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Large language models (LLMs) have demonstrated remarkable capabilities in various scientific domains, from natural language processing to complex problem-solving tasks. Their ability to understand and generate human-like text has opened up new possibilities for advancing scientific research, enabling tasks such as data analysis, literature review, and even experimental design. One of the most promising applications of LLMs in this context is hypothesis generation, where they can identify novel research directions by analyzing existing knowledge. However, despite their potential, LLMs are prone to generating ``hallucinations'', outputs that are plausible-sounding but factually incorrect. Such a problem presents significant challenges in scientific fields that demand rigorous accuracy and verifiability, potentially leading to erroneous or misleading conclusions. To overcome these challenges, we propose KG-CoI (Knowledge Grounded Chain of Ideas), a novel system that enhances LLM hypothesis generation by integrating external, structured knowledge from knowledge graphs (KGs). KG-CoI guides LLMs through a structured reasoning process, organizing their output as a chain of ideas (CoI), and includes a KG-supported module for the detection of hallucinations. With experiments on our newly constructed hypothesis generation dataset, we demonstrate that KG-CoI not only improves the accuracy of LLM-generated hypotheses but also reduces the hallucination in their reasoning chains, highlighting its effectiveness in advancing real-world scientific research.

Large Language Models (LLMs) have transformed how people interact with artificial intelligence (AI) systems, achieving state-of-the-art results in various tasks, including scientific discovery and hypothesis generation. However, the lack of a comprehensive and systematic evaluation framework for generating research ideas using LLMs poses a significant obstacle to understanding and assessing their generative capabilities in scientific discovery. To address this gap, we propose IdeaBench, a benchmark system that includes a comprehensive dataset and an evaluation framework for standardizing the assessment of research idea generation using LLMs. Our dataset comprises titles and abstracts from a diverse range of influential papers, along with their referenced works. To emulate the human process of generating research ideas, we profile LLMs as domain-specific researchers and ground them in the same context considered by human researchers. This maximizes the utilization of the LLMs' parametric knowledge to dynamically generate new research ideas. We also introduce an evaluation framework for assessing the quality of generated research ideas. Our evaluation framework is a two-stage process: first, using GPT-4o to rank ideas based on user-specified quality indicators such as novelty and feasibility, enabling scalable personalization; and second, calculating relative ranking based "Insight Score" to quantify the chosen quality indicator. The proposed benchmark system will be a valuable asset for the community to measure and compare different LLMs, ultimately advancing the automation of the scientific discovery process.

Large language models (LLMs) represent a transformative class of AI tools capable of revolutionizing various aspects of healthcare by generating human-like responses across diverse contexts and adapting to novel tasks following human instructions. Their potential application spans a broad range of medical tasks, such as clinical documentation, matching patients to clinical trials, and answering medical questions. In this primer paper, we propose an actionable guideline to help healthcare professionals more efficiently utilize LLMs in their work, along with a set of best practices. This approach consists of several main phases, including formulating the task, choosing LLMs, prompt engineering, fine-tuning, and deployment. We start with the discussion of critical considerations in identifying healthcare tasks that align with the core capabilities of LLMs and selecting models based on the selected task and data, performance requirements, and model interface. We then review the strategies, such as prompt engineering and fine-tuning, to adapt standard LLMs to specialized medical tasks. Deployment considerations, including regulatory compliance, ethical guidelines, and continuous monitoring for fairness and bias, are also discussed. By providing a structured step-by-step methodology, this tutorial aims to equip healthcare professionals with the tools necessary to effectively integrate LLMs into clinical practice, ensuring that these powerful technologies are applied in a safe, reliable, and impactful manner.

The rising need for explainable deep neural network architectures has utilized semantic concepts as explainable units. Several approaches utilizing disentangled representation learning estimate the generative factors and utilize them as concepts for explaining DNNs. However, even though the generative factors for a dataset remain fixed, concepts are not fixed entities and vary based on downstream tasks. In this paper, we propose a disentanglement mechanism utilizing a variational autoencoder (VAE) for learning mutually independent generative factors for a given dataset and subsequently learning task-specific concepts using a structural causal model (SCM). Our method assumes generative factors and concepts to form a bipartite graph, with directed causal edges from generative factors to concepts. Experiments are conducted on datasets with known generative factors: D-sprites and Shapes3D. On specific downstream tasks, our proposed method successfully learns task-specific concepts which are explained well by the causal edges from the generative factors. Lastly, separate from current causal concept discovery methods, our methodology is generalizable to an arbitrary number of concepts and flexible to any downstream tasks.

