Yi Nian

Haiyue Zhang, Yi Nian, Yue Zhao

What should a developer inspect before deploying an LLM agent: the model, the tool code, the deployment configuration, or all three? In practice, many security failures in agent systems arise not from model weights alone, but from the surrounding software stack: tool functions that pass untrusted inputs to dangerous operations, exposed credentials in deployment artifacts, and over-privileged Model Context Protocol (MCP) configurations. We present Agent Audit, a security analysis system for LLM agent applications. Agent Audit analyzes Python agent code and deployment artifacts through an agent-aware pipeline that combines dataflow analysis, credential detection, structured configuration parsing, and privilege-risk checks. The system reports findings in terminal, JSON, and SARIF formats, enabling direct integration with local development workflows and CI/CD pipelines. On a benchmark of 22 samples with 42 annotated vulnerabilities, Agent Audit detects 40 vulnerabilities with 6 false positives, substantially improving recall over common SAST baselines while maintaining sub-second scan times. Agent Audit is open source and installable via pip, making security auditing accessible for agent systems. In the live demonstration, attendees scan vulnerable agent repositories and observe how Agent Audit identifies security risks in tool functions, prompts, and more. Findings are linked to source locations and configuration paths, and can be exported into VS Code and GitHub Code Scanning for interactive inspection.

Yi Nian, Aojie Yuan, Haiyue Zhang et al.

LLM agents call tools, query databases, delegate tasks, and trigger external side effects. Once an agent system can act in the world, the question is no longer only whether harmful actions can be prevented--it is whether those actions remain answerable after deployment. We distinguish accountability (the ability to determine compliance and assign responsibility), auditability (the system property that makes accountability possible), and auditing (the process of reconstructing behavior from trustworthy evidence). Our claim is direct: no agent system can be accountable without auditability. To make this operational, we define five dimensions of agent auditability, i.e., action recoverability, lifecycle coverage, policy checkability, responsibility attribution, and evidence integrity, and identify three mechanism classes (detect, enforce, recover) whose temporal information-and-intervention constraints explain why, in practice, no single approach suffices. We support the position with layered evidence rather than a single benchmark: lower-bound ecosystem measurements suggest that even basic security prerequisites for auditability are widely unmet (617 security findings across six prominent open-source projects); runtime feasibility results show that pre-execution mediation with tamper-evident records adds only 8.3 ms median overhead; and controlled recovery experiments show that responsibility-relevant information can be partially recovered even when conventional logs are missing. We propose an Auditability Card for agent systems and identify six open research problems organized by mechanism class.

Yi Nian, Yurui Chang, Wei Jin et al.

Graph neural networks (GNNs) have emerged as a powerful model to capture critical graph patterns. Instead of treating them as black boxes in an end-to-end fashion, attempts are arising to explain the model behavior. Existing works mainly focus on local interpretation to reveal the discriminative pattern for each individual instance, which however cannot directly reflect the high-level model behavior across instances. To gain global insights, we aim to answer an important question that is not yet well studied: how to provide a global interpretation for the graph learning procedure? We formulate this problem as globally interpretable graph learning, which targets on distilling high-level and human-intelligible patterns that dominate the learning procedure, such that training on this pattern can recover a similar model. As a start, we propose a novel model fidelity metric, tailored for evaluating the fidelity of the resulting model trained on interpretations. Our preliminary analysis shows that interpretative patterns generated by existing global methods fail to recover the model training procedure. Thus, we further propose our solution, Graph Distribution Matching (GDM), which synthesizes interpretive graphs by matching the distribution of the original and interpretive graphs in the GNN's feature space as its training proceeds, thus capturing the most informative patterns the model learns during training. Extensive experiments on graph classification datasets demonstrate multiple advantages of the proposed method, including high model fidelity, predictive accuracy and time efficiency, as well as the ability to reveal class-relevant structure.

Fang Li, Yi Nian, Zenan Sun et al.

