signal. We observe that multi-hop question answering is a typical form of step-by-step computation, and that this structured process aligns closely with how code-specialized language models are trained to operate. Motivated by this, we introduce \pyrag, a framework that reformulates multi-hop RAG as program synthesis and execution. Instead of free-form reasoning trajectories, \pyrag represents the reasoning process as an executable Python program over retrieval and QA tools, exposing intermediate states as variables, producing deterministic feedback through execution, and yielding an inspectable trace of the entire reasoning process. This formulation further enables compiler-grounded self-repair and execution-driven adaptive retrieval without any additional training. Experiments on five QA benchmarks (PopQA, HotpotQA, 2WikiMultihopQA, MuSiQue, and Bamboogle) show that \pyrag consistently outperforms strong baselines under both training-free and RL-trained settings, with especially large gains on compositional multi-hop datasets. Our code, data and models are publicly available at https://github.com/GasolSun36/PyRAG.

cs.AI↗

arXiv2026

TaSR-RAG: Taxonomy-guided Structured Reasoning for Retrieval-Augmented Generation

Retrieval-Augmented Generation (RAG) helps large language models (LLMs) answer knowledge-intensive and time-sensitive questions by conditioning generation on external evidence. However, most RAG systems still retrieve unstructured chunks and rely on one-shot generation, which often yields redundant context, low information density, and brittle multi-hop reasoning. While structured RAG pipelines can improve grounding, they typically require costly and error-prone graph construction or impose rigid entity-centric structures that do not align with the query's reasoning chain. We propose \textsc{TaSR-RAG}, a taxonomy-guided structured reasoning framework for evidence selection. We represent both queries and documents as relational triples, and constrain entity semantics with a lightweight two-level taxonomy to balance generalization and precision. Given a complex question, \textsc{TaSR-RAG} decomposes it into an ordered sequence of triple sub-queries with explicit latent variables, then performs step-wise evidence selection via hybrid triple matching that combines semantic similarity over raw triples with structural consistency over typed triples. By maintaining an explicit entity binding table across steps, \textsc{TaSR-RAG} resolves intermediate variables and reduces entity conflation without explicit graph construction or exhaustive search. Experiments on multiple multi-hop question answering benchmarks show that \textsc{TaSR-RAG} consistently outperforms strong RAG and structured-RAG baselines by up to 14\%, while producing clearer evidence attribution and more faithful reasoning traces.

cs.CL↗

arXiv2026

Any Model, Any Place, Any Time: Get Remote Sensing Foundation Model Embeddings On Demand

The remote sensing community is witnessing a rapid growth of foundation models, which provide powerful embeddings for a wide range of downstream tasks. However, practical adoption and fair comparison remain challenging due to substantial heterogeneity in model release formats, platforms and interfaces, and input data specifications. These inconsistencies significantly increase the cost of obtaining, using, and benchmarking embeddings across models. To address this issue, we propose rs-embed, a Python library that offers a unified, region of interst (ROI) centric interface: with a single line of code, users can retrieve embeddings from any supported model for any location and any time range. The library also provides efficient batch processing to enable large-scale embedding generation and evaluation. The code is available at: https://github.com/cybergis/rs-embed

cs.CV↗

arXiv2026

MultiCube-RAG for Multi-hop Question Answering

Multi-hop question answering (QA) necessitates multi-step reasoning and retrieval across interconnected subjects, attributes, and relations. Existing retrieval-augmented generation (RAG) methods struggle to capture these structural semantics accurately, resulting in suboptimal performance. Graph-based RAGs structure such information in graphs, but the resulting graphs are often noisy and computationally expensive. Moreover, most methods rely on single-step retrieval, neglecting the need for multi-hop reasoning processes. Recent training-based approaches attempt to incentivize the large language models (LLMs) for iterative reasoning and retrieval, but their training processes are prone to unstable convergence and high computational overhead. To address these limitations, we devise an ontology-based cube structure with multiple and orthogonal dimensions to model structural subjects, attributes, and relations. Built on the cube structure, we propose MultiCube-RAG, a training-free method consisting of multiple cubes for multi-step reasoning and retrieval. Each cube specializes in modeling a class of subjects, so that MultiCube-RAG flexibly selects the most suitable cubes to acquire the relevant knowledge precisely. To enhance the query-based reasoning and retrieval, our method decomposes a complex multi-hop query into a set of simple subqueries along cube dimensions and conquers each of them sequentially. Experiments on four multi-hop QA datasets show that MultiCube-RAG improves response accuracy by 8.9% over the average performance of various baselines. Notably, we also demonstrate that our method performs with greater efficiency and inherent explainability.

