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A computational workflow, also known as workflow, consists of tasks that must be executed in a specific order to attain a specific goal. Often, in fields such as biology, chemistry, physics, and data science, among others, these workflows are complex and are executed in large-scale, distributed, and heterogeneous computing environments prone to failures and performance degradation. Therefore, anomaly detection for workflows is an important paradigm that aims to identify unexpected behavior or errors in workflow execution. This crucial task to improve the reliability of workflow executions can be further assisted by machine learning-based techniques. However, such application is limited, in large part, due to the lack of open datasets and benchmarking. To address this gap, we make the following contributions in this paper: (1) we systematically inject anomalies and collect raw execution logs from workflows executing on distributed infrastructures; (2) we summarize the statistics of new datasets, and provide insightful analyses; (3) we convert workflows into tabular, graph and text data, and benchmark with supervised and unsupervised anomaly detection techniques correspondingly. The presented dataset and benchmarks allow examining the effectiveness and efficiency of scientific computational workflows and identifying potential research opportunities for improvement and generalization. The dataset and benchmark code are publicly available \url{//poseidon-workflows.github.io/FlowBench/} under the MIT License.

Foundation Models (FMs) serve as a general class for the development of artificial intelligence systems, offering broad potential for generalization across a spectrum of downstream tasks. Despite extensive research into self-supervised learning as the cornerstone of FMs, several outstanding issues persist in Graph Foundation Models that rely on graph self-supervised learning, namely: 1) Homogenization. The extent of generalization capability on downstream tasks remains unclear. 2) Scalability. It is unknown how effectively these models can scale to large datasets. 3) Efficiency. The training time and memory usage of these models require evaluation. 4) Training Stop Criteria. Determining the optimal stopping strategy for pre-training across multiple tasks to maximize performance on downstream tasks. To address these questions, we have constructed a rigorous benchmark that thoroughly analyzes and studies the generalization and scalability of self-supervised Graph Neural Network (GNN) models. Regarding generalization, we have implemented and compared the performance of various self-supervised GNN models, trained to generate node representations, across tasks such as node classification, link prediction, and node clustering. For scalability, we have compared the performance of various models after training using full-batch and mini-batch strategies. Additionally, we have assessed the training efficiency of these models by conducting experiments to test their GPU memory usage and throughput. Through these experiments, we aim to provide insights to motivate future research. The code for this benchmark is publicly available at //github.com/NYUSHCS/GraphFM.

Developing interactive systems that leverage natural language instructions to solve complex robotic control tasks has been a long-desired goal in the robotics community. Large Language Models (LLMs) have demonstrated exceptional abilities in handling complex tasks, including logical reasoning, in-context learning, and code generation. However, predicting low-level robotic actions using LLMs poses significant challenges. Additionally, the complexity of such tasks usually demands the acquisition of policies to execute diverse subtasks and combine them to attain the ultimate objective. Hierarchical Reinforcement Learning (HRL) is an elegant approach for solving such tasks, which provides the intuitive benefits of temporal abstraction and improved exploration. However, HRL faces the recurring issue of non-stationarity due to unstable lower primitive behaviour. In this work, we propose LGR2, a novel HRL framework that leverages language instructions to generate a stationary reward function for the higher-level policy. Since the language-guided reward is unaffected by the lower primitive behaviour, LGR2 mitigates non-stationarity and is thus an elegant method for leveraging language instructions to solve robotic control tasks. To analyze the efficacy of our approach, we perform empirical analysis and demonstrate that LGR2 effectively alleviates non-stationarity in HRL. Our approach attains success rates exceeding 70$\%$ in challenging, sparse-reward robotic navigation and manipulation environments where the baselines fail to achieve any significant progress. Additionally, we conduct real-world robotic manipulation experiments and demonstrate that CRISP shows impressive generalization in real-world scenarios.

No existing dataset adequately tests how well language models can incrementally update entity summaries - a crucial ability as these models rapidly advance. The Incremental Entity Summarization (IES) task is vital for maintaining accurate, up-to-date knowledge. To address this, we introduce SUMIE, a fully synthetic dataset designed to expose real-world IES challenges. This dataset effectively highlights problems like incorrect entity association and incomplete information presentation. Unlike common synthetic datasets, ours captures the complexity and nuances found in real-world data. We generate informative and diverse attributes, summaries, and unstructured paragraphs in sequence, ensuring high quality. The alignment between generated summaries and paragraphs exceeds 96%, confirming the dataset's quality. Extensive experiments demonstrate the dataset's difficulty - state-of-the-art LLMs struggle to update summaries with an F1 higher than 80.4%. We will open source the benchmark and the evaluation metrics to help the community make progress on IES tasks.

Graph Neural Networks (GNNs) have advanced the field of machine learning by utilizing graph-structured data, which is ubiquitous in the real world. GNNs have applications in various fields, ranging from social network analysis to drug discovery. GNN training is strenuous, requiring significant computational resources and human expertise. It makes a trained GNN an indispensable Intellectual Property (IP) for its owner. Recent studies have shown GNNs to be vulnerable to model-stealing attacks, which raises concerns over IP rights protection. Watermarking has been shown to be effective at protecting the IP of a GNN model. Existing efforts to develop a watermarking scheme for GNNs have only focused on the node classification and the graph classification tasks. To the best of our knowledge, we introduce the first-ever watermarking scheme for GNNs tailored to the Link Prediction (LP) task. We call our proposed watermarking scheme GENIE (watermarking Graph nEural Networks for lInk prEdiction). We design GENIE using a novel backdoor attack to create a trigger set for two key methods of LP: (1) node representation-based and (2) subgraph-based. In GENIE, the watermark is embedded into the GNN model by training it on both the trigger set and a modified training set, resulting in a watermarked GNN model. To assess a suspect model, we verify the watermark against the trigger set. We extensively evaluate GENIE across 3 model architectures (i.e., SEAL, GCN, and GraphSAGE) and 7 real-world datasets. Furthermore, we validate the robustness of GENIE against 11 state-of-the-art watermark removal techniques and 3 model extraction attacks. We also demonstrate that GENIE is robust against ownership piracy attack. Our ownership demonstration scheme statistically guarantees both False Positive Rate (FPR) and False Negative Rate (FNR) to be less than $10^{-6}$.

