Mingchen Li

Davoud Ataee Tarzanagh, Mingchen Li, Christos Thrampoulidis et al.

Standard federated optimization methods successfully apply to stochastic problems with single-level structure. However, many contemporary ML problems -- including adversarial robustness, hyperparameter tuning, and actor-critic -- fall under nested bilevel programming that subsumes minimax and compositional optimization. In this work, we propose \fedblo: A federated alternating stochastic gradient method to address general nested problems. We establish provable convergence rates for \fedblo in the presence of heterogeneous data and introduce variations for bilevel, minimax, and compositional optimization. \fedblo 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. Code is available at https://github.com/ucr-optml/FedNest.

Yingcong Li, Mingchen Li, M. Salman Asif et al.

In continual learning (CL), the goal is to design models that can learn a sequence of tasks without catastrophic forgetting. While there is a rich set of techniques for CL, relatively little understanding exists on how representations built by previous tasks benefit new tasks that are added to the network. To address this, we study the problem of continual representation learning (CRL) where we learn an evolving representation as new tasks arrive. Focusing on zero-forgetting methods where tasks are embedded in subnetworks (e.g., PackNet), we first provide experiments demonstrating CRL can significantly boost sample efficiency when learning new tasks. To explain this, we establish theoretical guarantees for CRL by providing sample complexity and generalization error bounds for new tasks by formalizing the statistical benefits of previously-learned representations. Our analysis and experiments also highlight the importance of the order in which we learn the tasks. Specifically, we show that CL benefits if the initial tasks have large sample size and high "representation diversity". Diversity ensures that adding new tasks incurs small representation mismatch and can be learned with few samples while training only few additional nonzero weights. Finally, we ask whether one can ensure each task subnetwork to be efficient during inference time while retaining the benefits of representation learning. To this end, we propose an inference-efficient variation of PackNet called Efficient Sparse PackNet (ESPN) which employs joint channel & weight pruning. ESPN embeds tasks in channel-sparse subnets requiring up to 80% less FLOPs to compute while approximately retaining accuracy and is very competitive with a variety of baselines. In summary, this work takes a step towards data and compute-efficient CL with a representation learning perspective. GitHub page: https://github.com/ucr-optml/CtRL

Jiatan Huang, Mingchen Li, Ziming Li et al.

Multi-agent LLM systems often treat agreement as evidence: when many agents in a panel give the same answer, that answer is assumed to be more reliable. We show that this assumption can fail after agents communicate. Communication can induce correlated failures and false consensus, so the same vote share may reflect reliable agreement in one topology but over-confidence in another. We propose CAGE-CAL, a counterfactual agent-graph calibration framework for multi-agent LLMs. For each query, CAGE-CAL compares an observed post-communication agent graph with a matched counterfactual no-communication graph, capturing both pairwise failure correlations and group-level dependencies. Rather than simply counting how many agents agree, CAGE-CAL estimates the counterfactual shift between observed and no-communication dependence, and calibrates confidence accordingly. Across five benchmarks, CAGE-CAL improves reliability discrimination with competitive ECE, and its calibrated confidence further improves topology selection over the best fixed-topology strategy.

Mingchen Li, Liqi Kang, Yi Xiong et al.

Deep learning has been widely used for protein engineering. However, it is limited by the lack of sufficient experimental data to train an accurate model for predicting the functional fitness of high-order mutants. Here, we develop SESNet, a supervised deep-learning model to predict the fitness for protein mutants by leveraging both sequence and structure information, and exploiting attention mechanism. Our model integrates local evolutionary context from homologous sequences, the global evolutionary context encoding rich semantic from the universal protein sequence space and the structure information accounting for the microenvironment around each residue in a protein. We show that SESNet outperforms state-of-the-art models for predicting the sequence-function relationship on 26 deep mutational scanning datasets. More importantly, we propose a data augmentation strategy by leveraging the data from unsupervised models to pre-train our model. After that, our model can achieve strikingly high accuracy in prediction of the fitness of protein mutants, especially for the higher order variants (> 4 mutation sites), when finetuned by using only a small number of experimental mutation data (<50). The strategy proposed is of great practical value as the required experimental effort, i.e., producing a few tens of experimental mutation data on a given protein, is generally affordable by an ordinary biochemical group and can be applied on almost any protein.

Xuechen Zhang, Mingchen Li, Xiangyu Chang et al.

The growth and diversity of machine learning applications motivate a rethinking of learning with mobile and edge devices. How can we address diverse client goals and learn with scarce heterogeneous data? While federated learning aims to address these issues, it has challenges hindering a unified solution. Large transformer models have been shown to work across a variety of tasks achieving remarkable few-shot adaptation. This raises the question: Can clients use a single general-purpose model, rather than custom models for each task, while obeying device and network constraints? In this work, we investigate pretrained transformers (PTF) to achieve these on-device learning goals and thoroughly explore the roles of model size and modularity, where the latter refers to adaptation through modules such as prompts or adapters. Focusing on federated learning, we demonstrate that: (1) Larger scale shrinks the accuracy gaps between alternative approaches and improves heterogeneity robustness. Scale allows clients to run more local SGD epochs which can significantly reduce the number of communication rounds. At the extreme, clients can achieve respectable accuracy locally highlighting the potential of fully-local learning. (2) Modularity, by design, enables $>$100$\times$ less communication in bits. Surprisingly, it also boosts the generalization capability of local adaptation methods and the robustness of smaller PTFs. Finally, it enables clients to solve multiple unrelated tasks simultaneously using a single PTF, whereas full updates are prone to catastrophic forgetting. These insights on scale and modularity motivate a new federated learning approach we call "You Only Load Once" (FedYolo): The clients load a full PTF model once and all future updates are accomplished through communication-efficient modules with limited catastrophic-forgetting, where each task is assigned to its own module.

Yang Tan, Yuanxi Yu, Can Wu et al.