Graph representation learning (GRL) has emerged as a pivotal field that has contributed significantly to breakthroughs in various fields, including biomedicine. The objective of this survey is to review the latest advancements in GRL methods and their applications in the biomedical field. We also highlight key challenges currently faced by GRL and outline potential directions for future research.

Yi Nian, Haosen Cao, Shenzhe Zhu et al.

When a multi-agent system produces an incorrect or harmful answer, who is accountable if execution logs and agent identifiers are unavailable? Multi-agent language systems increasingly rely on structured interactions such as delegation and iterative refinement, yet the final output often obscures the underlying interaction topology and agent contributions. We introduce IET (Implicit Execution Tracing), a metadata-independent framework that enables token-level attribution directly from generated text and a simple mechanism for interaction topology reconstruction. During generation, agent-specific keyed signals are embedded into the token distribution, transforming the text into a self-describing execution trace detectable only with a secret key. At detection time, a transition-aware scoring method identifies agent handover points and reconstructs the interaction graph. Experiments show that IET recovers agent segments and coordination structure with high accuracy while preserving generation quality, enabling privacy-preserving auditing for multi-agent language systems.

Xinyue Hu, Zenan Sun, Yi Nian et al.

Background: Alzheimer's disease and related dementias (ADRD) ranks as the sixth leading cause of death in the US, underlining the importance of accurate ADRD risk prediction. While recent advancement in ADRD risk prediction have primarily relied on imaging analysis, yet not all patients undergo medical imaging before an ADRD diagnosis. Merging machine learning with claims data can reveal additional risk factors and uncover interconnections among diverse medical codes. Objective: Our goal is to utilize Graph Neural Networks (GNNs) with claims data for ADRD risk prediction. Addressing the lack of human-interpretable reasons behind these predictions, we introduce an innovative method to evaluate relationship importance and its influence on ADRD risk prediction, ensuring comprehensive interpretation. Methods: We employed Variationally Regularized Encoder-decoder Graph Neural Network (VGNN) for estimating ADRD likelihood. We created three scenarios to assess the model's efficiency, using Random Forest and Light Gradient Boost Machine as baselines. We further used our relation importance method to clarify the key relationships for ADRD risk prediction. Results: VGNN surpassed other baseline models by 10% in the area under the receiver operating characteristic. The integration of the GNN model and relation importance interpretation could potentially play an essential role in providing valuable insight into factors that may contribute to or delay ADRD progression. Conclusions: Employing a GNN approach with claims data enhances ADRD risk prediction and provides insights into the impact of interconnected medical code relationships. This methodology not only enables ADRD risk modeling but also shows potential for other image analysis predictions using claims data.

Tiankai Yang, Yi Nian, Xinyuan Li et al.

Aligning large language models with human preferences must balance two competing goals: responding helpfully to legitimate requests and reliably refusing harmful ones. Most preference-based safety alignment methods collapse safety into a single scalar that is applied uniformly to every preference pair. The result is a model that looks safe on average but stays relatively unsafe on a minority of harm categories. We cast safety alignment as a per-category constrained optimization problem and derive Cat-DPO, a direct-preference-optimization algorithm with a separate adaptive safety margin for each harm category. The margin tightens when the model still produces unsafe responses on a category and relaxes once the model catches up, so the training signal tracks each category's current difficulty rather than averaging under one global rate. Across two LLM backbones and six preference-learning baselines, Cat-DPO improves aggregate helpfulness and harmlessness and compresses per-category safety variance and the best-to-worst gap, offering a drop-in per-category refinement of direct preference safety alignment.

Yuangang Li, Jiaqi Li, Zhuo Xiao et al.

