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Mingchen Li

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12 papers

2 author rows

AAAI Conference 2026 Conference Paper

OrgaCast: A Trustworthy Spatiotemporal Diffusion Model for Fluorescence Organoid Forecasting

Dawei Gao
Angello Huerta Gomez
Mingchen Li
Marcel El-Mokahal
Huaxiao Yang
Yunhe Feng

Accurately forecasting the spatiotemporal dynamics of biological systems, such as human pluripotent stem cell (hPSC)-derived cardiac organoids, from microscopy time-series is a critical challenge in biomedicine with profound implications for drug discovery. Existing generative models often fail to capture the intricate dynamics of organoid development, struggling with their irregular morphology, indistinct boundaries, and complex spatiotemporal patterns. To overcome these limitations, we introduce OrgaCast, a novel multimodal conditional diffusion model for high-fidelity organoid forecasting. OrgaCast uniquely conditions the generative process on three synergistic modalities: (i) historical image sequences, captured by a dedicated spatiotemporal control module; (ii) structured numerical metadata defining experimental conditions; and (iii) descriptive text captions summarizing the biological context. This comprehensive conditioning enables the generation of forecasts with high visual accuracy and biological plausibility. Furthermore, to enhance the model's utility in critical research settings, we introduce a post-hoc uncertainty quantification method that produces intuitive confidence maps, bolstering the interpretability and trustworthiness of predictions. Extensive experiments on a challenging cardiac organoid dataset demonstrate that OrgaCast outperforms baselines in metrics such as SSIM, PSNR, and LPIPS. Our framework presents a robust solution for biological forecasting, promising to accelerate research discovery while minimizing experimental costs and manual effort.

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IJCAI Conference 2025 Conference Paper

ContextAware: A Multi-Agent Framework for Detecting Harmful Image-Based Comments on Social Media

Zheng Wei
Mingchen Li
Pu Zhang
Xinyu Liu
Huamin Qu
Pan Hui

Detecting hidden stigmatization in social media poses significant challenges due to semantic misalignments between textual and visual modalities, as well as the subtlety of implicit stigmatization. Traditional approaches often fail to capture these complexities in real-world, multimodal content. To address this gap, we introduce ContextAware, an agent-based framework that leverages specialized modules to collaboratively process and analyze images, textual context, and social interactions. Our approach begins by clustering image embeddings to identify recurring content, activating high-likes agents for deeper analysis of images receiving substantial user engagement, while comprehensive agents handle lower-engagement images. By integrating case-based learning, textual sentiment, and vision-language models (VLMs), ContextAware refines its detection of harmful content. We evaluate ContextAware on a self-collected Douyin dataset focused on interracial relationships, comprising 871 short videos and 885, 502 comments—of which a notable portion are image-based. Experimental results show that ContextAware not only outperforms state-of-the-art methods in accuracy and F1 score but also effectively detects implicit stigmatization within the highly contextual environment of social media. Our findings underscore the importance of agent-based architectures and multimodal alignment in capturing nuanced, culturally specific forms of harmful content.

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AAAI Conference 2025 Conference Paper

On the Power of Convolution-Augmented Transformer

Mingchen Li
Xuechen Zhang
Yixiao Huang
Samet Oymak

The transformer architecture has catalyzed revolutionary advances in language modeling. However, recent architectural recipes, such as state-space models, have bridged the performance gap. Motivated by this, we examine the benefits of Convolution-Augmented Transformer (CAT) for recall, copying, and length generalization tasks. CAT incorporates convolutional filters in the K/Q/V embeddings of an attention layer. Through CAT, we show that the locality of the convolution synergizes with the global view of the attention. Unlike comparable architectures, such as Mamba or transformer, CAT can provably solve the associative recall (AR) and copying tasks using a single layer while also enjoying guaranteed length generalization. We also establish computational tradeoffs between convolution and attention by characterizing how convolution can mitigate the need for full attention by summarizing the context window and creating salient summary tokens to attend. Evaluations on real datasets corroborate our findings and demonstrate that CAT and its variations indeed enhance the language modeling performance.

