Evaluating Cellularity Estimation Methods: Comparing AI Counting with Pathologists’ Visual Estimates

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The development of next-generation sequencing (NGS) has enabled the discovery of cancer-specific driver gene alternations, making precision medicine possible. However, accurategenetic testing requires a sufficient amount of tumor cells in the specimen. The evaluation of tumor content ratio (TCR) from hematoxylin and eosin (H&E)-stained images has been found to vary between pathologists, making it an important challenge to obtain an accurate TCR. In this study, three pathologists exhaustively labeled all cells in 41 regions from 41 lung cancer cases as either tumor, non-tumor or indistinguishable, thus establishing a “gold standard” TCR. We then compared the accuracy of the TCR estimated by 13 pathologists based on visual assessment and the TCR calculated by an AI model that we have developed. It is a compact and fast model that follows a fully convolutional neural network architecture and produces cell detection maps which can be efficiently post-processed to obtain tumor and non-tumor cell counts from which TCR is calculated. Its raw cell detection accuracy is 92% while its classification accuracy is 84%. The results show that the error between the gold standard TCR and the AI calculation was significantly smaller than that between the gold standard TCR and the pathologist’s visual assessment (p < 0.05). Additionally, the robustness of AI models across institutions is a key issue and we demonstrate that the variation in AI was smallerthan that in the average of pathologists when evaluated by institution. These findings suggest that the accuracy of tumor cellularity assessments in clinical workflows is significantly improved by the introduction of robust AI models, leading to more efficient genetic testing and ultimately to better patient outcomes.

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Impeller: A Path-based Heterogeneous Graph Learning Method for Spatial Transcriptomic Data Imputation

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Recent advances in spatial transcriptomics allow spatially resolved gene expression measurements with cellular or even sub-cellular resolution, directly characterizing the complex spatiotemporal gene expression landscape and cell-to-cell interactions in their native microenvironments. Due to technology limitations, most spatial transcriptomic technologies still yield incomplete expression measurements with excessive missing values. Therefore, gene imputation is critical to filling in missing data, enhancing resolution, and improving overall interpretability. However, existing methods either require additional matched single-cell RNA-seq data, which is rarely available, or ignore spatial proximity or expression similarity information

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Improving Test-Time Adaptation For Histopathology Image Segmentation: Gradient-To-Parameter Ratio Guided Feature Alignment

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In the field of histopathology, computer-aided systems face significant challenges due to diverse domain shifts. They include variations in tissue source organ, preparation and scanningprotocols. These domain shifts can significantly impact algorithms’ performance in histopathology tasks, such as cancer segmentation. In this paper, we address this problem byproposing a new multi-task extension of test-time adaptation (TTA) for simultaneous semantic, and instance segmentation of nuclei. First, to mitigate domain shifts during testing, weuse a feature alignment TTA method, through which we adapt the feature vectors of the target data based on the feature vectors’ statistics derived from the source data. Second, the ratioof Gradient norm to Parameter norm (G2P) is proposed to guide the feature alignment procedure. Our approach requires a pre-trained model on the source data, without requiringaccess to the source dataset during TTA. This is particularly crucial in medical applications where access to training data may be restricted due to privacy concerns or patient consent. Through experimental validation, we demonstrate that the proposed method consistently yields competitive results when applied to out-of-distribution data across multiple datasets.

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MULAN: Multi-modal Causal Structure Learning and Root Cause Analysis for Microservice Systems

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Effective root cause analysis (RCA) is vital for swiftly restoring services, minimizing losses, and ensuring the smooth operation and management of complex systems. Previous data-driven RCA methods, particularly those employing causal discovery techniques, have primarily focused on constructing dependency or causal graphs for backtracking the root causes. However, these methods often fall short as they rely solely on data from a single modality, thereby resulting in suboptimal solutions. In this work, we propose Mulan, a unified multi-modal causal structure learning method designed to identify root causes in microservice systems. We leverage a log-tailored language model to facilitate log representation learning, converting log sequences into time-series data. To explore intricate relationships across different modalities, we propose a contrastive learning-based approach to extract modality-invariant and modality-specific representations within a shared latent space. Additionally, we introduce a novel key performance indicator-aware attention mechanism for assessing modality reliability and co-learning a final causal graph. Finally, we employ random walk with restart to simulate system fault propagation and identify potential root causes. Extensive experiments on three real-world datasets validate the effectiveness of our proposed method.

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Long-HOT: A Modular Hierarchical Approach for Long-Horizon Object Transport

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We aim to address key challenges in long-horizon embodied exploration and navigation by proposing a long-horizon object transport task called Long-HOT and a novel modular framework for temporally extended navigation. Agents in Long-HOT need to efficiently find and pick up target objects that are scattered in the environment, carry them to a goal location with load constraints, and optionally have access to a container. We propose a modular topological graph-based transport policy (HTP) that explores efficiently with the help of weighted frontiers. Our hierarchical approach uses a combination of motion planning algorithms to reach point goals within explored locations and object navigation policies for moving towards semantic targets at unknown locations. Experiments on both our proposed Habitat transport task and on MultiOn benchmarks show that our method outperforms baselines and prior works. Further, we analyze the agent’s behavior for the usage of the container and demonstrate meaningful generalization to harder transport scenes with training only on simpler versions of the task.