Anomaly detection (AD) is an important machine learning task with applications in fraud detection, content moderation, and user behavior analysis. However, AD is relatively understudied in a natural language processing (NLP) context, limiting its effectiveness in detecting harmful content, phishing attempts, and spam reviews. We introduce NLP-ADBench, the most comprehensive NLP anomaly detection (NLP-AD) benchmark to date, which includes eight curated datasets and 19 state-of-the-art algorithms. These span 3 end-to-end methods and 16 two-step approaches that adapt classical, non-AD methods to language embeddings from BERT and OpenAI. Our empirical results show that no single model dominates across all datasets, indicating a need for automated model selection. Moreover, two-step methods with transformer-based embeddings consistently outperform specialized end-to-end approaches, with OpenAI embeddings outperforming those of BERT. We release NLP-ADBench at https://github.com/USC-FORTIS/NLP-ADBench, providing a unified framework for NLP-AD and supporting future investigations.

Shawn Li, Peilin Cai, Yuxiao Zhou et al.

Out-of-Distribution (OOD) detection is critical for ensuring the reliability of machine learning models in safety-critical applications such as autonomous driving and medical diagnosis. While deploying personalized OOD detection directly on edge devices is desirable, it remains challenging due to large model sizes and the computational infeasibility of on-device training. Federated learning partially addresses this but still requires gradient computation and backpropagation, exceeding the capabilities of many edge devices. To overcome these challenges, we propose SecDOOD, a secure cloud-device collaboration framework for efficient on-device OOD detection without requiring device-side backpropagation. SecDOOD utilizes cloud resources for model training while ensuring user data privacy by retaining sensitive information on-device. Central to SecDOOD is a HyperNetwork-based personalized parameter generation module, which adapts cloud-trained models to device-specific distributions by dynamically generating local weight adjustments, effectively combining central and local information without local fine-tuning. Additionally, our dynamic feature sampling and encryption strategy selectively encrypts only the most informative feature channels, largely reducing encryption overhead without compromising detection performance. Extensive experiments across multiple datasets and OOD scenarios demonstrate that SecDOOD achieves performance comparable to fully fine-tuned models, enabling secure, efficient, and personalized OOD detection on resource-limited edge devices. To enhance accessibility and reproducibility, our code is publicly available at https://github.com/Dystopians/SecDOOD.

Henry Peng Zou, Siffi Singh, Yi Nian et al.

Generalized Category Discovery (GCD) is a practical and challenging open-world task that aims to recognize both known and novel categories in unlabeled data using limited labeled data from known categories. Due to the lack of supervision, previous GCD methods face significant challenges, such as difficulty in rectifying errors for confusing instances, and inability to effectively uncover and leverage the semantic meanings of discovered clusters. Therefore, additional annotations are usually required for real-world applicability. However, human annotation is extremely costly and inefficient. To address these issues, we propose GLEAN, a unified framework for generalized category discovery that actively learns from diverse and quality-enhanced LLM feedback. Our approach leverages three different types of LLM feedback to: (1) improve instance-level contrastive features, (2) generate category descriptions, and (3) align uncertain instances with LLM-selected category descriptions. Extensive experiments demonstrate the superior performance of \MethodName over state-of-the-art models across diverse datasets, metrics, and supervision settings. Our code is available at https://github.com/amazon-science/Glean.

Henry Peng Zou, Chunyu Miao, Wei-Chieh Huang et al.

As LLM agents transition from short, static problem solving to executing complex, long-horizon tasks in dynamic environments, the ability to handle user interruptions, such as adding requirement or revising goals, during mid-task execution is becoming a core requirement for realistic deployment. However, existing benchmarks largely assume uninterrupted agent behavior or study interruptions only in short, unconstrained language tasks. In this paper, we present the first systematic study of interruptible agents in long-horizon, environmentally grounded web navigation tasks, where actions induce persistent state changes. We formalize three realistic interruption types, including addition, revision, and retraction, and introduce InterruptBench, a benchmark derived from WebArena-Lite that synthesizes high-quality interruption scenarios under strict semantic constraints. Using a unified interruption simulation framework, we evaluate six strong LLM backbones across single- and multi-turn interruption settings, analyzing both their effectiveness in adapting to updated intents and their efficiency in recovering from mid-task changes. Our results show that handling user interruptions effectively and efficiently during long-horizon agentic tasks remains challenging for powerful large-scale LLMs. Code and dataset are available at https://github.com/HenryPengZou/InterruptBench.

