arXiv subjects

Can Chen

Publications and source records attributed to Can Chen.

At least 55 records · Page 3Linked to original sources

arXiv2025

ParetoFlow: Guided Flows in Multi-Objective Optimization

In offline multi-objective optimization (MOO), we leverage an offline dataset of designs and their associated labels to simultaneously minimize multiple objectives. This setting more closely mirrors complex real-world problems compared to single-objective optimization. Recent works mainly employ evolutionary algorithms and Bayesian optimization, with limited attention given to the generative modeling capabilities inherent in such data. In this study, we explore generative modeling in offline MOO through flow matching, noted for its effectiveness and efficiency. We introduce ParetoFlow, specifically designed to guide flow sampling to approximate the Pareto front. Traditional predictor (classifier) guidance is inadequate for this purpose because it models only a single objective. In response, we propose a multi-objective predictor guidance module that assigns each sample a weight vector, representing a weighted distribution across multiple objective predictions. A local filtering scheme is introduced to address non-convex Pareto fronts. These weights uniformly cover the entire objective space, effectively directing sample generation towards the Pareto front. Since distributions with similar weights tend to generate similar samples, we introduce a neighboring evolution module to foster knowledge sharing among neighboring distributions. This module generates offspring from these distributions, and selects the most promising one for the next iteration. Our method achieves state-of-the-art performance across various tasks.

cs.CE↗

arXiv2025

Data-driven Control of T-Product-based Dynamical Systems

Data-driven control is a powerful tool that enables the design and implementation of control strategies directly from data without explicitly identifying the underlying system dynamics. While various data-driven control techniques, such as stabilization, linear quadratic regulation, and model predictive control, have been extensively developed, these methods are not inherently suited for multi-linear dynamical systems, where the states are represented as higher-order tensors. In this article, we propose a novel framework for data-driven control of T-product-based dynamical systems (TPDSs), where the system evolution is governed by the T-product between a third-order dynamic tensor and a third-order state tensor. In particular, we offer necessary and sufficient conditions to determine the data informativity for system identification, stabilization by state feedback, and T-product quadratic regulation of TPDSs with detailed complexity analyses. Finally, we validate our framework through numerical examples.

eess.SY↗

arXiv2025

AffinityFlow: Guided Flows for Antibody Affinity Maturation

Antibodies are widely used as therapeutics, but their development requires costly affinity maturation, involving iterative mutations to enhance binding affinity.This paper explores a sequence-only scenario for affinity maturation, using solely antibody and antigen sequences. Recently AlphaFlow wraps AlphaFold within flow matching to generate diverse protein structures, enabling a sequence-conditioned generative model of structure. Building on this, we propose an alternating optimization framework that (1) fixes the sequence to guide structure generation toward high binding affinity using a structure-based affinity predictor, then (2) applies inverse folding to create sequence mutations, refined by a sequence-based affinity predictor for post selection. A key challenge is the lack of labeled data for training both predictors. To address this, we develop a co-teaching module that incorporates valuable information from noisy biophysical energies into predictor refinement. The sequence-based predictor selects consensus samples to teach the structure-based predictor, and vice versa. Our method, AffinityFlow, achieves state-of-the-art performance in affinity maturation experiments. We plan to open-source our code after acceptance.

cs.LG↗

arXiv2025

HODDI: A Dataset of High-Order Drug-Drug Interactions for Computational Pharmacovigilance

Drug-side effect research is vital for understanding adverse reactions arising in complex multi-drug therapies. However, the scarcity of higher-order datasets that capture the combinatorial effects of multiple drugs severely limits progress in this field. Existing resources such as TWOSIDES primarily focus on pairwise interactions. To fill this critical gap, we introduce HODDI, the first Higher-Order Drug-Drug Interaction Dataset, constructed from U.S. Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) records spanning the past decade, to advance computational pharmacovigilance. HODDI contains 109,744 records involving 2,506 unique drugs and 4,569 unique side effects, specifically curated to capture multi-drug interactions and their collective impact on adverse effects. Comprehensive statistical analyses demonstrate HODDI's extensive coverage and robust analytical metrics, making it a valuable resource for studying higher-order drug relationships. Evaluating HODDI with multiple models, we found that simple Multi-Layer Perceptron (MLP) can outperform graph models, while hypergraph models demonstrate superior performance in capturing complex multi-drug interactions, further validating HODDI's effectiveness. Our findings highlight the inherent value of higher-order information in drug-side effect prediction and position HODDI as a benchmark dataset for advancing research in pharmacovigilance, drug safety, and personalized medicine. The dataset and codes are available at https://github.com/TIML-Group/HODDI.