Zero-shot mutation prediction is vital for low-resource protein engineering, yet existing protein language models (PLMs) often yield statistically confident results that ignore fundamental biophysical constraints. Currently, selecting candidates for wet-lab validation relies on manual expert auditing of PLM outputs, a process that is inefficient, subjective, and highly dependent on domain expertise. To address this, we propose Rank-and-Reason (VenusRAR), a two-stage agentic framework to automate this workflow and maximize expected wet-lab fitness. In the Rank-Stage, a Computational Expert and Virtual Biologist aggregate a context-aware multi-modal ensemble, establishing a new Spearman correlation record of 0.551 (vs. 0.518) on ProteinGym. In the Reason-Stage, an agentic Expert Panel employs chain-of-thought reasoning to audit candidates against geometric and structural constraints, improving the Top-5 Hit Rate by up to 367% on ProteinGym-DMS99. The wet-lab validation on Cas12i3 nuclease further confirms the framework's efficacy, achieving a 46.7% positive rate and identifying two novel mutants with 4.23-fold and 5.05-fold activity improvements. Code and datasets are released on GitHub (https://github.com/ai4protein/VenusRAR/).

Mingchen Li, Xuechen Zhang, Yixiao Huang et al.

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.

Mingchen Li, Junfan Chen, Samuel Mensah et al.

Due to the incompleteness of knowledge graphs (KGs), zero-shot link prediction (ZSLP) which aims to predict unobserved relations in KGs has attracted recent interest from researchers. A common solution is to use textual features of relations (e.g., surface name or textual descriptions) as auxiliary information to bridge the gap between seen and unseen relations. Current approaches learn an embedding for each word token in the text. These methods lack robustness as they suffer from the out-of-vocabulary (OOV) problem. Meanwhile, models built on character n-grams have the capability of generating expressive representations for OOV words. Thus, in this paper, we propose a Hierarchical N-Gram framework for Zero-Shot Link Prediction (HNZSLP), which considers the dependencies among character n-grams of the relation surface name for ZSLP. Our approach works by first constructing a hierarchical n-gram graph on the surface name to model the organizational structure of n-grams that leads to the surface name. A GramTransformer, based on the Transformer is then presented to model the hierarchical n-gram graph to construct the relation embedding for ZSLP. Experimental results show the proposed HNZSLP achieved state-of-the-art performance on two ZSLP datasets.

Yang Tan, Mingchen Li, Pan Tan et al.

Large protein language models are adept at capturing the underlying evolutionary information in primary structures, offering significant practical value for protein engineering. Compared to natural language models, protein amino acid sequences have a smaller data volume and a limited combinatorial space. Choosing an appropriate vocabulary size to optimize the pre-trained model is a pivotal issue. Moreover, despite the wealth of benchmarks and studies in the natural language community, there remains a lack of a comprehensive benchmark for systematically evaluating protein language model quality. Given these challenges, PETA trained language models with 14 different vocabulary sizes under three tokenization methods. It conducted thousands of tests on 33 diverse downstream datasets to assess the models' transfer learning capabilities, incorporating two classification heads and three random seeds to mitigate potential biases. Extensive experiments indicate that vocabulary sizes between 50 and 200 optimize the model, whereas sizes exceeding 800 detrimentally affect the model's representational performance. Our code, model weights and datasets are available at https://github.com/ginnm/ProteinPretraining.

Mingchen Li, Rui Zhang

Recent advancements in language models (LMs) have led to the emergence of powerful models such as Small LMs (e.g., T5) and Large LMs (e.g., GPT-4). These models have demonstrated exceptional capabilities across a wide range of tasks, such as name entity recognition (NER) in the general domain. (We define SLMs as pre-trained models with fewer parameters compared to models like GPT-3/3.5/4, such as T5, BERT, and others.) Nevertheless, their efficacy in the medical section remains uncertain and the performance of medical NER always needs high accuracy because of the particularity of the field. This paper aims to provide a thorough investigation to compare the performance of LMs in medical few-shot NER and answer How far is LMs from 100\% Few-shot NER in Medical Domain, and moreover to explore an effective entity recognizer to help improve the NER performance. Based on our extensive experiments conducted on 16 NER models spanning from 2018 to 2023, our findings clearly indicate that LLMs outperform SLMs in few-shot medical NER tasks, given the presence of suitable examples and appropriate logical frameworks. Despite the overall superiority of LLMs in few-shot medical NER tasks, it is important to note that they still encounter some challenges, such as misidentification, wrong template prediction, etc. Building on previous findings, we introduce a simple and effective method called \textsc{RT} (Retrieving and Thinking), which serves as retrievers, finding relevant examples, and as thinkers, employing a step-by-step reasoning process. Experimental results show that our proposed \textsc{RT} framework significantly outperforms the strong open baselines on the two open medical benchmark datasets

Mingchen Li, Shihao Ji

Building query graphs from natural language questions is an important step in complex question answering over knowledge graph (Complex KGQA). In general, a question can be correctly answered if its query graph is built correctly and the right answer is then retrieved by issuing the query graph against the KG. Therefore, this paper focuses on query graph generation from natural language questions. Existing approaches for query graph generation ignore the semantic structure of a question, resulting in a large number of noisy query graph candidates that undermine prediction accuracies. In this paper, we define six semantic structures from common questions in KGQA and develop a novel Structure-BERT to predict the semantic structure of a question. By doing so, we can first filter out noisy candidate query graphs, and then rank the remaining candidates with a BERT-based ranking model. Extensive experiments on two popular benchmarks MetaQA and WebQuestionsSP (WSP) demonstrate the effectiveness of our method as compared to state-of-the-arts.

Mingchen Li, Jiatan Huang, Chuxu Zhang et al.

In-context learning has recently been linked to implicit gradient descent in linear self-attention models, suggesting that context can induce a forward-pass update. Retrieval-augmented generation (RAG) also relies on context, but retrieved documents are usually treated as static evidence rather than signals for adaptation. We study RAG as an in-context optimization process. First, we show that one linear self-attention layer can implement one gradient-descent step on a unified linearized RAG objective covering both projection-based and dot-product retrieval interfaces. This gives an exact regime where retrieval-augmented prediction and in-context optimization coincide. We use this result not as a literal model of LLM computation, but as a guide for adapting the interaction between queries and retrieved evidence. We then test the boundary of this correspondence: it remains stable under controlled linear extensions, but becomes feature-distribution dependent under nonlinear architectures. Finally, we turn this view into a lightweight method for frozen RAG LLMs. The method keeps the retriever and backbone fixed, and predicts a context-conditioned update to a generator-side evidence-use interface. Across seven QA benchmarks, two retrievers, and two frozen LLM backbones, this forward-only update improves a shared-interface baseline, transfers to held-out tasks, and approaches test-time gradient adaptation at much lower per-query cost.