cs.CL↗

arXiv2025

Evaluating and Scoring Ebolavirus Protein-protein Docking Models Using PIsToN

Protein-protein docking is crucial for understanding how proteins interact. Numerous docking tools have been developed to discover possible conformations of two interacting proteins. However, the reliability and success of these docking tools rely on their scoring function. Accurate and efficient scoring functions are necessary to distinguish between native and non-native docking models to ensure the accuracy of a docking tool. Like in other fields where deep learning methods have been successfully utilized, these methods have also introduced innovative scoring functions. An outstanding tool for scoring and differentiating native-like docking models from non-native or incorrect conformations is called Protein binding Interfaces with Transformer Networks (PIsToN). PIsToN significantly outperforms state-of-the-art scoring functions. Using models of complexes obtained from binding the Ebola Virus Protein VP40 to the host cell's Sec24c protein as an example, we show how to evaluate docking models using PIsToN.

q-bio.BM↗

arXiv2025

Retrieval-Augmented Foundation Models for Water Level Prediction in the Everglades

Accurate water level forecasting in the Everglades is essential for flood mitigation, drought management, water resource planning, and biodiversity conservation. While recent time-series foundation models have shown strong performance on generic tasks (represented in their pre-training), their effectiveness in domain-specific applications remains insufficiently understood. In this work, we curate a domain-specific dataset for water-level forecasting in the Everglades and observe that the performance of current state-of-the-art models remains limited. To address this gap, we leverage a retrieval-augmented mechanism that retrieves analogous multivariate hydrological episodes from an external archive of historical observations to enrich the input context of those pre-trained models. We study two retrieval strategies, statistical similarity-based retrieval and mutual information-based retrieval, and analyze how incorporating retrieved historical contexts affects predictive performance. Extensive experiments show that retrieval augmentation consistently improves long-horizon water level forecasts and yields disproportionately larger gains during extreme events, which is particularly critical for environmental decision-making. Our study provides empirical evidence that analog-based retrieval can benefit pretrained time-series foundation models in environmental science, offering practical insights into their strengths, limitations, and failure modes when applied to hydrological forecasting in the Everglades. Although evaluated in the Everglades, the proposed framework is general and can be applied to other hydrological systems given time series data. The code and data have been made publicly available at https://github.com/rahuul2992000/WaterRAF.

cs.LG↗

arXiv2025

Uncovering Insights of Compound Flooding with Data-Driven AI

Compound flooding, driven by nonlinear interactions between multiple hydrometeorological factors, poses a significant challenge to hazard prevention. Existing forecasting approaches, whether physics-based or data-driven, often emphasize temporal patterns while underexploring how multiple interacting factors jointly shape flood dynamics. To address this problem, we conduct a large-scale data-driven analysis of compound flooding in South Florida, a typical area for compound flooding, by integrating tidal conditions, rainfall, groundwater stage, and human water management activities. Our analysis reveals three key findings: (i) models that capture temporal dynamics alone fail to represent multi-factor interactions during compound events; (ii) subsurface saturation, as reflected by groundwater levels, emerges as a dominant predictor of flood severity, often outweighing immediate rainfall intensity in this porous coastal region; and (iii) the spatial state of surrounding monitoring stations within a finite effective radius provides critical causal context for flooding, while extending temporal history yields diminishing returns during extreme events. These findings suggest that compound flooding is governed more by spatially coupled system states than by long-term temporal dependencies, challenging rain-centric and sequence-dominated forecasting paradigms. By framing data-driven models as tools for scientific inquiry rather than prediction alone, this study offers new insights into the mechanisms of compound flooding and informs the design of more physically grounded early-warning systems for coastal environments. Our dataset and code are publicly available at https://github.com/AslanDing/SFBench.