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ICLR Conference 2025 Conference Paper

TVNet: A Novel Time Series Analysis Method Based on Dynamic Convolution and 3D-Variation

Chenghan Li
Mingchen Li
Ruisheng Diao

With the recent development and advancement of Transformer and MLP architectures, significant strides have been made in time series analysis. Conversely, the performance of Convolutional Neural Networks (CNNs) in time series analysis has fallen short of expectations, diminishing their potential for future applications. Our research aims to enhance the representational capacity of Convolutional Neural Networks (CNNs) in time series analysis by introducing novel perspectives and design innovations. To be specific, We introduce a novel time series reshaping technique that considers the inter-patch, intra-patch, and cross-variable dimensions. Consequently, we propose TVNet, a dynamic convolutional network leveraging a 3D perspective to employ time series analysis. TVNet retains the computational efficiency of CNNs and achieves state-of-the-art results in five key time series analysis tasks, offering a superior balance of efficiency and performance over the state-of-the-art Transformer-based and MLP-based models. Additionally, our findings suggest that TVNet exhibits enhanced transferability and robustness. Therefore, it provides a new perspective for applying CNN in advanced time series analysis tasks.

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NeurIPS Conference 2025 Conference Paper

Venus-MAXWELL: Efficient Learning of Protein-Mutation Stability Landscapes using Protein Language Models

Yuanxi Yu
Fan Jiang
Xinzhu Ma
Liang Zhang
Bozitao Zhong
Wanli Ouyang
Guisheng Fan
Huiqun Yu

In-silico prediction of protein mutant stability, measured by the difference in Gibbs free energy change ($\Delta \Delta G$), is fundamental for protein engineering. Current sequence-to-label methods typically employ two-stage pipelines: (i) encoding mutant sequences using neural networks (e. g. , transformers), followed by (ii) the $\Delta \Delta G$ regression from the latent representations. Although these methods have demonstrated promising performance, their dependence on specialized neural network encoders significantly increases the complexity. Additionally, the requirement to compute latent representations individually for each mutant sequence negatively impacts computational efficiency and poses the risk of overfitting. This work proposes the Venus-MAXWELL framework, which reformulates mutation $\Delta \Delta G$ prediction as a sequence-to-landscape task. In Venus-MAXWELL, mutations of a protein and their corresponding $\Delta \Delta G$ values are organized into a landscape matrix, allowing our framework to learn the $\Delta \Delta G$ landscape of a protein with a single forward and backward pass during training. To this end, we curated a new $\Delta \Delta G$ benchmark dataset with strict controls on data leakage and redundancy to ensure robust evaluation. Leveraging the zero-shot scoring capability of protein language models (PLMs), Venus-MAXWELL effectively utilizes the evolutionary patterns learned by PLMs during pre-training. More importantly, Venus-MAXWELL is compatible with multiple protein language models. For example, when integrated with the ESM-IF, Venus-MAXWELL achieves higher accuracy than ThermoMPNN with 10$\times$ faster in inference speed (despite having 50$\times$ more parameters than ThermoMPNN). The training codes, model weights, and datasets are publicly available at https: //github. com/ai4protein/Venus-MAXWELL.

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EAAI Journal 2024 Journal Article

A new LASSO-BiLSTM-based ensemble learning approach for exchange rate forecasting

Siyuan Liu
Qiqian Huang
Mingchen Li
Yunjie Wei

Foreign exchange rate affects many countries' economic status and development. Therefore, it is essential to find the factors affecting the exchange rate price and make reasonable predictions. This paper proposes the novel LASSO-BiLSTM-based ensemble learning method by integrating least absolute shrinkage and selection operator (LASSO) and bidirectional long short-term memory (LSTM) to predict the USD/CNY exchange rate. First, 29 variables are selected to reflect economic activities on market and macroeconomic levels. Then, LASSO-BiLSTM-based ensemble learning approach is adopted with two steps: 1) LASSO is used to select six highly correlated variables with the exchange rate to reduce noises. 2) BiLSTM is employed to forecast the exchange rate with the six chosen variables. Last, to test the effectiveness of BiLSTM, comparisons with four deep learning algorithms, which are extreme learning machine (ELM), kernel extreme learning machine (KELM), long short-term memory (LSTM), and support vector regression (SVR), are conducted. The result shows that LASSO-BiLSTM outperforms the other models in 1-step forecast (MAE: 0. 051, RMSE: 0. 072, MDA: 0. 777). The same conclusion applies to 3-steps and 6-steps forecasts. Overall, the proposed LASSO-BiLSTM-based ensemble learning method demonstrates high potential in time series forecasting.