Mingchen Li, Hansi Zeng, Zhuo Qian et al.

Retrieval is increasingly moving from one-shot matching toward interactive reasoning, where language agents iteratively inspect evidence, reformulate queries, and search again. Training such agents raises a credit-assignment challenge: executable actions such as queries or summaries can be directly evaluated by the retriever, while latent reasoning steps are not directly observable and only affect future executable actions. This asymmetry makes outcome-level reward assignment unreliable, as the same final reward may credit reasoning steps that did not actually shape retrieval success. We propose RICE-PO, a critic-free policy optimization framework that converts retrieval interactions into localized learning signals. RICE-PO selects high-uncertainty executable actions as anchors, evaluates local counterfactual branches using retrieval metrics, and propagates credit to latent reasoning steps only when reasoning-to-action influence is strong and future residual effects are stable. On BRIGHT and BEIR, RICE-PO consistently outperforms prompt-based agents and group-based RL baselines under the same retriever setting. These results show that the structure of agent-environment interaction itself can provide useful supervision for training reasoning-based retrieval agents.

Mingchen Li, Lifu Huang

Open domain entity state tracking aims to predict reasonable state changes of entities (i.e., [attribute] of [entity] was [before_state] and [after_state] afterwards) given the action descriptions. It's important to many reasoning tasks to support human everyday activities. However, it's challenging as the model needs to predict an arbitrary number of entity state changes caused by the action while most of the entities are implicitly relevant to the actions and their attributes as well as states are from open vocabularies. To tackle these challenges, we propose a novel end-to-end Knowledge Informed framework for open domain Entity State Tracking, namely KIEST, which explicitly retrieves the relevant entities and attributes from external knowledge graph (i.e., ConceptNet) and incorporates them to autoregressively generate all the entity state changes with a novel dynamic knowledge grained encoder-decoder framework. To enforce the logical coherence among the predicted entities, attributes, and states, we design a new constraint decoding strategy and employ a coherence reward to improve the decoding process. Experimental results show that our proposed KIEST framework significantly outperforms the strong baselines on the public benchmark dataset OpenPI.

Davoud Ataee Tarzanagh, Mingchen Li, Pranay Sharma et al.

Stochastic approximation with multiple coupled sequences (MSA) has found broad applications in machine learning as it encompasses a rich class of problems including bilevel optimization (BLO), multi-level compositional optimization (MCO), and reinforcement learning (specifically, actor-critic methods). However, designing provably-efficient federated algorithms for MSA has been an elusive question even for the special case of double sequence approximation (DSA). Towards this goal, we develop FedMSA which is the first federated algorithm for MSA, and establish its near-optimal communication complexity. As core novelties, (i) FedMSA enables the provable estimation of hypergradients in BLO and MCO via local client updates, which has been a notable bottleneck in prior theory, and (ii) our convergence guarantees are sensitive to the heterogeneity-level of the problem. We also incorporate momentum and variance reduction techniques to achieve further acceleration leading to near-optimal rates. Finally, we provide experiments that support our theory and demonstrate the empirical benefits of FedMSA. As an example, FedMSA enables order-of-magnitude savings in communication rounds compared to prior federated BLO schemes.

Mingchen Li, Di Zhuang, J. Morris Chang

With the development of machine learning and data science, data sharing is very common between companies and research institutes to avoid data scarcity. However, sharing original datasets that contain private information can cause privacy leakage. A reliable solution is to utilize private synthetic datasets which preserve statistical information from original datasets. In this paper, we propose MC-GEN, a privacy-preserving synthetic data generation method under differential privacy guarantee for machine learning classification tasks. MC-GEN applies multi-level clustering and differential private generative model to improve the utility of synthetic data. In the experimental evaluation, we evaluated the effects of parameters and the effectiveness of MC-GEN. The results showed that MC-GEN can achieve significant effectiveness under certain privacy guarantees on multiple classification tasks. Moreover, we compare MC-GEN with three existing methods. The results showed that MC-GEN outperforms other methods in terms of utility.

Mingchen Li, Wajdi Aljedaani, Yingjie Liu et al.

Skin-toned emojis are crucial for fostering personal identity and social inclusion in online communication. As AI models, particularly Large Language Models (LLMs), increasingly mediate interactions on web platforms, the risk that these systems perpetuate societal biases through their representation of such symbols is a significant concern. This paper presents the first large-scale comparative study of bias in skin-toned emoji representations across two distinct model classes. We systematically evaluate dedicated emoji embedding models (emoji2vec, emoji-sw2v) against four modern LLMs (Llama, Gemma, Qwen, and Mistral). Our analysis first reveals a critical performance gap: while LLMs demonstrate robust support for skin tone modifiers, widely-used specialized emoji models exhibit severe deficiencies. More importantly, a multi-faceted investigation into semantic consistency, representational similarity, sentiment polarity, and core biases uncovers systemic disparities. We find evidence of skewed sentiment and inconsistent meanings associated with emojis across different skin tones, highlighting latent biases within these foundational models. Our findings underscore the urgent need for developers and platforms to audit and mitigate these representational harms, ensuring that AI's role on the web promotes genuine equity rather than reinforcing societal biases.

Jiatan Huang, Zheyuan Zhang, Tianyi Ma et al.