Tiankai Yang, Jiate Li, Yi Nian et al.

LLM-based agents increasingly operate across repeated sessions, maintaining task states to ensure continuity. In many deployments, a single agent serves multiple users within a team or organization, reusing a shared knowledge layer across user identities. This shared persistence expands the failure surface: information that is locally valid for one user can silently degrade another user's outcome when the agent reapplies it without regard for scope. We refer to this failure mode as unintentional cross-user contamination (UCC). Unlike adversarial memory poisoning, UCC requires no attacker; it arises from benign interactions whose scope-bound artifacts persist and are later misapplied. We formalize UCC through a controlled evaluation protocol, introduce a taxonomy of three contamination types, and evaluate the problem in two shared-state mechanisms. Under raw shared state, benign interactions alone produce contamination rates of 57--71%. A write-time sanitization is effective when shared state is conversational, but leaves substantial residual risk when shared state includes executable artifacts, with contamination often manifesting as silent wrong answers. These results indicate that shared-state agents need artifact-level defenses beyond text-level sanitization to prevent silent cross-user failures.

Yuangang Li, Yiqing Shen, Yi Nian et al.

Large language models (LLMs) exhibit logically inconsistent hallucinations that appear coherent yet violate reasoning principles, with recent research suggesting an inverse relationship between causal reasoning capabilities and such hallucinations. However, existing reasoning approaches in LLMs, such as Chain-of-Thought (CoT) and its graph-based variants, operate at the linguistic token level rather than modeling the underlying causal relationships between variables, lacking the ability to represent conditional independencies or satisfy causal identification assumptions. To bridge this gap, we introduce causal-DAG construction and reasoning (CDCR-SFT), a supervised fine-tuning framework that trains LLMs to explicitly construct variable-level directed acyclic graph (DAG) and then perform reasoning over it. Moreover, we present a dataset comprising 25,368 samples (CausalDR), where each sample includes an input question, explicit causal DAG, graph-based reasoning trace, and validated answer. Experiments on four LLMs across eight tasks show that CDCR-SFT improves the causal reasoning capability with the state-of-the-art 95.33% accuracy on CLADDER (surpassing human performance of 94.8% for the first time) and reduces the hallucination on HaluEval with 10% improvements. It demonstrates that explicit causal structure modeling in LLMs can effectively mitigate logical inconsistencies in LLM outputs. Code is available at https://github.com/MrLYG/CDCR-SFT.

Aojie Yuan, Zhiyuan Julian Su, Haiyue Zhang et al.

Chain-of-thought (CoT) prompting assumes that generated reasoning reflects a model's internal computation. We show this assumption is wrong in a specific, measurable way: models internally detect their own reasoning errors but outwardly express confidence in them. A linear probe on hidden states predicts trace correctness with 0.95 AUROC -- from the very first reasoning step (0.79) -- while verbalized confidence for wrong traces is 4.55/5, nearly identical to correct ones (4.87/5). A text-surface classifier achieves only 0.59 on the same data, confirming a 0.20-point gap invisible in the generated text. This hidden error awareness holds across three model families (Qwen, Llama, Phi), 1.5B-72B parameters, and RL-trained reasoning models (DeepSeek-R1, 0.852 AUROC). The natural question is whether this signal can fix the errors it detects. It cannot. Four interventions -- activation steering, probe-guided best-of-N, self-correction, and activation patching -- all fail; patching destroys output coherence entirely. The signal is diagnostic, not causal: a readout of computation quality, not a lever to redirect it. This delineates a boundary for mechanistic interpretability: error representations during reasoning are fundamentally different from the factual knowledge representations that prior work has successfully edited.

Panfeng Li, Qikai Yang, Xieming Geng et al.