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AAAI Conference 2024 Conference Paper

Class-Attribute Priors: Adapting Optimization to Heterogeneity and Fairness Objective

Xuechen Zhang
Mingchen Li
Jiasi Chen
Christos Thrampoulidis
Samet Oymak

Modern classification problems exhibit heterogeneities across individual classes: Each class may have unique attributes, such as sample size, label quality, or predictability (easy vs difficult), and variable importance at test-time. Without care, these heterogeneities impede the learning process, most notably, when optimizing fairness objectives. Confirming this, under a gaussian mixture setting, we show that the optimal SVM classifier for balanced accuracy needs to be adaptive to the class attributes. This motivates us to propose CAP: An effective and general method that generates a class-specific learning strategy (e.g.~hyperparameter) based on the attributes of that class. This way, optimization process better adapts to heterogeneities. CAP leads to substantial improvements over the naive approach of assigning separate hyperparameters to each class. We instantiate CAP for loss function design and post-hoc logit adjustment, with emphasis on label-imbalanced problems. We show that CAP is competitive with prior art and its flexibility unlocks clear benefits for fairness objectives beyond balanced accuracy. Finally, we evaluate CAP on problems with label noise as well as weighted test objectives to showcase how CAP can jointly adapt to different heterogeneities.

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NeurIPS Conference 2024 Conference Paper

ProSST: Protein Language Modeling with Quantized Structure and Disentangled Attention

Mingchen Li
Yang Tan
Xinzhu Ma
Bozitao Zhong
Huiqun Yu
Ziyi Zhou
Wanli Ouyang
Bingxin Zhou

Protein language models (PLMs) have shown remarkable capabilities in various protein function prediction tasks. However, while protein function is intricately tied to structure, most existing PLMs do not incorporate protein structure information. To address this issue, we introduce ProSST, a Transformer-based protein language model that seamlessly integrates both protein sequences and structures. ProSST incorporates a structure quantization module and a Transformer architecture with disentangled attention. The structure quantization module translates a 3D protein structure into a sequence of discrete tokens by first serializing the protein structure into residue-level local structures and then embeds them into dense vector space. These vectors are then quantized into discrete structure tokens by a pre-trained clustering model. These tokens serve as an effective protein structure representation. Furthermore, ProSST explicitly learns the relationship between protein residue token sequences and structure token sequences through the sequence-structure disentangled attention. We pre-train ProSST on millions of protein structures using a masked language model objective, enabling it to learn comprehensive contextual representations of proteins. To evaluate the proposed ProSST, we conduct extensive experiments on the zero-shot mutation effect prediction and several supervised downstream tasks, where ProSST achieves the state-of-the-art performance among all baselines. Our code and pre-trained models are publicly available.

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NeurIPS Conference 2024 Conference Paper

Selective Attention: Enhancing Transformer through Principled Context Control

Xuechen Zhang
Xiangyu Chang
Mingchen Li
Amit Roy-Chowdhury
Jiasi Chen
Samet Oymak