Nutritional interventions are important for managing chronic health conditions, but current computational methods provide limited support for personalized dietary guidance. We identify three key gaps: (1) dietary pattern studies often ignore real-world constraints such as socioeconomic status, comorbidities, and limited food access; (2) recommendation systems rarely explain why a particular food helps a given patient; and (3) no unified benchmark evaluates methods across the connected tasks needed for nutritional interventions. We introduce GLEN-Bench, the first comprehensive graph-language based benchmark for nutritional health assessment. We combine NHANES health records, FNDDS food composition data, and USDA food-access metrics to build a knowledge graph that links demographics, health conditions, dietary behaviors, poverty-related constraints, and nutrient needs. We test the benchmark using opioid use disorder, where models must detect subtle nutritional differences across disease stages. GLEN-Bench includes three linked tasks: risk detection identifies at-risk individuals from dietary and socioeconomic patterns; recommendation suggests personalized foods that meet clinical needs within resource constraints; and question answering provides graph-grounded, natural-language explanations to facilitate comprehension. We evaluate these graph-language approaches, including graph neural networks, large language models, and hybrid architectures, to establish solid baselines and identify practical design choices. Our analysis identifies clear dietary patterns linked to health risks, providing insights that can guide practical interventions.

Mingchen Li, Huixue Zhou, Rui Zhang

Biomedical triple extraction systems aim to automatically extract biomedical entities and relations between entities. The exploration of applying large language models (LLM) to triple extraction is still relatively unexplored. In this work, we mainly focus on sentence-level biomedical triple extraction. Furthermore, the absence of a high-quality biomedical triple extraction dataset impedes the progress in developing robust triple extraction systems. To address these challenges, initially, we compare the performance of various large language models. Additionally, we present GIT, an expert-annotated biomedical triple extraction dataset that covers a wider range of relation types.

Ying Liu, Haozhu Wang, Huixue Zhou et al.

Reinforcement learning (RL) has emerged as a powerful approach for tackling complex medical decision-making problems such as treatment planning, personalized medicine, and optimizing the scheduling of surgeries and appointments. It has gained significant attention in the field of Natural Language Processing (NLP) due to its ability to learn optimal strategies for tasks such as dialogue systems, machine translation, and question-answering. This paper presents a review of the RL techniques in NLP, highlighting key advancements, challenges, and applications in healthcare. The review begins by visualizing a roadmap of machine learning and its applications in healthcare. And then it explores the integration of RL with NLP tasks. We examined dialogue systems where RL enables the learning of conversational strategies, RL-based machine translation models, question-answering systems, text summarization, and information extraction. Additionally, ethical considerations and biases in RL-NLP systems are addressed.

Yang Tan, Mingchen Li, Bingxin Zhou et al.

Fine-tuning Pre-trained protein language models (PLMs) has emerged as a prominent strategy for enhancing downstream prediction tasks, often outperforming traditional supervised learning approaches. As a widely applied powerful technique in natural language processing, employing Parameter-Efficient Fine-Tuning techniques could potentially enhance the performance of PLMs. However, the direct transfer to life science tasks is non-trivial due to the different training strategies and data forms. To address this gap, we introduce SES-Adapter, a simple, efficient, and scalable adapter method for enhancing the representation learning of PLMs. SES-Adapter incorporates PLM embeddings with structural sequence embeddings to create structure-aware representations. We show that the proposed method is compatible with different PLM architectures and across diverse tasks. Extensive evaluations are conducted on 2 types of folding structures with notable quality differences, 9 state-of-the-art baselines, and 9 benchmark datasets across distinct downstream tasks. Results show that compared to vanilla PLMs, SES-Adapter improves downstream task performance by a maximum of 11% and an average of 3%, with significantly accelerated training speed by a maximum of 1034% and an average of 362%, the convergence rate is also improved by approximately 2 times. Moreover, positive optimization is observed even with low-quality predicted structures. The source code for SES-Adapter is available at https://github.com/tyang816/SES-Adapter.

Yang Tan, Lingrong Zhang, Mingchen Li et al.

Protein scientific discovery is bottlenecked by the manual orchestration of information and algorithms, while general agents are insufficient in complex domain projects. VenusFactory2 provides an autonomous framework that shifts from static tool usage to dynamic workflow synthesis via a self-evolving multi-agent infrastructure to address protein-related demands. It outperforms a set of well-known agents on the VenusAgentEval benchmark, and autonomously organizes the discovery and optimization of proteins from a single natural language prompt.

Yang Tan, Chen Liu, Jingyuan Gao et al.

Natural language processing (NLP) has significantly influenced scientific domains beyond human language, including protein engineering, where pre-trained protein language models (PLMs) have demonstrated remarkable success. However, interdisciplinary adoption remains limited due to challenges in data collection, task benchmarking, and application. This work presents VenusFactory, a versatile engine that integrates biological data retrieval, standardized task benchmarking, and modular fine-tuning of PLMs. VenusFactory supports both computer science and biology communities with choices of both a command-line execution and a Gradio-based no-code interface, integrating $40+$ protein-related datasets and $40+$ popular PLMs. All implementations are open-sourced on https://github.com/tyang816/VenusFactory.

Mingchen Li, Heng Fan, Song Fu et al.

Prompt privacy is crucial, especially when using online large language models (LLMs), due to the sensitive information often contained within prompts. While LLMs can enhance prompt privacy through text rewriting, existing methods primarily focus on document-level rewriting, neglecting the rich, multi-granular representations of text. This limitation restricts LLM utilization to specific tasks, overlooking their generalization and in-context learning capabilities, thus hindering practical application. To address this gap, we introduce DP-GTR, a novel three-stage framework that leverages local differential privacy (DP) and the composition theorem via group text rewriting. DP-GTR is the first framework to integrate both document-level and word-level information while exploiting in-context learning to simultaneously improve privacy and utility, effectively bridging local and global DP mechanisms at the individual data point level. Experiments on CommonSense QA and DocVQA demonstrate that DP-GTR outperforms existing approaches, achieving a superior privacy-utility trade-off. Furthermore, our framework is compatible with existing rewriting techniques, serving as a plug-in to enhance privacy protection. Our code is publicly available at github.com/ResponsibleAILab/DP-GTR.