This study explores innovative methods for improving Visual Question Answering (VQA) using Generative Adversarial Networks (GANs), autoencoders, and attention mechanisms. Leveraging a balanced VQA dataset, we investigate three distinct strategies. Firstly, GAN-based approaches aim to generate answer embeddings conditioned on image and question inputs, showing potential but struggling with more complex tasks. Secondly, autoencoder-based techniques focus on learning optimal embeddings for questions and images, achieving comparable results with GAN due to better ability on complex questions. Lastly, attention mechanisms, incorporating Multimodal Compact Bilinear pooling (MCB), address language priors and attention modeling, albeit with a complexity-performance trade-off. This study underscores the challenges and opportunities in VQA and suggests avenues for future research, including alternative GAN formulations and attentional mechanisms.

Qikai Yang, Panfeng Li, Xinhe Xu et al.

In the ever-evolving landscape of social network advertising, the volume and accuracy of data play a critical role in the performance of predictive models. However, the development of robust predictive algorithms is often hampered by the limited size and potential bias present in real-world datasets. This study presents and explores a generative augmentation framework of social network advertising data. Our framework explores three generative models for data augmentation - Generative Adversarial Networks (GANs), Variational Autoencoders (VAEs), and Gaussian Mixture Models (GMMs) - to enrich data availability and diversity in the context of social network advertising analytics effectiveness. By performing synthetic extensions of the feature space, we find that through data augmentation, the performance of various classifiers has been quantitatively improved. Furthermore, we compare the relative performance gains brought by each data augmentation technique, providing insights for practitioners to select appropriate techniques to enhance model performance. This paper contributes to the literature by showing that synthetic data augmentation alleviates the limitations imposed by small or imbalanced datasets in the field of social network advertising. At the same time, this article also provides a comparative perspective on the practicality of different data augmentation methods, thereby guiding practitioners to choose appropriate techniques to enhance model performance.

Tiankai Yang, Yi Nian, Shawn Li et al.

Anomaly detection (AD) is an important machine learning task with many real-world uses, including fraud detection, medical diagnosis, and industrial monitoring. Within natural language processing (NLP), AD helps detect issues like spam, misinformation, and unusual user activity. Although large language models (LLMs) have had a strong impact on tasks such as text generation and summarization, their potential in AD has not been studied enough. This paper introduces AD-LLM, the first benchmark that evaluates how LLMs can help with NLP anomaly detection. We examine three key tasks: (i) zero-shot detection, using LLMs' pre-trained knowledge to perform AD without tasks-specific training; (ii) data augmentation, generating synthetic data and category descriptions to improve AD models; and (iii) model selection, using LLMs to suggest unsupervised AD models. Through experiments with different datasets, we find that LLMs can work well in zero-shot AD, that carefully designed augmentation methods are useful, and that explaining model selection for specific datasets remains challenging. Based on these results, we outline six future research directions on LLMs for AD.

Yuehan Qin, Shawn Li, Yi Nian et al.

Large language models (LLMs) have shown substantial capacity for generating fluent, contextually appropriate responses. However, they can produce hallucinated outputs, especially when a user query includes one or more false premises-claims that contradict established facts. Such premises can mislead LLMs into offering fabricated or misleading details. Existing approaches include pretraining, fine-tuning, and inference-time techniques that often rely on access to logits or address hallucinations after they occur. These methods tend to be computationally expensive, require extensive training data, or lack proactive mechanisms to prevent hallucination before generation, limiting their efficiency in real-time applications. We propose a retrieval-based framework that identifies and addresses false premises before generation. Our method first transforms a user's query into a logical representation, then applies retrieval-augmented generation (RAG) to assess the validity of each premise using factual sources. Finally, we incorporate the verification results into the LLM's prompt to maintain factual consistency in the final output. Experiments show that this approach effectively reduces hallucinations, improves factual accuracy, and does not require access to model logits or large-scale fine-tuning.

Mahnaz Koupaee, Jake W. Vincent, Saab Mansour et al.

