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Recent years in NLP have seen the continued development of domain-specific information extraction tools for scientific documents, alongside the release of increasingly multimodal pretrained transformer models. While the opportunity for scientists outside of NLP to evaluate and apply such systems to their own domains has never been clearer, these models are difficult to compare: they accept different input formats, are often black-box and give little insight into processing failures, and rarely handle PDF documents, the most common format of scientific publication. In this work, we present Collage, a tool designed for rapid prototyping, visualization, and evaluation of different information extraction models on scientific PDFs. Collage allows the use and evaluation of any HuggingFace token classifier, several LLMs, and multiple other task-specific models out of the box, and provides extensible software interfaces to accelerate experimentation with new models. Further, we enable both developers and users of NLP-based tools to inspect, debug, and better understand modeling pipelines by providing granular views of intermediate states of processing. We demonstrate our system in the context of information extraction to assist with literature review in materials science.

Vision Transformers (ViTs) have achieved remarkable success over various vision tasks, yet their robustness against data distribution shifts and inherent inductive biases remain underexplored. To enhance the robustness of ViT models for image Out-of-Distribution (OOD) detection, we introduce a novel and generic framework named Prior-augmented Vision Transformer (PViT). PViT identifies OOD samples by quantifying the divergence between the predicted class logits and the prior logits obtained from pre-trained models. Unlike existing state-of-the-art OOD detection methods, PViT shapes the decision boundary between ID and OOD by utilizing the proposed prior guide confidence, without requiring additional data modeling, generation methods, or structural modifications. Extensive experiments on the large-scale ImageNet benchmark demonstrate that PViT significantly outperforms existing state-of-the-art OOD detection methods. Additionally, through comprehensive analyses, ablation studies, and discussions, we show how PViT can strategically address specific challenges in managing large vision models, paving the way for new advancements in OOD detection.

Deep learning has revolutionized medical and biological imaging, particularly in segmentation tasks. However, segmenting biological cells remains challenging due to the high variability and complexity of cell shapes. Addressing this challenge requires high-quality datasets that accurately represent the diverse morphologies found in biological cells. Existing cell segmentation datasets are often limited by their focus on regular and uniform shapes. In this paper, we introduce a novel benchmark dataset of Ntera-2 (NT2) cells, a pluripotent carcinoma cell line, exhibiting diverse morphologies across multiple stages of differentiation, capturing the intricate and heterogeneous cellular structures that complicate segmentation tasks. To address these challenges, we propose an uncertainty-aware deep learning framework for complex cellular morphology segmentation (MorphoSeg) by incorporating sampling of virtual outliers from low-likelihood regions during training. Our comprehensive experimental evaluations against state-of-the-art baselines demonstrate that MorphoSeg significantly enhances segmentation accuracy, achieving up to a 7.74% increase in the Dice Similarity Coefficient (DSC) and a 28.36% reduction in the Hausdorff Distance. These findings highlight the effectiveness of our dataset and methodology in advancing cell segmentation capabilities, especially for complex and variable cell morphologies. The dataset and source code is publicly available at https://github.com/RanchoGoose/MorphoSeg.

Foundation models for natural language processing, powered by the transformer architecture, exhibit remarkable in-context learning (ICL) capabilities, allowing pre-trained models to adapt to downstream tasks using few-shot prompts without updating their weights. Recently, transformer-based foundation models have also emerged as versatile tools for solving scientific problems, particularly in the realm of partial differential equations (PDEs). However, the theoretical foundations of the ICL capabilities in these scientific models remain largely unexplored. This work develops a rigorous error analysis for transformer-based ICL applied to solution operators associated with a family of linear elliptic PDEs. We first demonstrate that a linear transformer, defined by a linear self-attention layer, can provably learn in-context to invert linear systems arising from the spatial discretization of PDEs. This is achieved by deriving theoretical scaling laws for the prediction risk of the proposed linear transformers in terms of spatial discretization size, the number of training tasks, and the lengths of prompts used during training and inference. These scaling laws also enable us to establish quantitative error bounds for learning PDE solutions. Furthermore, we quantify the adaptability of the pre-trained transformer on downstream PDE tasks that experience distribution shifts in both tasks (represented by PDE coefficients) and input covariates (represented by the source term). To analyze task distribution shifts, we introduce a novel concept of task diversity and characterize the transformer's prediction error in terms of the magnitude of task shift, assuming sufficient diversity in the pre-training tasks. We also establish sufficient conditions to ensure task diversity. Finally, we validate the ICL-capabilities of transformers through extensive numerical experiments., Comment: Code available at https://github.com/ LuGroupUMN/ICL-EllipticPDEs

Generative models have gained significant prominence in Natural Language Processing (NLP), especially in tackling the complex task of modeling and evaluating long text sequences. This task is crucial for advancing various downstream applications, such as text generation and machine translation. Recent methods that utilize stochastic processes to capture the intrinsic dynamics of sequences have shown superior performance in generative modeling. However, the accurate encoding of both temporal and structural dependencies from text datasets, as well as leveraging this encoded information for sequence evaluation, remains an open area of research. In this paper, we propose a novel approach to learn the stochastic dynamics of long text sequences, utilizing a negative log-likelihood-based encoder that outperforms contrastive learning methods. We also introduce a likelihood-based evaluation metric for long-text assessment, which measures sequence coherence and can be applied to downstream tasks such as Human-AI discrimination. Our encoder preserves sequence coherence effectively and performs robustly on out-of-domain datasets. Additionally, the proposed evaluation metric captures both temporal and structural information comprehensively. Theoretical analysis demonstrates the superiority of our metric in sequence evaluation, and experimental results highlight its flexibility and exceptional performance across a variety of tasks, showcasing its utility in diverse NLP applications.