Zifan Peng, Mingchen Li

Personalized computer-use agents are rapidly moving from expert communities into mainstream use. Unlike conventional chatbots, these systems can install skills, invoke tools, access private resources, and modify local environments on users' behalf. Yet users often do not know what authority they have delegated, what the agent actually did during task execution, or whether the system has been safely removed afterward. We investigate this gap as a combined problem of risk understanding and post-hoc auditability, using OpenClaw as a motivating case. We first build a multi-source corpus of the OpenClaw ecosystem, including incidents, advisories, malicious-skill reports, news coverage, tutorials, and social-media narratives. We then conduct an interview study to examine how users and practitioners understand skills, autonomy, privilege, persistence, and uninstallation. Our findings suggest that participants often recognized these systems as risky in the abstract, but lacked concrete mental models of what skills can do, what resources agents can access, and what changes may remain after execution or removal. Motivated by these findings, we propose AgentTrace, a traceability framework and prototype interface for visualizing agent actions, touched resources, permission history, provenance, and persistent side effects. A scenario-based evaluation suggests that traceability-oriented interfaces can improve understanding of agent behavior, support anomaly detection, and foster more calibrated trust.

Wenrui Gou, Wenhui Ge, Yang Tan et al.

Protein structures are important for understanding their functions and interactions. Currently, many protein structure prediction methods are enriching the structure database. Discriminating the origin of structures is crucial for distinguishing between experimentally resolved and computationally predicted structures, evaluating the reliability of prediction methods, and guiding downstream biological studies. Building on works in structure prediction, We developed a structure-sensitive supervised deep learning model, Crystal vs Predicted Evaluator for Protein Structure (CPE-Pro), to represent and discriminate the origin of protein structures. CPE-Pro learns the structural information of proteins and captures inter-structural differences to achieve accurate traceability on four data classes, and is expected to be extended to more. Simultaneously, we utilized Foldseek to encode protein structures into "structure-sequences" and trained a protein Structural Sequence Language Model, SSLM. Preliminary experiments demonstrated that, compared to large-scale protein language models pre-trained on vast amounts of amino acid sequences, the "structure-sequence" enables the language model to learn more informative protein features, enhancing and optimizing structural representations. We have provided the code, model weights, and all related materials on https://github.com/GouWenrui/CPE-Pro-main.git.

Yang Tan, Mingchen Li, Zijie Huang et al.

Generative large language models (LLMs) have shown great success in various applications, including question-answering (QA) and dialogue systems. However, in specialized domains like traditional Chinese medical QA, these models may perform unsatisfactorily without fine-tuning on domain-specific datasets. To address this, we introduce MedChatZH, a dialogue model designed specifically for traditional Chinese medical QA. Our model is pre-trained on Chinese traditional medical books and fine-tuned with a carefully curated medical instruction dataset. It outperforms several solid baselines on a real-world medical dialogue dataset. We release our model, code, and dataset on https://github.com/tyang816/MedChatZH to facilitate further research in the domain of traditional Chinese medicine and LLMs.

Mingchen Li, Xuechen Zhang, Christos Thrampoulidis et al.

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 train-validation split. All code is available open-source.

Keyu Chen, Di Zhuang, Mingchen Li et al.

Neural Machine Translation (NMT) models have become successful, but their performance remains poor when translating on new domains with a limited number of data. In this paper, we present a novel approach Epi-Curriculum to address low-resource domain adaptation (DA), which contains a new episodic training framework along with denoised curriculum learning. Our episodic training framework enhances the model's robustness to domain shift by episodically exposing the encoder/decoder to an inexperienced decoder/encoder. The denoised curriculum learning filters the noised data and further improves the model's adaptability by gradually guiding the learning process from easy to more difficult tasks. Experiments on English-German and English-Romanian translation show that: (i) Epi-Curriculum improves both model's robustness and adaptability in seen and unseen domains; (ii) Our episodic training framework enhances the encoder and decoder's robustness to domain shift.

Mingchen Li, Halil Kilicoglu, Hua Xu et al.

Large Language Models (LLMs) have swiftly emerged as vital resources for different applications in the biomedical and healthcare domains; however, these models encounter issues such as generating inaccurate information or hallucinations. Retrieval-augmented generation provided a solution for these models to update knowledge and enhance their performance. In contrast to previous retrieval-augmented LMs, which utilize specialized cross-attention mechanisms to help LLM encode retrieved text, BiomedRAG adopts a simpler approach by directly inputting the retrieved chunk-based documents into the LLM. This straightforward design is easily applicable to existing retrieval and language models, effectively bypassing noise information in retrieved documents, particularly in noise-intensive tasks. Moreover, we demonstrate the potential for utilizing the LLM to supervise the retrieval model in the biomedical domain, enabling it to retrieve the document that assists the LM in improving its predictions. Our experiments reveal that with the tuned scorer,\textsc{ BiomedRAG} attains superior performance across 5 biomedical NLP tasks, encompassing information extraction (triple extraction, relation extraction), text classification, link prediction, and question-answering, leveraging over 9 datasets. For instance, in the triple extraction task, \textsc{BiomedRAG} outperforms other triple extraction systems with micro-F1 scores of 81.42 and 88.83 on GIT and ChemProt corpora, respectively.

Zaifu Zhan, Shuang Zhou, Mingchen Li et al.

\textbf{Objective:} We aimed to develop an advanced multi-task large language model (LLM) framework to extract multiple types of information about dietary supplements (DS) from clinical records. \textbf{Methods:} We used four core DS information extraction tasks - namely, named entity recognition (NER: 2,949 clinical sentences), relation extraction (RE: 4,892 sentences), triple extraction (TE: 2,949 sentences), and usage classification (UC: 2,460 sentences) as our multitasks. We introduced a novel Retrieval-Augmented Multi-task Information Extraction (RAMIE) Framework, including: 1) employed instruction fine-tuning techniques with task-specific prompts, 2) trained LLMs for multiple tasks with improved storage efficiency and lower training costs, and 3) incorporated retrieval augmentation generation (RAG) techniques by retrieving similar examples from the training set. We compared RAMIE's performance to LLMs with instruction fine-tuning alone and conducted an ablation study to assess the contributions of multi-task learning and RAG to improved multitasking performance. \textbf{Results:} With the aid of the RAMIE framework, Llama2-13B achieved an F1 score of 87.39 (3.51\% improvement) on the NER task and demonstrated outstanding performance on the RE task with an F1 score of 93.74 (1.15\% improvement). For the TE task, Llama2-7B scored 79.45 (14.26\% improvement), and MedAlpaca-7B achieved the highest F1 score of 93.45 (0.94\% improvement) on the UC task. The ablation study revealed that while MTL increased efficiency with a slight trade-off in performance, RAG significantly boosted overall accuracy. \textbf{Conclusion:} This study presents a novel RAMIE framework that demonstrates substantial improvements in multi-task information extraction for DS-related data from clinical records. Our framework can potentially be applied to other domains.