Generalized additive models (GAMs) have long been a powerful white-box tool for the intelligible analysis of tabular data, revealing the influence of each feature on the model predictions. Despite the success of neural networks (NNs) in various domains, their application as NN-based GAMs in tabular data analysis remains suboptimal compared to tree-based ones, and the opacity of encoders in NN-GAMs also prevents users from understanding how networks learn the functions. In this work, we propose a new deep tabular learning method, termed Prototypical Neural Additive Model (ProtoNAM), which introduces prototypes into neural networks in the framework of GAMs. With the introduced prototype-based feature activation, ProtoNAM can flexibly model the irregular mapping from tabular features to the outputs while maintaining the explainability of the final prediction. We also propose a gradient-boosting inspired hierarchical shape function modeling method, facilitating the discovery of complex feature patterns and bringing transparency into the learning process of each network layer. Our empirical evaluations demonstrate that ProtoNAM outperforms all existing NN-based GAMs, while providing additional insights into the shape function learned for each feature. The source code of ProtoNAM is available at \url{https://github.com/Teddy-XiongGZ/ProtoNAM}.

Few-shot image classifiers are designed to recognize and classify new data with minimal supervision and limited data but often show reliance on spurious correlations between classes and spurious attributes, known as spurious bias. Spurious correlations commonly hold in certain samples and few-shot classifiers can suffer from spurious bias induced from them. There is an absence of an automatic benchmarking system to assess the robustness of few-shot classifiers against spurious bias. In this paper, we propose a systematic and rigorous benchmark framework, termed FewSTAB, to fairly demonstrate and quantify varied degrees of robustness of few-shot classifiers to spurious bias. FewSTAB creates few-shot evaluation tasks with biased attributes so that using them for predictions can demonstrate poor performance. To construct these tasks, we propose attribute-based sample selection strategies based on a pre-trained vision-language model, eliminating the need for manual dataset curation. This allows FewSTAB to automatically benchmark spurious bias using any existing test data. FewSTAB offers evaluation results in a new dimension along with a new design guideline for building robust classifiers. Moreover, it can benchmark spurious bias in varied degrees and enable designs for varied degrees of robustness. Its effectiveness is demonstrated through experiments on ten few-shot learning methods across three datasets. We hope our framework can inspire new designs of robust few-shot classifiers. Our code is available at https://github.com/gtzheng/FewSTAB., Comment: Accepted to ECCV 2024

The emergent abilities of large language models (LLMs) have demonstrated great potential in solving medical questions. They can possess considerable medical knowledge, but may still hallucinate and are inflexible in the knowledge updates. While Retrieval-Augmented Generation (RAG) has been proposed to enhance the medical question-answering capabilities of LLMs with external knowledge bases, it may still fail in complex cases where multiple rounds of information-seeking are required. To address such an issue, we propose iterative RAG for medicine (i-MedRAG), where LLMs can iteratively ask follow-up queries based on previous information-seeking attempts. In each iteration of i-MedRAG, the follow-up queries will be answered by a conventional RAG system and they will be further used to guide the query generation in the next iteration. Our experiments show the improved performance of various LLMs brought by i-MedRAG compared with conventional RAG on complex questions from clinical vignettes in the United States Medical Licensing Examination (USMLE), as well as various knowledge tests in the Massive Multitask Language Understanding (MMLU) dataset. Notably, our zero-shot i-MedRAG outperforms all existing prompt engineering and fine-tuning methods on GPT-3.5, achieving an accuracy of 69.68% on the MedQA dataset. In addition, we characterize the scaling properties of i-MedRAG with different iterations of follow-up queries and different numbers of queries per iteration. Our case studies show that i-MedRAG can flexibly ask follow-up queries to form reasoning chains, providing an in-depth analysis of medical questions. To the best of our knowledge, this is the first-of-its-kind study on incorporating follow-up queries into medical RAG. The implementation of i-MedRAG is available at https://github.com/Teddy-XiongGZ/MedRAG., Comment: Accepted to PSB 2025

Interpretability of Deep Neural Networks using concept-based models offers a promising way to explain model behavior through human-understandable concepts. A parallel line of research focuses on disentangling the data distribution into its underlying generative factors, in turn explaining the data generation process. While both directions have received extensive attention, little work has been done on explaining concepts in terms of generative factors to unify mathematically disentangled representations and human-understandable concepts as an explanation for downstream tasks. In this paper, we propose a novel method CoLiDR - which utilizes a disentangled representation learning setup for learning mutually independent generative factors and subsequently learns to aggregate the said representations into human-understandable concepts using a novel aggregation/decomposition module. Experiments are conducted on datasets with both known and unknown latent generative factors. Our method successfully aggregates disentangled generative factors into concepts while maintaining parity with state-of-the-art concept-based approaches. Quantitative and visual analysis of the learned aggregation procedure demonstrates the advantages of our work compared to commonly used concept-based models over four challenging datasets. Lastly, our work is generalizable to an arbitrary number of concepts and generative factors - making it flexible enough to be suitable for various types of data., Comment: KDD 2024