Measuring the coherence of text is a vital aspect of evaluating the quality of written content. Recent advancements in neural coherence modeling have demonstrated their efficacy in capturing entity coreference and discourse relations, thereby enhancing coherence evaluation. However, many existing methods heavily depend on static embeddings or focus narrowly on nearby context, constraining their capacity to measure the overarching coherence of long texts. In this paper, we posit that coherent texts inherently manifest a sequential and cohesive interplay among sentences, effectively conveying the central theme, purpose, or standpoint. To explore this abstract relationship, we introduce the "BBScore," a novel reference-free metric grounded in Brownian bridge theory for assessing text coherence. Our findings showcase that when synergized with a simple additional classification component, this metric attains a performance level comparable to state-of-the-art techniques on standard artificial discrimination tasks. We also establish in downstream tasks that this metric effectively differentiates between human-written documents and text generated by large language models under a specific domain. Furthermore, we illustrate the efficacy of this approach in detecting written styles attributed to diverse large language models, underscoring its potential for generalizability. In summary, we present a novel Brownian bridge coherence metric capable of measuring both local and global text coherence, while circumventing the need for end-to-end model training. This flexibility allows for its application in various downstream tasks., Comment: Accepted to the 38th Annual AAAI Conference on Artificial Intelligence (AAAI-24)

The superior performance of object detectors is often established under the condition that the test samples are in the same distribution as the training data. However, in many practical applications, out-of-distribution (OOD) instances are inevitable and usually lead to uncertainty in the results. In this paper, we propose a novel, intuitive, and scalable probabilistic object detection method for OOD detection. Unlike other uncertainty-modeling methods that either require huge computational costs to infer the weight distributions or rely on model training through synthetic outlier data, our method is able to distinguish between in-distribution (ID) data and OOD data via weight parameter sampling from proposed Gaussian distributions based on pre-trained networks. We demonstrate that our Bayesian object detector can achieve satisfactory OOD identification performance by reducing the FPR95 score by up to 8.19% and increasing the AUROC score by up to 13.94% when trained on BDD100k and VOC datasets as the ID datasets and evaluated on COCO2017 dataset as the OOD dataset.

The multiple scattering of light makes materials opaque and obstructs imaging. Wavefront shaping can reverse the scattering process, but imaging with physical wavefront shaping has limitations such as requiring physical guidestars, being restricted within a small isoplanatic volume, and relying on slow wavefront updates, with some approaches only working for planar targets outside the scattering media. Here, we introduce scattering matrix tomography (SMT): measure the hyperspectral scattering matrix of the sample, use it to digitally scan a synthesized confocal spatiotemporal focus and construct a volumetric image of the sample, and then use the tomograms as virtual guidestars in a nonconvex optimization to find the pulse shape, input wavefront, and output wavefront that can compensate for aberrations and scattering. SMT combines the strengths of wavefront shaping, spatiotemporal gating, and computational adaptive optics, eliminating physical guidestars and enabling digital double-path wavefront corrections tailored for every isoplanatic volume. We demonstrate sub-micron lateral resolution and one-micron axial resolution at one millimeter beneath ex vivo mouse brain tissue and over three transport mean free paths inside an opaque colloid, where existing imaging methods all fail due to the overwhelming multiple scattering. As a noninvasive and label-free method that works both inside and outside the scattering media, SMT may be applied broadly across medical imaging, biological science, device inspection, and colloidal physics.

No-reference video quality assessment (NR-VQA) for user generated content (UGC) is crucial for understanding and improving visual experience. Unlike video recognition tasks, VQA tasks are sensitive to changes in input resolution. Since large amounts of UGC videos nowadays are 720p or above, the fixed and relatively small input used in conventional NR-VQA methods results in missing high-frequency details for many videos. In this paper, we propose a novel Transformer-based NR-VQA framework that preserves the high-resolution quality information. With the multi-resolution input representation and a novel multi-resolution patch sampling mechanism, our method enables a comprehensive view of both the global video composition and local high-resolution details. The proposed approach can effectively aggregate quality information across different granularities in spatial and temporal dimensions, making the model robust to input resolution variations. Our method achieves state-of-the-art performance on large-scale UGC VQA datasets LSVQ and LSVQ-1080p, and on KoNViD-1k and LIVE-VQC without fine-tuning., Comment: Frontiers Signal Processing in Computational Video and Video Streaming (https://www.frontiersin.org/articles/10.3389/frsip.2023.1137006/full)

Congestion Control (CC), as the core networking task to efficiently utilize network capacity, received great attention and widely used in various Internet communication applications such as 5G, Internet-of-Things, UAN, and more. Various CC algorithms have been proposed both on network and transport layers such as Active Queue Management (AQM) algorithm and Transmission Control Protocol (TCP) congestion control mechanism. But it is hard to model dynamic AQM/TCP system and cooperate two algorithms to obtain excellent performance under different communication scenarios. In this paper, we explore the performance of multi-agent reinforcement learning-based cross-layer congestion control algorithms and present cooperation performance of two agents, known as MACC (Multi-agent Congestion Control). We implement MACC in NS3. The simulation results show that our scheme outperforms other congestion control combination in terms of throughput and delay, etc. Not only does it proves that networking protocols based on multi-agent deep reinforcement learning is efficient for communication managing, but also verifies that networking area can be used as new playground for machine learning algorithms., Comment: 7 pages, 8 figures