Xuechen Zhang, Xiangyu Chang, Mingchen Li et al.

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 $\textit{Selective Self-Attention}$ (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.

Mingchen Li, Zaifu Zhan, Han Yang et al.

Large language models (LLM) have demonstrated remarkable capabilities in various biomedical natural language processing (NLP) tasks, leveraging the demonstration within the input context to adapt to new tasks. However, LLM is sensitive to the selection of demonstrations. To address the hallucination issue inherent in LLM, retrieval-augmented LLM (RAL) offers a solution by retrieving pertinent information from an established database. Nonetheless, existing research work lacks rigorous evaluation of the impact of retrieval-augmented large language models on different biomedical NLP tasks. This deficiency makes it challenging to ascertain the capabilities of RAL within the biomedical domain. Moreover, the outputs from RAL are affected by retrieving the unlabeled, counterfactual, or diverse knowledge that is not well studied in the biomedical domain. However, such knowledge is common in the real world. Finally, exploring the self-awareness ability is also crucial for the RAL system. So, in this paper, we systematically investigate the impact of RALs on 5 different biomedical tasks (triple extraction, link prediction, classification, question answering, and natural language inference). We analyze the performance of RALs in four fundamental abilities, including unlabeled robustness, counterfactual robustness, diverse robustness, and negative awareness. To this end, we proposed an evaluation framework to assess the RALs' performance on different biomedical NLP tasks and establish four different testbeds based on the aforementioned fundamental abilities. Then, we evaluate 3 representative LLMs with 3 different retrievers on 5 tasks over 9 datasets.

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.

Zeren Luo, Zifan Peng, Yule Liu et al.

Recent advancements in Large Language Models (LLMs) have significantly enhanced the capabilities of AI-Powered Search Engines (AIPSEs), offering precise and efficient responses by integrating external databases with pre-existing knowledge. However, we observe that these AIPSEs raise risks such as quoting malicious content or citing malicious websites, leading to harmful or unverified information dissemination. In this study, we conduct the first safety risk quantification on seven production AIPSEs by systematically defining the threat model, risk type, and evaluating responses to various query types. With data collected from PhishTank, ThreatBook, and LevelBlue, our findings reveal that AIPSEs frequently generate harmful content that contains malicious URLs even with benign queries (e.g., with benign keywords). We also observe that directly querying a URL will increase the number of main risk-inclusive responses, while querying with natural language will slightly mitigate such risk. Compared to traditional search engines, AIPSEs outperform in both utility and safety. We further perform two case studies on online document spoofing and phishing to show the ease of deceiving AIPSEs in the real-world setting. To mitigate these risks, we develop an agent-based defense with a GPT-4.1-based content refinement tool and a URL detector. Our evaluation shows that our defense can effectively reduce the risk, with only a minor cost of reducing available information by approximately 10.7%. Our research highlights the urgent need for robust safety measures in AIPSEs.

Zifan Peng, Yule Liu, Zhen Sun et al.

Audio Language Models (ALMs) have made significant progress recently. These models integrate the audio modality directly into the model, rather than converting speech into text and inputting text to Large Language Models (LLMs). While jailbreak attacks on LLMs have been extensively studied, the security of ALMs with audio modalities remains largely unexplored. Currently, there is a lack of an adversarial audio dataset and a unified framework specifically designed to evaluate and compare attacks and ALMs. In this paper, we present JALMBench, a comprehensive benchmark to assess the safety of ALMs against jailbreak attacks. JALMBench includes a dataset containing 11,316 text samples and 245,355 audio samples with over 1,000 hours. It supports 12 mainstream ALMs, 4 text-transferred and 4 audio-originated attack methods, and 5 defense methods. Using JALMBench, we provide an in-depth analysis of attack efficiency, topic sensitivity, voice diversity, and architecture. Additionally, we explore mitigation strategies for the attacks at both the prompt level and the response level.

Jiatan Huang, Mingchen Li, Zonghai Yao et al.

Answering complex real-world questions often requires accurate retrieval from textual knowledge graphs (TKGs). The scarcity of annotated data, along with intricate topological structures, makes this task particularly challenging. As the nature of relational path information could enhance the inference ability of Large Language Models (LLMs), efficiently retrieving more complex relational path information from TKGs presents another key challenge. To tackle these challenges, we first develop a Dataset for LLMs Complex Reasoning over Textual Knowledge Graphs (RiTeK) with a broad topological structure coverage.We synthesize realistic user queries that integrate diverse topological structures, relational information, and complex textual descriptions. We conduct rigorous expert evaluation to validate the quality of our synthesized queries. And then, we introduce an enhanced Monte Carlo Tree Search (MCTS) method, Relational MCTS, to automatically extract relational path information from textual graphs for specific queries. Our dataset mainly covers the medical domain as the relation types and entity are complex and publicly available. Experimental results indicate that RiTeK poses significant challenges for current retrieval and LLM systems, while the proposed Relational MCTS method enhances LLM inference ability and achieves state-of-the-art performance on RiTeK.

Mingchen Li, Chen Ling, Rui Zhang et al.

Zero-shot link prediction (ZSLP) on knowledge graphs aims at automatically identifying relations between given entities. Existing methods primarily employ auxiliary information to predict tail entity given head entity and its relation, yet face challenges due to the occasional unavailability of such detailed information and the inherent simplicity of predicting tail entities based on semantic similarities. Even though Large Language Models (LLMs) offer a promising solution to predict unobserved relations between the head and tail entity in a zero-shot manner, their performance is still restricted due to the inability to leverage all the (exponentially many) paths' information between two entities, which are critical in collectively indicating their relation types. To address this, in this work, we introduce a Condensed Transition Graph Framework for Zero-Shot Link Prediction (CTLP), which encodes all the paths' information in linear time complexity to predict unseen relations between entities, attaining both efficiency and information preservation. Specifically, we design a condensed transition graph encoder with theoretical guarantees on its coverage, expressiveness, and efficiency. It is learned by a transition graph contrastive learning strategy. Subsequently, we design a soft instruction tuning to learn and map the all-path embedding to the input of LLMs. Experimental results show that our proposed CTLP method achieves state-of-the-art performance on three standard ZSLP datasets

Mingchen Li, Jiatan Huang, Zonghai Yao et al.