Spurious bias, a tendency to use spurious correlations between non-essential input attributes and target variables for predictions, has revealed a severe robustness pitfall in deep learning models trained on single modality data. Multimodal Large Language Models (MLLMs), which integrate both vision and language models, have demonstrated strong capability in joint vision-language understanding. However, whether spurious biases are prevalent in MLLMs remains under-explored. We mitigate this gap by analyzing the spurious biases in a multimodal setting, uncovering the specific test data patterns that can manifest this problem when biases in the vision model cascade into the alignment between visual and text tokens in MLLMs. To better understand this problem, we introduce MM-SpuBench, a comprehensive visual question-answering (VQA) benchmark designed to evaluate MLLMs' reliance on nine distinct categories of spurious correlations from five open-source image datasets. The VQA dataset is built from human-understandable concept information (attributes). Leveraging this benchmark, we conduct a thorough evaluation of current state-of-the-art MLLMs. Our findings illuminate the persistence of the reliance on spurious correlations from these models and underscore the urge for new methodologies to mitigate spurious biases. To support the MLLM robustness research, we release our VQA benchmark at https://huggingface.co/datasets/mmbench/MM-SpuBench.

As opposed to evaluating computation and logic-based reasoning, current benchmarks for evaluating large language models (LLMs) in medicine are primarily focused on question-answering involving domain knowledge and descriptive reasoning. While such qualitative capabilities are vital to medical diagnosis, in real-world scenarios, doctors frequently use clinical calculators that follow quantitative equations and rule-based reasoning paradigms for evidence-based decision support. To this end, we propose MedCalc-Bench, a first-of-its-kind dataset focused on evaluating the medical calculation capability of LLMs. MedCalc-Bench contains an evaluation set of over 1000 manually reviewed instances from 55 different medical calculation tasks. Each instance in MedCalc-Bench consists of a patient note, a question requesting to compute a specific medical value, a ground truth answer, and a step-by-step explanation showing how the answer is obtained. While our evaluation results show the potential of LLMs in this area, none of them are effective enough for clinical settings. Common issues include extracting the incorrect entities, not using the correct equation or rules for a calculation task, or incorrectly performing the arithmetic for the computation. We hope our study highlights the quantitative knowledge and reasoning gaps in LLMs within medical settings, encouraging future improvements of LLMs for various clinical calculation tasks., Comment: Github link: https://github.com/ncbi-nlp/MedCalc-Bench HuggingFace link: https://huggingface.co/datasets/nsk7153/MedCalc-Bench

Spurious correlations are brittle associations between certain attributes of inputs and target variables, such as the correlation between an image background and an object class. Deep image classifiers often leverage them for predictions, leading to poor generalization on the data where the correlations do not hold. Mitigating the impact of spurious correlations is crucial towards robust model generalization, but it often requires annotations of the spurious correlations in data -- a strong assumption in practice. In this paper, we propose a novel learning framework based on meta-learning, termed SPUME -- SPUriousness-aware MEta-learning, to train an image classifier to be robust to spurious correlations. We design the framework to iteratively detect and mitigate the spurious correlations that the classifier excessively relies on for predictions. To achieve this, we first propose to utilize a pre-trained vision-language model to extract text-format attributes from images. These attributes enable us to curate data with various class-attribute correlations, and we formulate a novel metric to measure the degree of these correlations' spuriousness. Then, to mitigate the reliance on spurious correlations, we propose a meta-learning strategy in which the support (training) sets and query (test) sets in tasks are curated with different spurious correlations that have high degrees of spuriousness. By meta-training the classifier on these spuriousness-aware meta-learning tasks, our classifier can learn to be invariant to the spurious correlations. We demonstrate that our method is robust to spurious correlations without knowing them a priori and achieves the best on five benchmark datasets with different robustness measures., Comment: Accepted to KDD 2024

Adapting large language models (LLMs) to unseen tasks with in-context training samples without fine-tuning remains an important research problem. To learn a robust LLM that adapts well to unseen tasks, multiple meta-training approaches have been proposed such as MetaICL and MetaICT, which involve meta-training pre-trained LLMs on a wide variety of diverse tasks. These meta-training approaches essentially perform in-context multi-task fine-tuning and evaluate on a disjointed test set of tasks. Even though they achieve impressive performance, their goal is never to compute a truly general set of parameters. In this paper, we propose MAML-en-LLM, a novel method for meta-training LLMs, which can learn truly generalizable parameters that not only perform well on disjointed tasks but also adapts to unseen tasks. We see an average increase of 2% on unseen domains in the performance while a massive 4% improvement on adaptation performance. Furthermore, we demonstrate that MAML-en-LLM outperforms baselines in settings with limited amount of training data on both seen and unseen domains by an average of 2%. Finally, we discuss the effects of type of tasks, optimizers and task complexity, an avenue barely explored in meta-training literature. Exhaustive experiments across 7 task settings along with two data settings demonstrate that models trained with MAML-en-LLM outperform SOTA meta-training approaches., Comment: KDD 2024, 11 pages(9 main, 2 ref, 1 App) Openreview https://openreview.net/forum?id=JwecLNhWDy&referrer=%5BAuthor%20Console%5D(%2Fgroup%3Fid%3DKDD.org%2F2024%2FResearch_Track%2FAuthors%23your-submissions)