cs.LG↗

arXiv2025

Hypercube-Based Retrieval-Augmented Generation for Scientific Question-Answering

Large language models (LLMs) often need to incorporate external knowledge to solve theme-specific problems. Retrieval-augmented generation (RAG) has shown its high promise, empowering LLMs to generate more qualified responses with retrieved external data and knowledge. However, most RAG methods retrieve relevant documents based on either sparse or dense retrieval methods or their combinations, which overlooks the essential, multi-dimensional, and structured semantic information present in documents. This structured information plays a critical role in finding concise yet highly relevant information for domain knowledge-intensive tasks, such as scientific question-answering (QA). In this work, we introduce a multi-dimensional (cube) structure, Hypercube, which can index and allocate documents in a pre-defined multi-dimensional space. Built on the hypercube, we further propose Hypercube-RAG, a novel RAG framework for precise and efficient retrieval. Given a query, Hypercube-RAG first decomposes it based on its entities, phrases, and topics along with pre-defined hypercube dimensions, and then retrieves relevant documents from cubes by aligning these decomposed components with corresponding dimensions. Experiments on three datasets across different domains demonstrate that our method improves response accuracy by 3.7% and retrieval accuracy by 5.3% over the strongest RAG baseline. It also boosts retrieval efficiency (speed) by one or two magnitudes faster than graph-based RAG. Notably, our Hypercube-RAG inherently offers explainability by revealing those underlying dimensions used for retrieval. The code and data are available at https://github.com/JimengShi/Hypercube-RAG.

cs.LG↗

arXiv2025

How Effective are Large Time Series Models in Hydrology? A Study on Water Level Forecasting in Everglades

The Everglades play a crucial role in flood and drought regulation, water resource planning, and ecosystem management in the surrounding regions. However, traditional physics-based and statistical methods for predicting water levels often face significant challenges, including high computational costs and limited adaptability to diverse or unforeseen conditions. Recent advancements in large time series models have demonstrated the potential to address these limitations, with state-of-the-art deep learning and foundation models achieving remarkable success in time series forecasting across various domains. Despite this progress, their application to critical environmental systems, such as the Everglades, remains underexplored. In this study, we fill the gap by investigating twelve task-specific models and five time series foundation models across six categories for a real-world application focused on water level prediction in the Everglades. Our primary results show that the foundation model Chronos significantly outperforms all other models while the remaining foundation models exhibit relatively poor performance. We also noticed that the performance of task-specific models varies with the model architectures, and discussed the possible reasons. We hope our study and findings will inspire the community to explore the applicability of large time series models in hydrological applications. The code and data are available at https://github.com/rahuul2992000/Everglades-Benchmark.

cs.LG↗

arXiv2025

Deep Learning and Foundation Models for Weather Prediction: A Survey

Physics-based numerical models have been the bedrock of atmospheric sciences for decades, offering robust solutions but often at the cost of significant computational resources. Deep learning (DL) models have emerged as powerful tools in meteorology, capable of analyzing complex weather and climate data by learning intricate dependencies and providing rapid predictions once trained. While these models demonstrate promising performance in weather prediction, often surpassing traditional physics-based methods, they still face critical challenges. This paper presents a comprehensive survey of recent deep learning and foundation models for weather prediction. We propose a taxonomy to classify existing models based on their training paradigms: deterministic predictive learning, probabilistic generative learning, and pre-training and fine-tuning. For each paradigm, we delve into the underlying model architectures, address major challenges, offer key insights, and propose targeted directions for future research. Furthermore, we explore real-world applications of these methods and provide a curated summary of open-source code repositories and widely used datasets, aiming to bridge research advancements with practical implementations while fostering open and trustworthy scientific practices in adopting cutting-edge artificial intelligence for weather prediction. The related sources are available at https://github.com/JimengShi/ DL-Foundation-Models-Weather.

cs.LG↗

arXiv2024

ReFine: Boosting Time Series Prediction of Extreme Events by Reweighting and Fine-tuning