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Towards Robust Fidelity for Evaluating Explainability of Graph Neural Networks

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Graph Neural Networks (GNNs) are neural models that leverage the dependency structure in graphical data via message passing among the graph nodes. GNNs have emerged as pivotal architectures in analyzing graph-structured data, and their expansive application in sensitive domains requires a comprehensive understanding of their decision-making processes — necessitating a framework for GNN explainability. An explanation function for GNNs takes a pre-trained GNN along with a graph as input, to produce a ‘sufficient statistic’ subgraph with respect to the graph label. A main challenge in studying GNN explainability is to provide f idelity measures that evaluate the performance of these explanation functions. This paper studies this foundational challenge, spotlighting the inherent limitations of prevailing fidelity metrics, including Fid+, Fid?, and Fid?. Specifically, a formal, information-theoretic definition of explainability is introduced and it is shown that existing metrics often fail to align with this definition across various statistical scenarios. The reason is due to potential distribution shifts when subgraphs are removed in computing these fidelity measures. Subsequently, a robust class of fidelity measures are introduced, and it is shown analytically that they are resilient to distribution shift issues and are applicable in a wide range of scenarios. Extensive empirical analysis on both synthetic and real datasets are provided to illustrate that the proposed metrics are more coherent with gold standard metrics. The source code is available at https://trustai4s-lab.github.io/fidelity.

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Parametric Augmentation for Time Series Contrastive Learning

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Modern techniques like contrastive learning have been effectively used in many areas, including computer vision, natural language processing, and graph-structured data. Creating positive examples that assist the model in learning robust and discriminative representations is a crucial stage in contrastive learning approaches. Usually, preset human intuition directs the selection of relevant data augmentations. Due to patterns that are easily recognized by humans, this rule of thumb works well in the vision and language domains. However, it is impractical to visually inspect the temporal structures in time series. The diversity of time series augmentations at both the dataset and instance levels makes it difficult to choose meaningful augmentations on the fly. In this study, we address this gap by analyzing time series data augmentation using information theory and summarizing the most commonly adopted augmentations in a unified format. We then propose a contrastive learning framework with parametric augmentation, AutoTCL, which can be adaptively employed to support time series representation learning. The proposed approach is encoder-agnostic, allowing it to be seamlessly integrated with different backbone encoders. Experiments on univariate forecasting tasks demonstrate the highly competitive results of our method, with an average 6.5% reduction in MSE and 4.7% in MAE over the leading baselines. In classification tasks, AutoTCL achieves a 1.2% increase in average accuracy. The source code is available at https://github.com/AslanDing/AutoTCL.

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Improving Open Information Extraction with Large Language Models: A Study on Demonstration Uncertainty

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Open Information Extraction (OIE) task aims at extracting structured facts from unstructured text, typically in the form of (subject, relation, object) triples. Despite the potential of large language models (LLMs) like ChatGPT as a general task solver, they lag behind state-of-the-art (supervised) methods in OIE tasks due to two key issues. First, LLMs struggle to distinguish irrelevant context from relevant relations and generate structured output due to the restrictions on fine-tuning the model. Second, LLMs generate responses autoregressively based on probability, which makes the predicted relations lack confidence. In this paper, we assess the capabilities of LLMs in improving the OIE task. Particularly, we propose various in-context learning strategies to enhance LLM’s instruction-following ability and a demonstration uncertainty quantification module to enhance the confidence of the generated relations. Our experiments on three OIE benchmark datasets show that our approach holds its own against established supervised methods, both quantitatively and qualitatively.

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DNA-GPT: Divergent N-Gram Analysis for Training-Free Detection of GPT-Generated Text

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Large language models (LLMs) have notably enhanced the fluency and diversity of machine-generated text. However, this progress also presents a significant challenge in detecting the origin of a given text, and current research on detection methods lags behind the rapid evolution of LLMs. Conventional training-based methods have limitations in flexibility, particularly when adapting to new domains, and they often lack explanatory power. To address this gap, we propose a novel training-free detection strategy called Divergent N-Gram Analysis (DNA-GPT). Given a text, we first truncate it in the middle and then use only the preceding portion as input to the LLMs to regenerate the new remaining parts. By analyzing the differences between the original and new remaining parts through N-gram analysis in black-box or probability divergence in white-box, we can clearly illustrate significant discrepancies between machine-generated and human-written text. We conducted extensive experiments on the most advanced LLMs from OpenAI, including text-davinci-003, GPT-3.5-turbo, and GPT-4, as well as open-source models such as GPT-NeoX-20B and LLaMa-13B. Results show that our zero-shot approach exhibits state-of-the-art performance in distinguishing between human and GPT-generated text on four English and one German dataset, outperforming OpenAI’s own classifier, which is trained on millions of text. Additionally, our methods provide reasonable explanations and evidence to support our claim, which is a unique feature of explainable detection. Our method is also robust under the revised text attack and can additionally solve model sourcing.

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Deep Learning-Based Real-Time Rate Control for Live Streaming on Wireless Networks

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Providing wireless users with high-quality video content has become increasingly important. However, ensuring consistent video quality poses challenges due to variable encodedbitrate caused by dynamic video content and fluctuating channel bitrate caused by wireless fading effects. Suboptimal selection of encoder parameters can lead to video quality loss due to underutilized bandwidth or the introduction of video artifacts due to packet loss. To address this, a real-time deep learning-based H.264 controller is proposed. This controller leverages instantaneous channel quality data driven from the physical layer, along with the video chunk, to dynamically estimate the optimal encoder parameters with a negligible delay in real-time. The objective is to maintain an encoded video bitrate slightly below the available channel bitrate. Experimental results, conducted on both QCIF dataset and a diverse selection of random videos from public datasets, validate the effectiveness of the approach. Remarkably, improvements of 10-20 dB in PSNR with respect to the state-of-the art adaptive bitrate video streaming is achieved, with an average packet drop rate as low as 0.002.

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