Deep neural classifiers tend to rely on spurious correlations between spurious attributes of inputs and targets to make predictions, which could jeopardize their generalization capability. Training classifiers robust to spurious correlations typically relies on annotations of spurious correlations in data, which are often expensive to get. In this paper, we tackle an annotation-free setting and propose a self-guided spurious correlation mitigation framework. Our framework automatically constructs fine-grained training labels tailored for a classifier obtained with empirical risk minimization to improve its robustness against spurious correlations. The fine-grained training labels are formulated with different prediction behaviors of the classifier identified in a novel spuriousness embedding space. We construct the space with automatically detected conceptual attributes and a novel spuriousness metric which measures how likely a class-attribute correlation is exploited for predictions. We demonstrate that training the classifier to distinguish different prediction behaviors reduces its reliance on spurious correlations without knowing them a priori and outperforms prior methods on five real-world datasets., Comment: Accepted to IJCAI 2024

With the wide proliferation of Deep Neural Networks in high-stake applications, there is a growing demand for explainability behind their decision-making process. Concept learning models attempt to learn high-level 'concepts' - abstract entities that align with human understanding, and thus provide interpretability to DNN architectures. However, in this paper, we demonstrate that present SOTA concept learning approaches suffer from two major problems - lack of concept fidelity wherein the models fail to learn consistent concepts among similar classes and limited concept interoperability wherein the models fail to generalize learned concepts to new domains for the same task. Keeping these in mind, we propose a novel self-explaining architecture for concept learning across domains which - i) incorporates a new concept saliency network for representative concept selection, ii) utilizes contrastive learning to capture representative domain invariant concepts, and iii) uses a novel prototype-based concept grounding regularization to improve concept alignment across domains. We demonstrate the efficacy of our proposed approach over current SOTA concept learning approaches on four widely used real-world datasets. Empirical results show that our method improves both concept fidelity measured through concept overlap and concept interoperability measured through domain adaptation performance., Comment: IJCAI 2024. 16 pages (7 main content, 2 references, 7 Appendix) Code available at https://github.com/sanchit97/secl

While large language models (LLMs) have achieved state-of-the-art performance on a wide range of medical question answering (QA) tasks, they still face challenges with hallucinations and outdated knowledge. Retrieval-augmented generation (RAG) is a promising solution and has been widely adopted. However, a RAG system can involve multiple flexible components, and there is a lack of best practices regarding the optimal RAG setting for various medical purposes. To systematically evaluate such systems, we propose the Medical Information Retrieval-Augmented Generation Evaluation (MIRAGE), a first-of-its-kind benchmark including 7,663 questions from five medical QA datasets. Using MIRAGE, we conducted large-scale experiments with over 1.8 trillion prompt tokens on 41 combinations of different corpora, retrievers, and backbone LLMs through the MedRAG toolkit introduced in this work. Overall, MedRAG improves the accuracy of six different LLMs by up to 18% over chain-of-thought prompting, elevating the performance of GPT-3.5 and Mixtral to GPT-4-level. Our results show that the combination of various medical corpora and retrievers achieves the best performance. In addition, we discovered a log-linear scaling property and the "lost-in-the-middle" effects in medical RAG. We believe our comprehensive evaluations can serve as practical guidelines for implementing RAG systems for medicine., Comment: Homepage: https://teddy-xionggz.github.io/benchmark-medical-rag/

Machine learning systems are known to be sensitive to spurious correlations between non-essential features of the inputs (e.g., background, texture, and secondary objects) and the corresponding labels. These features and their correlations with the labels are known as "spurious" because they tend to change with shifts in real-world data distributions, which can negatively impact the model's generalization and robustness. In this paper, we provide a review of this issue, along with a taxonomy of current state-of-the-art methods for addressing spurious correlations in machine learning models. Additionally, we summarize existing datasets, benchmarks, and metrics to aid future research. The paper concludes with a discussion of the recent advancements and future challenges in this field, aiming to provide valuable insights for researchers in the related domains., Comment: Version 2; Github Link: https://github.com/wenqian-ye/Awesome-Spurious-Correlations

Single domain generalization (SDG) aims to train a robust model against unknown target domain shifts using data from a single source domain. Data augmentation has been proven an effective approach to SDG. However, the utility of standard augmentations, such as translate, or invert, has not been fully exploited in SDG; practically, these augmentations are used as a part of a data preprocessing procedure. Although it is intuitive to use many such augmentations to boost the robustness of a model to out-of-distribution domain shifts, we lack a principled approach to harvest the benefit brought from multiple these augmentations. Here, we conceptualize standard data augmentations with learnable parameters as semantics transformations that can manipulate certain semantics of a sample, such as the geometry or color of an image. Then, we propose Adversarial learning with Semantics Transformations (AdvST) that augments the source domain data with semantics transformations and learns a robust model with the augmented data. We theoretically show that AdvST essentially optimizes a distributionally robust optimization objective defined on a set of semantics distributions induced by the parameters of semantics transformations. We demonstrate that AdvST can produce samples that expand the coverage on target domain data. Compared with the state-of-the-art methods, AdvST, despite being a simple method, is surprisingly competitive and achieves the best average SDG performance on the Digits, PACS, and DomainNet datasets. Our code is available at https://github.com/gtzheng/AdvST., Comment: Accepted to AAAI 2024