Faithfulness evaluators based on large language models (LLMs) are often fooled by the fluency of the text and struggle with identifying errors in the summaries. We propose an approach to summary faithfulness evaluation in which multiple LLM-based agents are assigned initial stances (regardless of what their belief might be) and forced to come up with a reason to justify the imposed belief, thus engaging in a multi-round debate to reach an agreement. The uniformly distributed initial assignments result in a greater diversity of stances leading to more meaningful debates and ultimately more errors identified. Furthermore, by analyzing the recent faithfulness evaluation datasets, we observe that naturally, it is not always the case for a summary to be either faithful to the source document or not. We therefore introduce a new dimension, ambiguity, and a detailed taxonomy to identify such special cases. Experiments demonstrate our approach can help identify ambiguities, and have even a stronger performance on non-ambiguous summaries.

Zhendong Liu, Yi Nian, Henry Peng Zou et al.

How can models effectively detect out-of-distribution (OOD) samples in complex, multi-label settings without extensive retraining? Existing OOD detection methods struggle to capture the intricate semantic relationships and label co-occurrences inherent in multi-label settings, often requiring large amounts of training data and failing to generalize to unseen label combinations. While large language models have revolutionized zero-shot OOD detection, they primarily focus on single-label scenarios, leaving a critical gap in handling real-world tasks where samples can be associated with multiple interdependent labels. To address these challenges, we introduce COOD, a novel zero-shot multi-label OOD detection framework. COOD leverages pre-trained vision-language models, enhancing them with a concept-based label expansion strategy and a new scoring function. By enriching the semantic space with both positive and negative concepts for each label, our approach models complex label dependencies, precisely differentiating OOD samples without the need for additional training. Extensive experiments demonstrate that our method significantly outperforms existing approaches, achieving approximately 95% average AUROC on both VOC and COCO datasets, while maintaining robust performance across varying numbers of labels and different types of OOD samples.

Yinhong Liu, Jianfeng He, Hang Su et al.

Multimodal Dialogue Summarization (MDS) is a critical task with wide-ranging applications. To support the development of effective MDS models, robust automatic evaluation methods are essential for reducing both cost and human effort. However, such methods require a strong meta-evaluation benchmark grounded in human annotations. In this work, we introduce MDSEval, the first meta-evaluation benchmark for MDS, consisting image-sharing dialogues, corresponding summaries, and human judgments across eight well-defined quality aspects. To ensure data quality and richfulness, we propose a novel filtering framework leveraging Mutually Exclusive Key Information (MEKI) across modalities. Our work is the first to identify and formalize key evaluation dimensions specific to MDS. We benchmark state-of-the-art modal evaluation methods, revealing their limitations in distinguishing summaries from advanced MLLMs and their susceptibility to various bias.

Shenzhe Zhu, Jiao Sun, Yi Nian et al. · mit

AI agents are increasingly used in consumer-facing applications to assist with tasks such as product search, negotiation, and transaction execution. In this paper, we explore a future scenario where both consumers and merchants authorize AI agents to fully automate negotiations and transactions. We aim to answer two key questions: (1) Do different LLM agents vary in their ability to secure favorable deals for users? (2) What risks arise from fully automating deal-making with AI agents in consumer markets? To address these questions, we develop an experimental framework that evaluates the performance of various LLM agents in real-world negotiation and transaction settings. Our findings reveal that AI-mediated deal-making is an inherently imbalanced game -- different agents achieve significantly different outcomes for their users. Moreover, behavioral anomalies in LLMs can result in financial losses for both consumers and merchants, such as overspending or accepting unreasonable deals. These results underscore that while automation can improve efficiency, it also introduces substantial risks. Users should exercise caution when delegating business decisions to AI agents.

Yi Nian, Shenzhe Zhu, Yuehan Qin et al.