cs.LG↗

arXiv2025

3DMolFormer: A Dual-channel Framework for Structure-based Drug Discovery

Structure-based drug discovery, encompassing the tasks of protein-ligand docking and pocket-aware 3D drug design, represents a core challenge in drug discovery. However, no existing work can deal with both tasks to effectively leverage the duality between them, and current methods for each task are hindered by challenges in modeling 3D information and the limitations of available data. To address these issues, we propose 3DMolFormer, a unified dual-channel transformer-based framework applicable to both docking and 3D drug design tasks, which exploits their duality by utilizing docking functionalities within the drug design process. Specifically, we represent 3D pocket-ligand complexes using parallel sequences of discrete tokens and continuous numbers, and we design a corresponding dual-channel transformer model to handle this format, thereby overcoming the challenges of 3D information modeling. Additionally, we alleviate data limitations through large-scale pre-training on a mixed dataset, followed by supervised and reinforcement learning fine-tuning techniques respectively tailored for the two tasks. Experimental results demonstrate that 3DMolFormer outperforms previous approaches in both protein-ligand docking and pocket-aware 3D drug design, highlighting its promising application in structure-based drug discovery. The code is available at: https://github.com/HXYfighter/3DMolFormer .

cs.CE↗

arXiv2024

Fast and Interpretable Mixed-Integer Linear Program Solving by Learning Model Reduction

By exploiting the correlation between the structure and the solution of Mixed-Integer Linear Programming (MILP), Machine Learning (ML) has become a promising method for solving large-scale MILP problems. Existing ML-based MILP solvers mainly focus on end-to-end solution learning, which suffers from the scalability issue due to the high dimensionality of the solution space. Instead of directly learning the optimal solution, this paper aims to learn a reduced and equivalent model of the original MILP as an intermediate step. The reduced model often corresponds to interpretable operations and is much simpler, enabling us to solve large-scale MILP problems much faster than existing commercial solvers. However, current approaches rely only on the optimal reduced model, overlooking the significant preference information of all reduced models. To address this issue, this paper proposes a preference-based model reduction learning method, which considers the relative performance (i.e., objective cost and constraint feasibility) of all reduced models on each MILP instance as preferences. We also introduce an attention mechanism to capture and represent preference information, which helps improve the performance of model reduction learning tasks. Moreover, we propose a SetCover based pruning method to control the number of reduced models (i.e., labels), thereby simplifying the learning process. Evaluation on real-world MILP problems shows that 1) compared to the state-of-the-art model reduction ML methods, our method obtains nearly 20% improvement on solution accuracy, and 2) compared to the commercial solver Gurobi, two to four orders of magnitude speedups are achieved.

cs.LG↗

arXiv2024

Heterogeneous Entity Representation for Medicinal Synergy Prediction

Medicinal synergy prediction is a powerful tool in drug discovery and development that harnesses the principles of combination therapy to enhance therapeutic outcomes by improving efficacy, reducing toxicity, and preventing drug resistance. While a myriad of computational methods has emerged for predicting synergistic drug combinations, a large portion of them may overlook the intricate, yet critical relationships between various entities in drug interaction networks, such as drugs, cell lines, and diseases. These relationships are complex and multidimensional, requiring sophisticated modeling to capture nuanced interplay that can significantly influence therapeutic efficacy. We introduce a salient deep hypergraph learning method, namely, Heterogeneous Entity Representation for MEdicinal Synergy prediction (HERMES), to predict anti-cancer drug synergy. HERMES integrates heterogeneous data sources, encompassing drug, cell line, and disease information, to provide a comprehensive understanding of the interactions involved. By leveraging advanced hypergraph neural networks with gated residual mechanisms, HERMES can effectively learn complex relationships/interactions within the data. Our results show HERMES demonstrates state-of-the-art performance, particularly in forecasting new drug combinations, significantly surpassing previous methods. This advancement underscores the potential of HERMES to facilitate more effective and precise drug combination predictions, thereby enhancing the development of novel therapeutic strategies.