Federated Averaging (FedAvg) is known to experience convergence issues when encountering significant clients system heterogeneity and data heterogeneity. Server momentum has been proposed as an effective mitigation. However, existing server momentum works are restrictive in the momentum formulation, do not properly schedule hyperparameters and focus only on system homogeneous settings, which leaves the role of server momentum still an under-explored problem. In this paper, we propose a general framework for server momentum, that (a) covers a large class of momentum schemes that are unexplored in federated learning (FL), (b) enables a popular stagewise hyperparameter scheduler, (c) allows heterogeneous and asynchronous local computing. We provide rigorous convergence analysis for the proposed framework. To our best knowledge, this is the first work that thoroughly analyzes the performances of server momentum with a hyperparameter scheduler and system heterogeneity. Extensive experiments validate the effectiveness of our proposed framework., Comment: Accepted at AAAI 2024

Visually-rich document entity retrieval (VDER), which extracts key information (e.g. date, address) from document images like invoices and receipts, has become an important topic in industrial NLP applications. The emergence of new document types at a constant pace, each with its unique entity types, presents a unique challenge: many documents contain unseen entity types that occur only a couple of times. Addressing this challenge requires models to have the ability of learning entities in a few-shot manner. However, prior works for Few-shot VDER mainly address the problem at the document level with a predefined global entity space, which doesn't account for the entity-level few-shot scenario: target entity types are locally personalized by each task and entity occurrences vary significantly among documents. To address this unexplored scenario, this paper studies a novel entity-level few-shot VDER task. The challenges lie in the uniqueness of the label space for each task and the increased complexity of out-of-distribution (OOD) contents. To tackle this novel task, we present a task-aware meta-learning based framework, with a central focus on achieving effective task personalization that distinguishes between in-task and out-of-task distribution. Specifically, we adopt a hierarchical decoder (HC) and employ contrastive learning (ContrastProtoNet) to achieve this goal. Furthermore, we introduce a new dataset, FewVEX, to boost future research in the field of entity-level few-shot VDER. Experimental results demonstrate our approaches significantly improve the robustness of popular meta-learning baselines., Comment: Paper published at Findings of the Association for Computational Linguistics: EMNLP, 2023

The minimax problems arise throughout machine learning applications, ranging from adversarial training and policy evaluation in reinforcement learning to AUROC maximization. To address the large-scale data challenges across multiple clients with communication-efficient distributed training, federated learning (FL) is gaining popularity. Many optimization algorithms for minimax problems have been developed in the centralized setting (\emph{i.e.} single-machine). Nonetheless, the algorithm for minimax problems under FL is still underexplored. In this paper, we study a class of federated nonconvex minimax optimization problems. We propose FL algorithms (FedSGDA+ and FedSGDA-M) and reduce existing complexity results for the most common minimax problems. For nonconvex-concave problems, we propose FedSGDA+ and reduce the communication complexity to $O(\varepsilon^{-6})$. Under nonconvex-strongly-concave and nonconvex-PL minimax settings, we prove that FedSGDA-M has the best-known sample complexity of $O(\kappa^{3} N^{-1}\varepsilon^{-3})$ and the best-known communication complexity of $O(\kappa^{2}\varepsilon^{-2})$. FedSGDA-M is the first algorithm to match the best sample complexity $O(\varepsilon^{-3})$ achieved by the single-machine method under the nonconvex-strongly-concave setting. Extensive experimental results on fair classification and AUROC maximization show the efficiency of our algorithms.

Conditional stochastic optimization has found applications in a wide range of machine learning tasks, such as invariant learning, AUPRC maximization, and meta-learning. As the demand for training models with large-scale distributed data grows in these applications, there is an increasing need for communication-efficient distributed optimization algorithms, such as federated learning algorithms. This paper considers the nonconvex conditional stochastic optimization in federated learning and proposes the first federated conditional stochastic optimization algorithm (FCSG) with a conditional stochastic gradient estimator and a momentum-based algorithm (FCSG-M). To match the lower bound complexity in the single-machine setting, we design an accelerated algorithm (Acc-FCSG-M) via the variance reduction to achieve the best sample and communication complexity. Compared with the existing optimization analysis for MAML in FL, federated conditional stochastic optimization considers the sample of tasks. Extensive experimental results on various tasks validate the efficiency of these algorithms.