With recent rapid growth of large language models (LLMs), discrete speech tokenization has played an important role for injecting speech into LLMs. However, this discretization gives rise to a loss of information, consequently impairing overall performance. To improve the performance of these discrete speech tokens, we present RepCodec, a novel speech representation codec for semantic speech tokenization. In contrast to audio codecs which reconstruct the raw audio, RepCodec learns a vector quantization codebook through reconstructing speech representations from speech encoders like HuBERT or data2vec. Together, the speech encoder, the codec encoder and the vector quantization codebook form a pipeline for converting speech waveforms into semantic tokens. The extensive experiments illustrate that RepCodec, by virtue of its enhanced information retention capacity, significantly outperforms the widely used k-means clustering approach in both speech understanding and generation. Furthermore, this superiority extends across various speech encoders and languages, affirming the robustness of RepCodec. We believe our method can facilitate large language modeling research on speech processing.

Effective attention modules have played a crucial role in the success of Transformer-based large language models (LLMs), but the quadratic time and memory complexities of these attention modules also pose a challenge when processing long sequences. One potential solution for the long sequence problem is to utilize distributed clusters to parallelize the computation of attention modules across multiple devices (e.g., GPUs). However, adopting a distributed approach inevitably introduces extra memory overheads to store local attention results and incurs additional communication costs to aggregate local results into global ones. In this paper, we propose a distributed attention framework named ``BurstAttention'' to optimize memory access and communication operations at both the global cluster and local device levels. In our experiments, we compare BurstAttention with other competitive distributed attention solutions for long sequence processing. The experimental results under different length settings demonstrate that BurstAttention offers significant advantages for processing long sequences compared with these competitive baselines, reducing 40% communication overheads and achieving 1.37 X speedup during training 128K sequence length on 32 X A100.

Large language models (LLMs) have demonstrated impressive capabilities in natural language processing. However, their internal mechanisms are still unclear and this lack of transparency poses unwanted risks for downstream applications. Therefore, understanding and explaining these models is crucial for elucidating their behaviors, limitations, and social impacts. In this paper, we introduce a taxonomy of explainability techniques and provide a structured overview of methods for explaining Transformer-based language models. We categorize techniques based on the training paradigms of LLMs: traditional fine-tuning-based paradigm and prompting-based paradigm. For each paradigm, we summarize the goals and dominant approaches for generating local explanations of individual predictions and global explanations of overall model knowledge. We also discuss metrics for evaluating generated explanations, and discuss how explanations can be leveraged to debug models and improve performance. Lastly, we examine key challenges and emerging opportunities for explanation techniques in the era of LLMs in comparison to conventional machine learning models.

Following unprecedented success on the natural language tasks, Transformers have been successfully applied to several computer vision problems, achieving state-of-the-art results and prompting researchers to reconsider the supremacy of convolutional neural networks (CNNs) as {de facto} operators. Capitalizing on these advances in computer vision, the medical imaging field has also witnessed growing interest for Transformers that can capture global context compared to CNNs with local receptive fields. Inspired from this transition, in this survey, we attempt to provide a comprehensive review of the applications of Transformers in medical imaging covering various aspects, ranging from recently proposed architectural designs to unsolved issues. Specifically, we survey the use of Transformers in medical image segmentation, detection, classification, reconstruction, synthesis, registration, clinical report generation, and other tasks. In particular, for each of these applications, we develop taxonomy, identify application-specific challenges as well as provide insights to solve them, and highlight recent trends. Further, we provide a critical discussion of the field's current state as a whole, including the identification of key challenges, open problems, and outlining promising future directions. We hope this survey will ignite further interest in the community and provide researchers with an up-to-date reference regarding applications of Transformer models in medical imaging. Finally, to cope with the rapid development in this field, we intend to regularly update the relevant latest papers and their open-source implementations at \url{//github.com/fahadshamshad/awesome-transformers-in-medical-imaging}.

Graph representation learning resurges as a trending research subject owing to the widespread use of deep learning for Euclidean data, which inspire various creative designs of neural networks in the non-Euclidean domain, particularly graphs. With the success of these graph neural networks (GNN) in the static setting, we approach further practical scenarios where the graph dynamically evolves. Existing approaches typically resort to node embeddings and use a recurrent neural network (RNN, broadly speaking) to regulate the embeddings and learn the temporal dynamics. These methods require the knowledge of a node in the full time span (including both training and testing) and are less applicable to the frequent change of the node set. In some extreme scenarios, the node sets at different time steps may completely differ. To resolve this challenge, we propose EvolveGCN, which adapts the graph convolutional network (GCN) model along the temporal dimension without resorting to node embeddings. The proposed approach captures the dynamism of the graph sequence through using an RNN to evolve the GCN parameters. Two architectures are considered for the parameter evolution. We evaluate the proposed approach on tasks including link prediction, edge classification, and node classification. The experimental results indicate a generally higher performance of EvolveGCN compared with related approaches. The code is available at \url{//github.com/IBM/EvolveGCN}.