cs.CE↗

arXiv2024

Efficient and Robust Continual Graph Learning for Graph Classification in Biology

Graph classification is essential for understanding complex biological systems, where molecular structures and interactions are naturally represented as graphs. Traditional graph neural networks (GNNs) perform well on static tasks but struggle in dynamic settings due to catastrophic forgetting. We present Perturbed and Sparsified Continual Graph Learning (PSCGL), a robust and efficient continual graph learning framework for graph data classification, specifically targeting biological datasets. We introduce a perturbed sampling strategy to identify critical data points that contribute to model learning and a motif-based graph sparsification technique to reduce storage needs while maintaining performance. Additionally, our PSCGL framework inherently defends against graph backdoor attacks, which is crucial for applications in sensitive biological contexts. Extensive experiments on biological datasets demonstrate that PSCGL not only retains knowledge across tasks but also enhances the efficiency and robustness of graph classification models in biology.

cs.LG↗

arXiv2024

Data-driven Analysis of T-Product-based Dynamical Systems

A wide variety of data can be represented using third-order tensors, spanning applications in chemometrics, psychometrics, and image processing. However, traditional data-driven frameworks are not naturally equipped to process tensors without first unfolding or flattening the data, which can result in a loss of crucial higher-order structural information. In this article, we introduce a novel framework for the data-driven analysis of T-product-based dynamical systems (TPDSs), where the system evolution is governed by the T-product between a third-order dynamic tensor and a third-order state tensor. In particular, we examine the data informativity of TPDSs concerning system identification, stability, controllability, and stabilizability and illustrate significant computational improvements over traditional approaches by leveraging the unique properties of the T-product. The effectiveness of our framework is demonstrated through numerical examples.

eess.SY↗

arXiv2024

LLM-TS Integrator: Integrating LLM for Enhanced Time Series Modeling

Time series~(TS) modeling is essential in dynamic systems like weather prediction and anomaly detection. Recent studies utilize Large Language Models (LLMs) for TS modeling, leveraging their powerful pattern recognition capabilities. These methods primarily position LLMs as the predictive backbone, often omitting the mathematical modeling within traditional TS models, such as periodicity. However, disregarding the potential of LLMs also overlooks their pattern recognition capabilities. To address this gap, we introduce \textit{LLM-TS Integrator}, a novel framework that effectively integrates the capabilities of LLMs into traditional TS modeling. Central to this integration is our \textit{mutual information} module. The core of this \textit{mutual information} module is a traditional TS model enhanced with LLM-derived insights for improved predictive abilities. This enhancement is achieved by maximizing the mutual information between traditional model's TS representations and LLM's textual representation counterparts, bridging the two modalities. Moreover, we recognize that samples vary in importance for two losses: traditional prediction and mutual information maximization. To address this variability, we introduce the \textit{sample reweighting} module to improve information utilization. This module assigns dual weights to each sample: one for prediction loss and another for mutual information loss, dynamically optimizing these weights via bi-level optimization. Our method achieves state-of-the-art or comparable performance across five mainstream TS tasks, including short-term and long-term forecasting, imputation, classification, and anomaly detection.

cs.LG↗

arXiv2024

A Simple yet Effective Subway Self-positioning Method based on Aerial-view Sleeper Detection