Large language models (LLMs) hold significant promise for healthcare, yet their reliability in high-stakes clinical settings is often compromised by hallucinations and a lack of granular medical context. While Retrieval Augmented Generation (RAG) can mitigate these issues, standard supervised pipelines require computationally intensive searches over massive external knowledge bases, leading to high latency that is impractical for time-sensitive care. To address this, we introduce Keys to Knowledge (K2K), a novel framework that replaces external retrieval with internal, key-based knowledge access. By encoding essential clinical information directly into the model's parameter space, K2K enables rapid retrieval from internal key-value memory without inference-time overhead. We further enhance retrieval quality through activation-guided probe construction and cross-attention reranking. Experimental results demonstrate that K2K achieves state-of-the-art performance across four benchmark healthcare outcome prediction datasets.

Jingzhe Ding, Shengda Long, Changxin Pu et al.

Recent advances in coding agents suggest rapid progress toward autonomous software development, yet existing benchmarks fail to rigorously evaluate the long-horizon capabilities required to build complete software systems. Most prior evaluations focus on localized code generation, scaffolded completion, or short-term repair tasks, leaving open the question of whether agents can sustain coherent reasoning, planning, and execution over the extended horizons demanded by real-world repository construction. To address this gap, we present NL2Repo Bench, a benchmark explicitly designed to evaluate the long-horizon repository generation ability of coding agents. Given only a single natural-language requirements document and an empty workspace, agents must autonomously design the architecture, manage dependencies, implement multi-module logic, and produce a fully installable Python library. Our experiments across state-of-the-art open- and closed-source models reveal that long-horizon repository generation remains largely unsolved: even the strongest agents achieve below 40% average test pass rates and rarely complete an entire repository correctly. Detailed analysis uncovers fundamental long-horizon failure modes, including premature termination, loss of global coherence, fragile cross-file dependencies, and inadequate planning over hundreds of interaction steps. NL2Repo Bench establishes a rigorous, verifiable testbed for measuring sustained agentic competence and highlights long-horizon reasoning as a central bottleneck for the next generation of autonomous coding agents.

Zheng Wei, Mingchen Li, Zeqian Zhang et al.

Recent advancements in multi-agent systems have demonstrated significant potential for enhancing creative task performance, such as long video generation. This study introduces three innovations to improve multi-agent collaboration. First, we propose OmniAgent, a hierarchical, graph-based multi-agent framework for long video generation that leverages a film-production-inspired architecture to enable modular specialization and scalable inter-agent collaboration. Second, inspired by context engineering, we propose hypergraph nodes that enable temporary group discussions among agents lacking sufficient context, reducing individual memory requirements while ensuring adequate contextual information. Third, we transition from directed acyclic graphs (DAGs) to directed cyclic graphs with limited retries, allowing agents to reflect and refine outputs iteratively, thereby improving earlier stages through feedback from subsequent nodes. These contributions lay the groundwork for developing more robust multi-agent systems in creative tasks.

Chenghan Li, Mingchen Li, Yipu Liao et al.

Research on long-term time series prediction has primarily relied on Transformer and MLP models, while the potential of convolutional networks in this domain remains underexplored. To address this, we propose a novel multi-scale time series reshape module that effectively captures cross-period patch interactions and variable dependencies. Building on this, we develop MS-DFTVNet, the multi-scale 3D deformable convolutional framework tailored for long-term forecasting. Moreover, to handle the inherently uneven distribution of temporal features, we introduce a context-aware dynamic deformable convolution mechanism, which further enhances the model's ability to capture complex temporal patterns. Extensive experiments demonstrate that MS-DFTVNet not only significantly outperforms strong baselines but also achieves an average improvement of about 7.5% across six public datasets, setting new state-of-the-art results.

Chen Liu, Mingchen Li, Yang Tan et al.

A pivotal area of research in antibody engineering is to find effective modifications that enhance antibody-antigen binding affinity. Traditional wet-lab experiments assess mutants in a costly and time-consuming manner. Emerging deep learning solutions offer an alternative by modeling antibody structures to predict binding affinity changes. However, they heavily depend on high-quality complex structures, which are frequently unavailable in practice. Therefore, we propose ProtAttBA, a deep learning model that predicts binding affinity changes based solely on the sequence information of antibody-antigen complexes. ProtAttBA employs a pre-training phase to learn protein sequence patterns, following a supervised training phase using labeled antibody-antigen complex data to train a cross-attention-based regressor for predicting binding affinity changes. We evaluated ProtAttBA on three open benchmarks under different conditions. Compared to both sequence- and structure-based prediction methods, our approach achieves competitive performance, demonstrating notable robustness, especially with uncertain complex structures. Notably, our method possesses interpretability from the attention mechanism. We show that the learned attention scores can identify critical residues with impacts on binding affinity. This work introduces a rapid and cost-effective computational tool for antibody engineering, with the potential to accelerate the development of novel therapeutic antibodies.

Mingchen Li, Di Zhuang, Keyu Chen et al.

Link prediction in graph data uses various algorithms and Graph Nerual Network (GNN) models to predict potential relationships between graph nodes. These techniques have found widespread use in numerous real-world applications, including recommendation systems, community/social networks, and biological structures. However, recent research has highlighted the vulnerability of GNN models to adversarial attacks, such as poisoning and evasion attacks. Addressing the vulnerability of GNN models is crucial to ensure stable and robust performance in GNN applications. Although many works have focused on enhancing the robustness of node classification on GNN models, the robustness of link prediction has received less attention. To bridge this gap, this article introduces an unweighted graph poisoning attack that leverages meta-learning with weighted scheme strategies to degrade the link prediction performance of GNNs. We conducted comprehensive experiments on diverse datasets across multiple link prediction applications to evaluate the proposed method and its parameters, comparing it with existing approaches under similar conditions. Our results demonstrate that our approach significantly reduces link prediction performance and consistently outperforms other state-of-the-art baselines.