Multimodal large language models (MLLMs) excel in vision-language tasks but also pose significant risks of generating harmful content, particularly through jailbreak attacks. Jailbreak attacks refer to intentional manipulations that bypass safety mechanisms in models, leading to the generation of inappropriate or unsafe content. Detecting such attacks is critical to ensuring the responsible deployment of MLLMs. Existing jailbreak detection methods face three primary challenges: (1) Many rely on model hidden states or gradients, limiting their applicability to white-box models, where the internal workings of the model are accessible; (2) They involve high computational overhead from uncertainty-based analysis, which limits real-time detection, and (3) They require fully labeled harmful datasets, which are often scarce in real-world settings. To address these issues, we introduce a test-time adaptive framework called JAILDAM. Our method leverages a memory-based approach guided by policy-driven unsafe knowledge representations, eliminating the need for explicit exposure to harmful data. By dynamically updating unsafe knowledge during test-time, our framework improves generalization to unseen jailbreak strategies while maintaining efficiency. Experiments on multiple VLM jailbreak benchmarks demonstrate that JAILDAM delivers state-of-the-art performance in harmful content detection, improving both accuracy and speed.

Yi Nian, Xinyue Hu, Rui Zhang et al.

To date, there are no effective treatments for most neurodegenerative diseases. Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leveraged in many biomedical applications including drug repurposing. Our objective is to construct a knowledge graph from literature to study relations between Alzheimer's disease (AD) and chemicals, drugs and dietary supplements in order to identify opportunities to prevent or delay neurodegenerative progression. We collected biomedical annotations and extracted their relations using SemRep via SemMedDB. We used both a BERT-based classifier and rule-based methods during data preprocessing to exclude noise while preserving most AD-related semantic triples. The 1,672,110 filtered triples were used to train with knowledge graph completion algorithms (i.e., TransE, DistMult, and ComplEx) to predict candidates that might be helpful for AD treatment or prevention. Among three knowledge graph completion models, TransE outperformed the other two (MR = 13.45, Hits@1 = 0.306). We leveraged the time-slicing technique to further evaluate the prediction results. We found supporting evidence for most highly ranked candidates predicted by our model which indicates that our approach can inform reliable new knowledge. This paper shows that our graph mining model can predict reliable new relationships between AD and other entities (i.e., dietary supplements, chemicals, and drugs). The knowledge graph constructed can facilitate data-driven knowledge discoveries and the generation of novel hypotheses.

Yi Nian, Jingcheng Du, Larry Bu et al.

To date, there are no effective treatments for most neurodegenerative diseases. However, certain foods may be associated with these diseases and bring an opportunity to prevent or delay neurodegenerative progression. Our objective is to construct a knowledge graph for neurodegenerative diseases using literature mining to study their relations with diet. We collected biomedical annotations (Disease, Chemical, Gene, Species, SNP&Mutation) in the abstracts from 4,300 publications relevant to both neurodegenerative diseases and diet using PubTator, an NIH-supported tool that can extract biomedical concepts from literature. A knowledge graph was created from these annotations. Graph embeddings were then trained with the node2vec algorithm to support potential concept clustering and similar concept identification. We found several food-related species and chemicals that might come from diet and have an impact on neurodegenerative diseases.

Iddo Drori, Lu Liu, Yi Nian et al.

As a human choosing a supervised learning algorithm, it is natural to begin by reading a text description of the dataset and documentation for the algorithms you might use. We demonstrate that the same idea improves the performance of automated machine learning methods. We use language embeddings from modern NLP to improve state-of-the-art AutoML systems by augmenting their recommendations with vector embeddings of datasets and of algorithms. We use these embeddings in a neural architecture to learn the distance between best-performing pipelines. The resulting (meta-)AutoML framework improves on the performance of existing AutoML frameworks. Our zero-shot AutoML system using dataset metadata embeddings provides good solutions instantaneously, running in under one second of computation. Performance is competitive with AutoML systems OBOE, AutoSklearn, AlphaD3M, and TPOT when each framework is allocated a minute of computation. We make our data, models, and code publicly available.