With the rapid development of urban underground rail vehicles,subway positioning, which plays a fundamental role in the traffic navigation and collision avoidance systems, has become a research hot-spot these years. Most current subway positioning methods rely on localization beacons densely pre-installed alongside the railway tracks, requiring massive costs for infrastructure and maintenance, while commonly lacking flexibility and anti-interference ability. In this paper, we propose a low-cost and real-time visual-assisted self-localization framework to address the robust and convenient positioning problem for subways. Firstly, we perform aerial view rail sleeper detection based on the fast and efficient YOLOv8n network. The detection results are then used to achieve real-time correction of mileage values combined with geometric positioning information, obtaining precise subway locations. Front camera Videos for subway driving scenes along a 6.9 km route are collected and annotated from the simulator for validation of the proposed method. Experimental results show that our aerial view sleeper detection algorithm can efficiently detect sleeper positions with F1-score of 0.929 at 1111 fps, and that the proposed positioning framework achieves a mean percentage error of 0.1\%, demonstrating its continuous and high-precision self-localization capability.

cs.CV↗

arXiv2024

Large Language Model (LLM) for Telecommunications: A Comprehensive Survey on Principles, Key Techniques, and Opportunities

Large language models (LLMs) have received considerable attention recently due to their outstanding comprehension and reasoning capabilities, leading to great progress in many fields. The advancement of LLM techniques also offers promising opportunities to automate many tasks in the telecommunication (telecom) field. After pre-training and fine-tuning, LLMs can perform diverse downstream tasks based on human instructions, paving the way to artificial general intelligence (AGI)-enabled 6G. Given the great potential of LLM technologies, this work aims to provide a comprehensive overview of LLM-enabled telecom networks. In particular, we first present LLM fundamentals, including model architecture, pre-training, fine-tuning, inference and utilization, model evaluation, and telecom deployment. Then, we introduce LLM-enabled key techniques and telecom applications in terms of generation, classification, optimization, and prediction problems. Specifically, the LLM-enabled generation applications include telecom domain knowledge, code, and network configuration generation. After that, the LLM-based classification applications involve network security, text, image, and traffic classification problems. Moreover, multiple LLM-enabled optimization techniques are introduced, such as automated reward function design for reinforcement learning and verbal reinforcement learning. Furthermore, for LLM-aided prediction problems, we discussed time-series prediction models and multi-modality prediction problems for telecom. Finally, we highlight the challenges and identify the future directions of LLM-enabled telecom networks.

eess.SY↗

arXiv2024

Controllability and Observability of Temporal Hypergraphs

Numerous complex systems, such as those arisen in ecological networks, genomic contact networks, and social networks, exhibit higher-order and time-varying characteristics, which can be effectively modeled using temporal hypergraphs. However, analyzing and controlling temporal hypergraphs poses significant challenges due to their inherent time-varying and nonlinear nature, while most existing methods predominantly target static hypergraphs. In this article, we generalize the notions of controllability and observability to temporal hypergraphs by leveraging tensor and nonlinear systems theory. Specifically, we establish tensor-based rank conditions to determine the weak controllability and observability of temporal hypergraphs. The proposed framework is further demonstrated with synthetic and real-world examples.

eess.SY↗

arXiv2024

Kronecker Product of Tensors and Hypergraphs: Structure and Dynamics

Hypergraphs and tensors extend classic graph and matrix theory to account for multiway relationships, which are ubiquitous in engineering, biological, and social systems. While the Kronecker product is a potent tool for analyzing the coupling of systems in graph or matrix contexts, its effectiveness in capturing multiway interactions remains elusive. In this article, we present a comprehensive exploration of algebraic, structural, and spectral properties of the tensor Kronecker product. We express Tucker and tensor train decompositions and various tensor eigenvalues in terms of the tensor Kronecker product. Additionally, we utilize the tensor Kronecker product to form Kronecker hypergraphs, a tensor-based hypergraph product, and investigate the structure and stability of polynomial dynamics on Kronecker hypergraphs. Finally, we provide numerical examples to demonstrate the utility of the tensor Kronecker product in computing Z-eigenvectors, various tensor decompositions, and determining the stability of polynomial systems.