Fairness-aware machine learning has attracted a surge of attention in many domains, such as online advertising, personalized recommendation, and social media analysis in web applications. Fairness-aware machine learning aims to eliminate biases of learning models against certain subgroups described by certain protected (sensitive) attributes such as race, gender, and age. Among many existing fairness notions, counterfactual fairness is a popular notion defined from a causal perspective. It measures the fairness of a predictor by comparing the prediction of each individual in the original world and that in the counterfactual worlds in which the value of the sensitive attribute is modified. A prerequisite for existing methods to achieve counterfactual fairness is the prior human knowledge of the causal model for the data. However, in real-world scenarios, the underlying causal model is often unknown, and acquiring such human knowledge could be very difficult. In these scenarios, it is risky to directly trust the causal models obtained from information sources with unknown reliability and even causal discovery methods, as incorrect causal models can consequently bring biases to the predictor and lead to unfair predictions. In this work, we address the problem of counterfactually fair prediction from observational data without given causal models by proposing a novel framework CLAIRE. Specifically, under certain general assumptions, CLAIRE effectively mitigates the biases from the sensitive attribute with a representation learning framework based on counterfactual data augmentation and an invariant penalty. Experiments conducted on both synthetic and real-world datasets validate the superiority of CLAIRE in both counterfactual fairness and prediction performance.

Deep neural networks are susceptible to human imperceptible adversarial perturbations. One of the strongest defense mechanisms is \emph{Adversarial Training} (AT). In this paper, we aim to address two predominant problems in AT. First, there is still little consensus on how to set hyperparameters with a performance guarantee for AT research, and customized settings impede a fair comparison between different model designs in AT research. Second, the robustly trained neural networks struggle to generalize well and suffer from tremendous overfitting. This paper focuses on the primary AT framework - Projected Gradient Descent Adversarial Training (PGD-AT). We approximate the dynamic of PGD-AT by a continuous-time Stochastic Differential Equation (SDE), and show that the diffusion term of this SDE determines the robust generalization. An immediate implication of this theoretical finding is that robust generalization is positively correlated with the ratio between learning rate and batch size. We further propose a novel approach, \emph{Diffusion Enhanced Adversarial Training} (DEAT), to manipulate the diffusion term to improve robust generalization with virtually no extra computational burden. We theoretically show that DEAT obtains a tighter generalization bound than PGD-AT. Our empirical investigation is extensive and firmly attests that DEAT universally outperforms PGD-AT by a significant margin., Comment: Accepted at KDD 2023

Rising usage of deep neural networks to perform decision making in critical applications like medical diagnosis and financial analysis have raised concerns regarding their reliability and trustworthiness. As automated systems become more mainstream, it is important their decisions be transparent, reliable and understandable by humans for better trust and confidence. To this effect, concept-based models such as Concept Bottleneck Models (CBMs) and Self-Explaining Neural Networks (SENN) have been proposed which constrain the latent space of a model to represent high level concepts easily understood by domain experts in the field. Although concept-based models promise a good approach to both increasing explainability and reliability, it is yet to be shown if they demonstrate robustness and output consistent concepts under systematic perturbations to their inputs. To better understand performance of concept-based models on curated malicious samples, in this paper, we aim to study their robustness to adversarial perturbations, which are also known as the imperceptible changes to the input data that are crafted by an attacker to fool a well-learned concept-based model. Specifically, we first propose and analyze different malicious attacks to evaluate the security vulnerability of concept based models. Subsequently, we propose a potential general adversarial training-based defense mechanism to increase robustness of these systems to the proposed malicious attacks. Extensive experiments on one synthetic and two real-world datasets demonstrate the effectiveness of the proposed attacks and the defense approach., Comment: Accepted at AAAI 2023. Extended Version

Counterfactual explanations promote explainability in machine learning models by answering the question "how should an input instance be perturbed to obtain a desired predicted label?". The comparison of this instance before and after perturbation can enhance human interpretation. Most existing studies on counterfactual explanations are limited in tabular data or image data. In this work, we study the problem of counterfactual explanation generation on graphs. A few studies have explored counterfactual explanations on graphs, but many challenges of this problem are still not well-addressed: 1) optimizing in the discrete and disorganized space of graphs; 2) generalizing on unseen graphs; and 3) maintaining the causality in the generated counterfactuals without prior knowledge of the causal model. To tackle these challenges, we propose a novel framework CLEAR which aims to generate counterfactual explanations on graphs for graph-level prediction models. Specifically, CLEAR leverages a graph variational autoencoder based mechanism to facilitate its optimization and generalization, and promotes causality by leveraging an auxiliary variable to better identify the underlying causal model. Extensive experiments on both synthetic and real-world graphs validate the superiority of CLEAR over the state-of-the-art methods in different aspects., Comment: 18 pages, 9 figures