The attention mechanism within the transformer architecture enables the model to weigh and combine tokens based on their relevance to the query. While self-attention has enjoyed major success, it notably treats all queries $q$ in the same way by applying the mapping $V^\top\text{softmax}(Kq)$, where $V, K$ are the value and key embeddings respectively. In this work, we argue that this uniform treatment hinders the ability to control contextual sparsity and relevance. As a solution, we introduce the Selective Self-Attention (SSA) layer that augments the softmax nonlinearity with a principled temperature scaling strategy. By controlling temperature, SSA adapts the contextual sparsity of the attention map to the query embedding and its position in the context window. Through theory and experiments, we demonstrate that this alleviates attention dilution, aids the optimization process, and enhances the model's ability to control softmax spikiness of individual queries. We also incorporate temperature scaling for value embeddings and show that it boosts the model's ability to suppress irrelevant/noisy tokens. Notably, SSA is a lightweight method which introduces less than 0. 5\% new parameters through a weight-sharing strategy and can be fine-tuned on existing LLMs. Extensive empirical evaluations demonstrate that SSA-equipped models achieve a noticeable and consistent accuracy improvement on language modeling benchmarks.

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ICML Conference 2022 Conference Paper

FedNest: Federated Bilevel, Minimax, and Compositional Optimization

Davoud Ataee Tarzanagh
Mingchen Li
Christos Thrampoulidis
Samet Oymak

Standard federated optimization methods successfully apply to stochastic problems with single-level structure. However, many contemporary ML problems - including adversarial robustness, hyperparameter tuning, actor-critic - fall under nested bilevel programming that subsumes minimax and compositional optimization. In this work, we propose FedNest: A federated alternating stochastic gradient method to address general nested problems. We establish provable convergence rates for FedNest in the presence of heterogeneous data and introduce variations for bilevel, minimax, and compositional optimization. FedNest introduces multiple innovations including federated hypergradient computation and variance reduction to address inner-level heterogeneity. We complement our theory with experiments on hyperparameter & hyper-representation learning and minimax optimization that demonstrate the benefits of our method in practice.

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NeurIPS Conference 2021 Conference Paper

AutoBalance: Optimized Loss Functions for Imbalanced Data

Mingchen Li
Xuechen Zhang
Christos Thrampoulidis
Jiasi Chen
Samet Oymak

Imbalanced datasets are commonplace in modern machine learning problems. The presence of under-represented classes or groups with sensitive attributes results in concerns about generalization and fairness. Such concerns are further exacerbated by the fact that large capacity deep nets can perfectly fit the training data and appear to achieve perfect accuracy and fairness during training, but perform poorly during test. To address these challenges, we propose AutoBalance, a bi-level optimization framework that automatically designs a training loss function to optimize a blend of accuracy and fairness-seeking objectives. Specifically, a lower-level problem trains the model weights, and an upper-level problem tunes the loss function by monitoring and optimizing the desired objective over the validation data. Our loss design enables personalized treatment for classes/groups by employing a parametric cross-entropy loss and individualized data augmentation schemes. We evaluate the benefits and performance of our approach for the application scenarios of imbalanced and group-sensitive classification. Extensive empirical evaluations demonstrate the benefits of AutoBalance over state-of-the-art approaches. Our experimental findings are complemented with theoretical insights on loss function design and the benefits of the train-validation split. All code is available open-source.

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ICML Conference 2021 Conference Paper

Generalization Guarantees for Neural Architecture Search with Train-Validation Split

Samet Oymak
Mingchen Li
Mahdi Soltanolkotabi

Neural Architecture Search (NAS) is a popular method for automatically designing optimized deep-learning architectures. NAS methods commonly use bilevel optimization where one optimizes the weights over the training data (lower-level problem) and hyperparameters - such as the architecture - over the validation data (upper-level problem). This paper explores the statistical aspects of such problems with train-validation splits. In practice, the lower-level problem is often overparameterized and can easily achieve zero loss. Thus, a-priori, it seems impossible to distinguish the right hyperparameters based on training loss alone which motivates a better understanding of train-validation split. To this aim, we first show that refined properties of the validation loss such as risk and hyper-gradients are indicative of those of the true test loss and help prevent overfitting with a near-minimal validation sample size. Importantly, this is established for continuous search spaces which are relevant for differentiable search schemes. We then establish generalization bounds for NAS problems with an emphasis on an activation search problem and gradient-based methods. Finally, we show rigorous connections between NAS and low-rank matrix learning which leads to algorithmic insights where the solution of the upper problem can be accurately learned via spectral methods to achieve near-minimal risk.

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