math.DS↗

arXiv2024

Network Learning with Directional Sign Patterns

Complex systems can be effectively modeled via graphs that encode networked interactions, where relations between entities or nodes are often quantified by signed edge weights, e.g., promotion/inhibition in gene regulatory networks, or encoding political of friendship differences in social networks. However, it is often the case that only an aggregate consequence of such edge weights that characterize relations may be directly observable, as in protein expression of in gene regulatory networks. Thus, learning edge weights poses a significant challenge that is further exacerbated for intricate and large-scale networks. In this article, we address a model problem to determine the strength of sign-indefinite relations that explain marginal distributions that constitute our data. To this end, we develop a paradigm akin to that of the Schrödinger bridge problem and an efficient Sinkhorn type algorithm (more properly, Schrödinger-Fortet-Sinkhorn algorithm) that allows fast convergence to parameters that minimize a relative entropy/likelihood criterion between the sought signed adjacency matrix and a prior. The formalism that we present represents a novel generalization of the earlier Schrödinger formalism in that marginal computations may incorporate weights that model directionality in underlying relations, and further, that it can be extended to high-order networks -- the Schrödinger-Fortet-Sinkhorn algorithm that we derive is applicable all the same and allows geometric convergence to a sought sign-indefinite adjacency matrix or tensor, for high-order networks. We demonstrate our framework with synthetic and real-world examples.

math.OC↗

arXiv2024

On Complexity of Stability Analysis in Higher-order Ecological Networks through Tensor Decompositions

Complex ecological networks are often characterized by intricate interactions that extend beyond pairwise relationships. Understanding the stability of higher-order ecological networks is salient for species coexistence, biodiversity, and community persistence. In this article, we present complexity analyses for determining the linear stability of higher-order ecological networks through tensor decompositions. We are interested in the higher-order generalized Lotka-Volterra model, which captures high-order interactions using tensors of varying orders. To efficiently compute Jacobian matrices and thus determine stability in large ecological networks, we exploit various tensor decompositions, including higher-order singular value decomposition, Canonical Polyadic decomposition, and tensor train decomposition, accompanied by in-depth computational and memory complexity analyses. We demonstrate the effectiveness of our framework with numerical examples.

eess.SY↗

arXiv2024

Stability of Ecological Systems: A Theoretical Review

The stability of ecological systems is a fundamental concept in ecology, which offers profound insights into species coexistence, biodiversity, and community persistence. In this article, we provide a systematic and comprehensive review on the theoretical frameworks for analyzing the stability of ecological systems. Notably, we survey various stability notions, including linear stability, sign stability, diagonal stability, D-stability, total stability, sector stability, structural stability, and higher-order stability. For each of these stability notions, we examine necessary or sufficient conditions for achieving such stability and demonstrate the intricate interplay of these conditions on the network structures of ecological systems. Finally, we explore the future prospects of these stability notions.

math.DS↗

arXiv2023

Dual-space Hierarchical Learning for Goal-guided Conversational Recommendation

Proactively and naturally guiding the dialog from the non-recommendation context (e.g., Chit-chat) to the recommendation scenario (e.g., Music) is crucial for the Conversational Recommender System (CRS). Prior studies mainly focus on planning the next dialog goal~(e.g., chat on a movie star) conditioned on the previous dialog. However, we find the dialog goals can be simultaneously observed at different levels, which can be utilized to improve CRS. In this paper, we propose Dual-space Hierarchical Learning (DHL) to leverage multi-level goal sequences and their hierarchical relationships for conversational recommendation. Specifically, we exploit multi-level goal sequences from both the representation space and the optimization space. In the representation space, we propose the hierarchical representation learning where a cross attention module derives mutually enhanced multi-level goal representations. In the optimization space, we devise the hierarchical weight learning to reweight lower-level goal sequences, and introduce bi-level optimization for stable update. Additionally, we propose a soft labeling strategy to guide optimization gradually. Experiments on two real-world datasets verify the effectiveness of our approach. Code and data are available here.

cs.IR↗