Fair machine learning aims to mitigate the biases of model predictions against certain subpopulations regarding sensitive attributes such as race and gender. Among the many existing fairness notions, counterfactual fairness measures the model fairness from a causal perspective by comparing the predictions of each individual from the original data and the counterfactuals. In counterfactuals, the sensitive attribute values of this individual had been modified. Recently, a few works extend counterfactual fairness to graph data, but most of them neglect the following facts that can lead to biases: 1) the sensitive attributes of each node's neighbors may causally affect the prediction w.r.t. this node; 2) the sensitive attributes may causally affect other features and the graph structure. To tackle these issues, in this paper, we propose a novel fairness notion - graph counterfactual fairness, which considers the biases led by the above facts. To learn node representations towards graph counterfactual fairness, we propose a novel framework based on counterfactual data augmentation. In this framework, we generate counterfactuals corresponding to perturbations on each node's and their neighbors' sensitive attributes. Then we enforce fairness by minimizing the discrepancy between the representations learned from the original graph and the counterfactuals for each node. Experiments on both synthetic and real-world graphs show that our framework outperforms the state-of-the-art baselines in graph counterfactual fairness, and also achieves comparable prediction performance., Comment: 9 pages, 4 figures

Dynamic quadrupedal locomotion over rough terrains reveals remarkable progress over the last few decades. Small-scale quadruped robots are adequately flexible and adaptable to traverse uneven terrains along sagittal direction, such as slopes and stairs. To accomplish autonomous locomotion navigation in complex environments, spinning is a fundamental yet indispensable functionality for legged robots. However, spinning behaviors of quadruped robots on uneven terrain often exhibit position drifts. Motivated by this problem, this study presents an algorithmic method to enable accurate spinning motions over uneven terrain and constrain the spinning radius of the Center of Mass (CoM) to be bounded within a small range to minimize the drift risks. A modified spherical foot kinematics representation is proposed to improve the foot kinematic model and rolling dynamics of the quadruped during locomotion. A CoM planner is proposed to generate stable spinning motion based on projected stability margins. Accurate motion tracking is accomplished with Linear Quadratic Regulator (LQR) to bound the position drift during the spinning movement. Experiments are conducted on a small-scale quadruped robot and the effectiveness of the proposed method is verified on versatile terrains including flat ground, stairs and slopes.

Existing gradient-based meta-learning approaches to few-shot learning assume that all tasks have the same input feature space. However, in the real world scenarios, there are many cases that the input structures of tasks can be different, that is, different tasks may vary in the number of input modalities or data types. Existing meta-learners cannot handle the heterogeneous task distribution (HTD) as there is not only global meta-knowledge shared across tasks but also type-specific knowledge that distinguishes each type of tasks. To deal with task heterogeneity and promote fast within-task adaptions for each type of tasks, in this paper, we propose HetMAML, a task-heterogeneous model-agnostic meta-learning framework, which can capture both the type-specific and globally shared knowledge and can achieve the balance between knowledge customization and generalization. Specifically, we design a multi-channel backbone module that encodes the input of each type of tasks into the same length sequence of modality-specific embeddings. Then, we propose a task-aware iterative feature aggregation network which can automatically take into account the context of task-specific input structures and adaptively project the heterogeneous input spaces to the same lower-dimensional embedding space of concepts. Our experiments on six task-heterogeneous datasets demonstrate that HetMAML successfully leverages type-specific and globally shared meta-parameters for heterogeneous tasks and achieves fast within-task adaptions for each type of tasks., Comment: Accepted by CIKM 2021

Causal inference is a critical research topic across many domains, such as statistics, computer science, education, public policy and economics, for decades. Nowadays, estimating causal effect from observational data has become an appealing research direction owing to the large amount of available data and low budget requirement, compared with randomized controlled trials. Embraced with the rapidly developed machine learning area, various causal effect estimation methods for observational data have sprung up. In this survey, we provide a comprehensive review of causal inference methods under the potential outcome framework, one of the well known causal inference framework. The methods are divided into two categories depending on whether they require all three assumptions of the potential outcome framework or not. For each category, both the traditional statistical methods and the recent machine learning enhanced methods are discussed and compared. The plausible applications of these methods are also presented, including the applications in advertising, recommendation, medicine and so on. Moreover, the commonly used benchmark datasets as well as the open-source codes are also summarized, which facilitate researchers and practitioners to explore, evaluate and apply the causal inference methods.

While deep learning has achieved great success in many fields, one common criticism about deep learning is its lack of interpretability. In most cases, the hidden units in a deep neural network do not have a clear semantic meaning or correspond to any physical entities. However, model interpretability and explainability are crucial in many biomedical applications. To address this challenge, we developed the Factor Graph Neural Network model that is interpretable and predictable by combining probabilistic graphical models with deep learning. We directly encode biological knowledge such as Gene Ontology as a factor graph into the model architecture, making the model transparent and interpretable. Furthermore, we devised an attention mechanism that can capture multi-scale hierarchical interactions among biological entities such as genes and Gene Ontology terms. With parameter sharing mechanism, the unrolled Factor Graph Neural Network model can be trained with stochastic depth and generalize well. We applied our model to two cancer genomic datasets to predict target clinical variables and achieved better results than other traditional machine learning and deep learning models. Our model can also be used for gene set enrichment analysis and selecting Gene Ontology terms that are important to target clinical variables., Comment: 12 pages, 4 figures