Extreme events are of great importance since they often represent impactive occurrences. For instance, in terms of climate and weather, extreme events might be major storms, floods, extreme heat or cold waves, and more. However, they are often located at the tail of the data distribution. Consequently, accurately predicting these extreme events is challenging due to their rarity and irregularity. Prior studies have also referred to this as the out-of-distribution (OOD) problem, which occurs when the distribution of the test data is substantially different from that used for training. In this work, we propose two strategies, reweighting and fine-tuning, to tackle the challenge. Reweighting is a strategy used to force machine learning models to focus on extreme events, which is achieved by a weighted loss function that assigns greater penalties to the prediction errors for the extreme samples relative to those on the remainder of the data. Unlike previous intuitive reweighting methods based on simple heuristics of data distribution, we employ meta-learning to dynamically optimize these penalty weights. To further boost the performance on extreme samples, we start from the reweighted models and fine-tune them using only rare extreme samples. Through extensive experiments on multiple data sets, we empirically validate that our meta-learning-based reweighting outperforms existing heuristic ones, and the fine-tuning strategy can further increase the model performance. More importantly, these two strategies are model-agnostic, which can be implemented on any type of neural network for time series forecasting. The open-sourced code is available at \url{https://github.com/JimengShi/ReFine}.

cs.LG↗

arXiv2024

CoDiCast: Conditional Diffusion Model for Global Weather Prediction with Uncertainty Quantification

Accurate weather forecasting is critical for science and society. Yet, existing methods have not managed to simultaneously have the properties of high accuracy, low uncertainty, and high computational efficiency. On one hand, to quantify the uncertainty in weather predictions, the strategy of ensemble forecast (i.e., generating a set of diverse predictions) is often employed. However, traditional ensemble numerical weather prediction (NWP) is computationally intensive. On the other hand, most existing machine learning-based weather prediction (MLWP) approaches are efficient and accurate. Nevertheless, they are deterministic and cannot capture the uncertainty of weather forecasting. In this work, we propose CoDiCast, a conditional diffusion model to generate accurate global weather prediction, while achieving uncertainty quantification with ensemble forecasts and modest computational cost. The key idea is to simulate a conditional version of the reverse denoising process in diffusion models, which starts from pure Gaussian noise to generate realistic weather scenarios for a future time point. Each denoising step is conditioned on observations from the recent past. Ensemble forecasts are achieved by repeatedly sampling from stochastic Gaussian noise to represent uncertainty quantification. CoDiCast is trained on a decade of ERA5 reanalysis data from the European Centre for Medium-Range Weather Forecasts (ECMWF). Experimental results demonstrate that our approach outperforms several existing data-driven methods in accuracy. Our conditional diffusion model, CoDiCast, can generate 6-day global weather forecasts, at 6-hour steps and $5.625^\circ$ latitude-longitude resolution, for over 5 variables, in about 12 minutes on a commodity A100 GPU machine with 80GB memory. The open-souced code is provided at https://github.com/JimengShi/CoDiCast.

cs.LG↗

arXiv2024

TimeX++: Learning Time-Series Explanations with Information Bottleneck

Explaining deep learning models operating on time series data is crucial in various applications of interest which require interpretable and transparent insights from time series signals. In this work, we investigate this problem from an information theoretic perspective and show that most existing measures of explainability may suffer from trivial solutions and distributional shift issues. To address these issues, we introduce a simple yet practical objective function for time series explainable learning. The design of the objective function builds upon the principle of information bottleneck (IB), and modifies the IB objective function to avoid trivial solutions and distributional shift issues. We further present TimeX++, a novel explanation framework that leverages a parametric network to produce explanation-embedded instances that are both in-distributed and label-preserving. We evaluate TimeX++ on both synthetic and real-world datasets comparing its performance against leading baselines, and validate its practical efficacy through case studies in a real-world environmental application. Quantitative and qualitative evaluations show that TimeX++ outperforms baselines across all datasets, demonstrating a substantial improvement in explanation quality for time series data. The source code is available at \url{https://github.com/zichuan-liu/TimeXplusplus}.