Xiang Liu, Mingchen Li, Xia Li et al.

Modern applications require lightweight neural network models. Most existing neural network pruning methods focus on removing unimportant filters; however, these may result in the loss of statistical information after pruning due to failing to consider the class-wise information. In this paper, we employ the structured lasso from the perspective of utilizing precise class-wise information for model pruning with the help of Information Bottleneck theory, which guides us to ensure the retention of statistical information before and after pruning. With these techniques, we propose two novel adaptive network pruning schemes in parallel: sparse graph-structured lasso pruning with Information Bottleneck (sGLP-IB) and sparse tree-guided lasso pruning with Information Bottleneck (sTLP-IB). The key component is that we prune the model filters utilizing sGLP-IB and sTLP-IB with more precise structured class-wise relatedness. Compared to multiple state-of-the-art methods, our approaches achieve the best performance across three datasets and six model structures on extensive experiments. For example, with the VGG16 model based on the CIFAR-10 dataset, we can reduce the parameters by 85%, decrease the FLOPs by 61%, and maintain an accuracy of 94.10% (0.14% better than the original). For large-scale ImageNet, we can reduce the parameters by 55% while keeping the accuracy at 76.12% (only drop 0.03%) using the ResNet architecture. In summary, we succeed in reducing the model size and computational resource usage while maintaining the effectiveness of accuracy.

Mingchen Li, Jiatan Huang, Jeremy Yeung et al.

Medical Large Language Models (LLMs) have demonstrated impressive performance on a wide variety of medical NLP tasks; however, there still lacks a LLM specifically designed for phenotyping identification and diagnosis in cancer domain. Moreover, these LLMs typically have several billions of parameters, making them computationally expensive for healthcare systems. Thus, in this study, we propose CancerLLM, a model with 7 billion parameters and a Mistral-style architecture, pre-trained on nearly 2.7M clinical notes and over 515K pathology reports covering 17 cancer types, followed by fine-tuning on two cancer-relevant tasks, including cancer phenotypes extraction and cancer diagnosis generation. Our evaluation demonstrated that the CancerLLM achieves state-of-the-art results with F1 score of 91.78% on phenotyping extraction and 86.81% on disganois generation. It outperformed existing LLMs, with an average F1 score improvement of 9.23%. Additionally, the CancerLLM demonstrated its efficiency on time and GPU usage, and robustness comparing with other LLMs. We demonstrated that CancerLLM can potentially provide an effective and robust solution to advance clinical research and practice in cancer domain

Xuechen Zhang, Mingchen Li, Jiasi Chen et al.

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.

Mingchen Li, Yang Ye, Jeremy Yeung et al.

Contrastive learning has become a popular solution for few-shot Name Entity Recognization (NER). The conventional configuration strives to reduce the distance between tokens with the same labels and increase the distance between tokens with different labels. The effect of this setup may, however, in the medical domain, there are a lot of entities annotated as OUTSIDE (O), and they are undesirably pushed apart to other entities that are not labeled as OUTSIDE (O) by the current contrastive learning method end up with a noisy prototype for the semantic representation of the label, though there are many OUTSIDE (O) labeled entities are relevant to the labeled entities. To address this challenge, we propose a novel method named Weighted Prototypical Contrastive Learning for Medical Few Shot Named Entity Recognization (W-PROCER). Our approach primarily revolves around constructing the prototype-based contractive loss and weighting network. These components play a crucial role in assisting the model in differentiating the negative samples from OUTSIDE (O) tokens and enhancing the discrimination ability of contrastive learning. Experimental results show that our proposed W-PROCER framework significantly outperforms the strong baselines on the three medical benchmark datasets.

Di Zhuang, Mingchen Li, J. Morris Chang

Deep learning often requires a large amount of data. In real-world applications, e.g., healthcare applications, the data collected by a single organization (e.g., hospital) is often limited, and the majority of massive and diverse data is often segregated across multiple organizations. As such, it motivates the researchers to conduct distributed deep learning, where the data user would like to build DL models using the data segregated across multiple different data owners. However, this could lead to severe privacy concerns due to the sensitive nature of the data, thus the data owners would be hesitant and reluctant to participate. We propose LDP-DL, a privacy-preserving distributed deep learning framework via local differential privacy and knowledge distillation, where each data owner learns a teacher model using its own (local) private dataset, and the data user learns a student model to mimic the output of the ensemble of the teacher models. In the experimental evaluation, a comprehensive comparison has been made among our proposed approach (i.e., LDP-DL), DP-SGD, PATE and DP-FL, using three popular deep learning benchmark datasets (i.e., CIFAR10, MNIST and FashionMNIST). The experimental results show that LDP-DL consistently outperforms the other competitors in terms of privacy budget and model accuracy.

Samet Oymak, Mingchen Li, Mahdi Soltanolkotabi

Neural Architecture Search (NAS) is a popular method for automatically designing optimized architectures for high-performance deep learning. In this approach, it is common to use bilevel optimization where one optimizes the model weights over the training data (inner problem) and various hyperparameters such as the configuration of the architecture over the validation data (outer problem). This paper explores the statistical aspects of such problems with train-validation splits. In practice, the inner 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 the role of train-validation split. To this aim this work establishes the following results. (1) We show that refined properties of the validation loss such as risk and hyper-gradients are indicative of those of the true test loss. This reveals that the outer problem helps select the most generalizable model and prevent overfitting with a near-minimal validation sample size. This is established for continuous search spaces which are relevant for differentiable schemes. Extensions to transfer learning are developed in terms of the mismatch between training & validation distributions. (2) We establish generalization bounds for NAS problems with an emphasis on an activation search problem. When optimized with gradient-descent, we show that the train-validation procedure returns the best (model, architecture) pair even if all architectures can perfectly fit the training data to achieve zero error. (3) Finally, we highlight connections between NAS, multiple kernel learning, and low-rank matrix learning. The latter leads to novel insights where the solution of the outer problem can be accurately learned via efficient spectral methods to achieve near-minimal risk.