Multi-omic data provides multiple views of the same patients. Integrative analysis of multi-omic data is crucial to elucidate the molecular underpinning of disease etiology. However, multi-omic data has the "big p, small N" problem (the number of features is large, but the number of samples is small), it is challenging to train a complicated machine learning model from the multi-omic data alone and make it generalize well. Here we propose a framework termed Multi-view Factorization AutoEncoder with network constraints to integrate multi-omic data with domain knowledge (biological interactions networks). Our framework employs deep representation learning to learn feature embeddings and patient embeddings simultaneously, enabling us to integrate feature interaction network and patient view similarity network constraints into the training objective. The whole framework is end-to-end differentiable. We applied our approach to the TCGA Pan-cancer dataset and achieved satisfactory results to predict disease progression-free interval (PFI) and patient overall survival (OS) events. Code will be made publicly available., Comment: 12 pages, 2 figures

Defining subtypes of complex diseases such as cancer and stratifying patient groups with the same disease but different subtypes for targeted treatments is important for personalized and precision medicine. Approaches that incorporate multi-omic data are more advantageous to those using only one data type for patient clustering and disease subtype discovery. However, it is challenging to integrate multi-omic data as they are heterogeneous and noisy. In this paper, we present Affinity Network Fusion (ANF) to integrate multi-omic data for patient clustering. ANF first constructs patient affinity networks for each omic data type, and then calculates a fused network for spectral clustering. We applied ANF to a processed harmonized cancer dataset downloaded from GDC data portal consisting of 2193 patients, and generated promising results on clustering patients into correct disease types. Moreover, we developed a semi-supervised model combining ANF and neural network for few-shot learning. In several cases, the model can achieve greater than 90% acccuracy on test set with training less than 1% of the data. This demonstrates the power of ANF in learning a good representation of patients, and shows the great potential of semi-supervised learning in cancer patient clustering., Comment: Accepted to Methods (https://www.journals.elsevier.com/methods). arXiv admin note: text overlap with arXiv:1708.07136

While deep learning has achieved great success in computer vision and many other fields, currently it does not work very well on patient genomic data with the "big p, small N" problem (i.e., a relatively small number of samples with high-dimensional features). In order to make deep learning work with a small amount of training data, we have to design new models that facilitate few-shot learning. Here we present the Affinity Network Model (AffinityNet), a data efficient deep learning model that can learn from a limited number of training examples and generalize well. The backbone of the AffinityNet model consists of stacked k-Nearest-Neighbor (kNN) attention pooling layers. The kNN attention pooling layer is a generalization of the Graph Attention Model (GAM), and can be applied to not only graphs but also any set of objects regardless of whether a graph is given or not. As a new deep learning module, kNN attention pooling layers can be plugged into any neural network model just like convolutional layers. As a simple special case of kNN attention pooling layer, feature attention layer can directly select important features that are useful for classification tasks. Experiments on both synthetic data and cancer genomic data from TCGA projects show that our AffinityNet model has better generalization power than conventional neural network models with little training data. The code is freely available at https://github.com/BeautyOfWeb/AffinityNet ., Comment: 14 pages, 6 figures

Clustering cancer patients into subgroups and identifying cancer subtypes is an important task in cancer genomics. Clustering based on comprehensive multi-omic molecular profiling can often achieve better results than those using a single data type, since each omic data type (representing one view of patients) may contain complementary information. However, it is challenging to integrate heterogeneous omic data types directly. Based on one popular method -- Similarity Network Fusion (SNF), we presented Affinity Network Fusion (ANF) in this paper, an "upgrade" of SNF with several advantages. Similar to SNF, ANF treats each omic data type as one view of patients and learns a fused affinity (transition) matrix for clustering. We applied ANF to a carefully processed harmonized cancer dataset downloaded from GDC data portals consisting of 2193 patients, and generated promising results on clustering patients into correct disease types. Our experimental results also demonstrated the power of feature selection and transformation combined with using ANF in patient clustering. Moreover, eigengap analysis suggests that the learned affinity matrices of four cancer types using our proposed framework may have successfully captured patient group structure and can be used for discovering unknown cancer subtypes., Comment: submitted to BIBM2017 (https://muii.missouri.edu/bibm2017/)

Knowledge of the association information between the attributes in a data set provides insight into the underlying structure of the data and explains the relationships (independence, synergy, redundancy) between the attributes and class (if present). Complex models learnt computationally from the data are more interpretable to a human analyst when such interdependencies are known. In this paper, we focus on mining two types of association information among the attributes - correlation information and interaction information for both supervised (class attribute present) and unsupervised analysis (class attribute absent). Identifying the statistically significant attribute associations is a computationally challenging task - the number of possible associations increases exponentially and many associations contain redundant information when a number of correlated attributes are present. In this paper, we explore efficient data mining methods to discover non-redundant attribute sets that contain significant association information indicating the presence of informative patterns in the data., Comment: 16 pages, 7 figures