cs.LG↗

arXiv2024

FIDLAR: Forecast-Informed Deep Learning Architecture for Flood Mitigation

In coastal river systems, frequent floods, often occurring during major storms or king tides, pose a severe threat to lives and property. However, these floods can be mitigated or even prevented by strategically releasing water before extreme weather events with hydraulic structures such as dams, gates, pumps, and reservoirs. A standard approach used by local water management agencies is the "rule-based" method, which specifies predetermined pre-releases of water based on historical and time-tested human experience, but which tends to result in excess or inadequate water release. The model predictive control (MPC), a physics-based model for prediction, is an alternative approach, albeit involving computationally intensive calculations. In this paper, we propose a Forecast Informed Deep Learning Architecture, FIDLAR, to achieve rapid and optimal flood management with precise water pre-releases. FIDLAR seamlessly integrates two neural network modules: one called the Flood Manager, which is responsible for generating water pre-release schedules, and another called the Flood Evaluator, which assesses these generated schedules. The Evaluator module is pre-trained separately, and its gradient-based feedback is used to train the Manager model, ensuring optimal water pre-releases. We have conducted experiments using FIDLAR with data from a flood-prone coastal area in South Florida, particularly susceptible to frequent storms. Results show that FIDLAR is several orders of magnitude faster than currently used physics-based approaches while outperforming baseline methods with improved water pre-release schedules.

cs.LG↗

arXiv2023

The Power of Explainability in Forecast-Informed Deep Learning Models for Flood Mitigation

Floods can cause horrific harm to life and property. However, they can be mitigated or even avoided by the effective use of hydraulic structures such as dams, gates, and pumps. By pre-releasing water via these structures in advance of extreme weather events, water levels are sufficiently lowered to prevent floods. In this work, we propose FIDLAR, a Forecast Informed Deep Learning Architecture, achieving flood management in watersheds with hydraulic structures in an optimal manner by balancing out flood mitigation and unnecessary wastage of water via pre-releases. We perform experiments with FIDLAR using data from the South Florida Water Management District, which manages a coastal area that is highly prone to frequent storms and floods. Results show that FIDLAR performs better than the current state-of-the-art with several orders of magnitude speedup and with provably better pre-release schedules. The dramatic speedups make it possible for FIDLAR to be used for real-time flood management. The main contribution of this paper is the effective use of tools for model explainability, allowing us to understand the contribution of the various environmental factors towards its decisions.

cs.LG↗

arXiv2023

Graph Transformer Network for Flood Forecasting with Heterogeneous Covariates

Floods can be very destructive causing heavy damage to life, property, and livelihoods. Global climate change and the consequent sea-level rise have increased the occurrence of extreme weather events, resulting in elevated and frequent flood risk. Therefore, accurate and timely flood forecasting in coastal river systems is critical to facilitate good flood management. However, the computational tools currently used are either slow or inaccurate. In this paper, we propose a Flood prediction tool using Graph Transformer Network (FloodGTN) for river systems. More specifically, FloodGTN learns the spatio-temporal dependencies of water levels at different monitoring stations using Graph Neural Networks (GNNs) and an LSTM. It is currently implemented to consider external covariates such as rainfall, tide, and the settings of hydraulic structures (e.g., outflows of dams, gates, pumps, etc.) along the river. We use a Transformer to learn the attention given to external covariates in computing water levels. We apply the FloodGTN tool to data from the South Florida Water Management District, which manages a coastal area prone to frequent storms and hurricanes. Experimental results show that FloodGTN outperforms the physics-based model (HEC-RAS) by achieving higher accuracy with 70% improvement while speeding up run times by at least 500x.

cs.LG↗

arXiv2023

Deep Learning Models for Flood Predictions in South Florida

Simulating and predicting the water level/stage in river systems is essential for flood warnings, hydraulic operations, and flood mitigations. Physics-based detailed hydrological and hydraulic computational tools, such as HEC-RAS, MIKE, and SWMM, can be used to simulate a complete watershed and compute the water stage at any point in the river system. However, these physics-based models are computationally intensive, especially for large watersheds and for longer simulations, since they use detailed grid representations of terrain elevation maps of the entire watershed and solve complex partial differential equations (PDEs) for each grid cell. To overcome this problem, we train several deep learning (DL) models for use as surrogate models to rapidly predict the water stage. A portion of the Miami River in South Florida was chosen as a case study for this paper. Extensive experiments show that the performance of various DL models (MLP, RNN, CNN, LSTM, and RCNN) is significantly better than that of the physics-based model, HEC-RAS, even during extreme precipitation conditions (i.e., tropical storms), and with speedups exceeding 500x. To predict the water stages more accurately, our DL models use both measured variables of the river system from the recent past and covariates for which predictions are typically available for the near future.

cs.LG↗