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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

Recently, image captioning has aroused great interest in both academic and industrial worlds. Most existing systems are built upon large-scale datasets consisting of image-sentence pairs, which, however, are time-consuming to construct. In addition, even for the most advanced image captioning systems, it is still difficult to realize deep image understanding. In this work, we achieve unpaired image captioning by bridging the vision and the language domains with high-level semantic information. The motivation stems from the fact that the semantic concepts with the same modality can be extracted from both images and descriptions. To further improve the quality of captions generated by the model, we propose the Semantic Relationship Explorer, which explores the relationships between semantic concepts for better understanding of the image. Extensive experiments on MSCOCO dataset show that we can generate desirable captions without paired datasets. Furthermore, the proposed approach boosts five strong baselines under the paired setting, where the most significant improvement in CIDEr score reaches 8%, demonstrating that it is effective and generalizes well to a wide range of models.

In this paper, the circle formation control problem is addressed for a group of cooperative underactuated fish-like robots involving unknown nonlinear dynamics and disturbances. Based on the reinforcement learning and cognitive consistency theory, we propose a decentralized controller without the knowledge of the dynamics of the fish-like robots. The proposed controller can be transferred from simulation to reality. It is only trained in our established simulation environment, and the trained controller can be deployed to real robots without any manual tuning. Simulation results confirm that the proposed model-free robust formation control method is scalable with respect to the group size of the robots and outperforms other representative RL algorithms. Several experiments in the real world verify the effectiveness of our RL-based approach for circle formation control., Comment: to be published in ICRA2021

In recent years, text-guided image manipulation has gained increasing attention in the multimedia and computer vision community. The input to conditional image generation has evolved from image-only to multimodality. In this paper, we study a setting that allows users to edit an image with multiple objects using complex text instructions to add, remove, or change the objects. The inputs of the task are multimodal including (1) a reference image and (2) an instruction in natural language that describes desired modifications to the image. We propose a GAN-based method to tackle this problem. The key idea is to treat text as neural operators to locally modify the image feature. We show that the proposed model performs favorably against recent strong baselines on three public datasets. Specifically, it generates images of greater fidelity and semantic relevance, and when used as a image query, leads to better retrieval performance.

We use the data of tenured and tenure-track faculty at ten public and private math departments of various tiered rankings in the United States, as a case study to demonstrate the statistical and mathematical relationships among several variables, e.g., the number of publications and citations, the rank of professorship and AMS fellow status. At first we do an exploratory data analysis of the math departments. Then various statistical tools, including regression, artificial neural network, and unsupervised learning, are applied and the results obtained from different methods are compared. We conclude that with more advanced models, it may be possible to design an automatic promotion algorithm that has the potential to be fairer, more efficient and more consistent than human approach., Comment: 26 pages, 8 figures

Many tasks in computer vision and graphics fall within the framework of conditional image synthesis. In recent years, generative adversarial nets (GANs) have delivered impressive advances in quality of synthesized images. However, it remains a challenge to generate both diverse and plausible images for the same input, due to the problem of mode collapse. In this paper, we develop a new generic multimodal conditional image synthesis method based on Implicit Maximum Likelihood Estimation (IMLE) and demonstrate improved multimodal image synthesis performance on two tasks, single image super-resolution and image synthesis from scene layouts. We make our implementation publicly available., Comment: To appear in International Journal of Computer Vision (IJCV). arXiv admin note: text overlap with arXiv:1811.12373

We give a constructive proof of the classical Cauchy-Kovalevskaya theorem in the ODE setting which provides a sufficient condition for an initial value problem to have a unique analytic solution. Our proof is inspired by a modern functional analytic technique for rigorously solving nonlinear problems known as the radii polynomial approach. The main idea is to recast the existence and uniqueness of analytic solutions as a fixed point problem for an appropriately chosen Banach space. A key aspect of this method is the usage of an approximate solution which plays a crucial role in the theoretical proof. Our proof is constructive in the sense that we provide an explicit recipe for constructing the fixed point problem, an approximate solution, and the bounds necessary to prove the existence of the fixed point.

The internal states of most deep neural networks are difficult to interpret, which makes diagnosis and debugging during training challenging. Activation maximization methods are widely used, but lead to multiple optima and are hard to interpret (appear noise-like) for complex neurons. Image-based methods use maximally-activating image regions which are easier to interpret, but do not provide pixel-level insight into why the neuron responds to them. In this work we introduce an MCMC method: Langevin Dynamics Activation Maximization (LDAM), which is designed for diagnostic visualization. LDAM provides two affordances in combination: the ability to explore the set of maximally activating pre-images, and the ability to trade-off interpretability and pixel-level accuracy using a GAN-style discriminator as a regularizer. We present case studies on MNIST, CIFAR and ImageNet datasets exploring these trade-offs. Finally we show that diagnostic visualization using LDAM leads to a novel insight into the parameter averaging method for deep net training.

Most existing methods for conditional image synthesis are only able to generate a single plausible image for any given input, or at best a fixed number of plausible images. In this paper, we focus on the problem of generating images from semantic segmentation maps and present a simple new method that can generate an arbitrary number of images with diverse appearance for the same semantic layout. Unlike most existing approaches which adopt the GAN framework, our method is based on the recently introduced Implicit Maximum Likelihood Estimation (IMLE) framework. Compared to the leading approach, our method is able to generate more diverse images while producing fewer artifacts despite using the same architecture. The learned latent space also has sensible structure despite the lack of supervision that encourages such behaviour. Videos and code are available at https://people.eecs.berkeley.edu/~ke.li/projects/imle/scene_layouts/., Comment: 18 pages, 16 figures; IEEE International Conference on Computer Vision (ICCV), 2019

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset., Comment: The International Multimodal Brain Tumor Segmentation (BraTS) Challenge

Humans and animals are capable of learning a new behavior by observing others perform the skill just once. We consider the problem of allowing a robot to do the same -- learning from a raw video pixels of a human, even when there is substantial domain shift in the perspective, environment, and embodiment between the robot and the observed human. Prior approaches to this problem have hand-specified how human and robot actions correspond and often relied on explicit human pose detection systems. In this work, we present an approach for one-shot learning from a video of a human by using human and robot demonstration data from a variety of previous tasks to build up prior knowledge through meta-learning. Then, combining this prior knowledge and only a single video demonstration from a human, the robot can perform the task that the human demonstrated. We show experiments on both a PR2 arm and a Sawyer arm, demonstrating that after meta-learning, the robot can learn to place, push, and pick-and-place new objects using just one video of a human performing the manipulation., Comment: First two authors contributed equally. Video available at https://sites.google.com/view/daml

Imitation learning is a powerful paradigm for robot skill acquisition. However, obtaining demonstrations suitable for learning a policy that maps from raw pixels to actions can be challenging. In this paper we describe how consumer-grade Virtual Reality headsets and hand tracking hardware can be used to naturally teleoperate robots to perform complex tasks. We also describe how imitation learning can learn deep neural network policies (mapping from pixels to actions) that can acquire the demonstrated skills. Our experiments showcase the effectiveness of our approach for learning visuomotor skills., Comment: First two authors contributed equally. Video available at https://sites.google.com/view/vrlfd/

In order for a robot to be a generalist that can perform a wide range of jobs, it must be able to acquire a wide variety of skills quickly and efficiently in complex unstructured environments. High-capacity models such as deep neural networks can enable a robot to represent complex skills, but learning each skill from scratch then becomes infeasible. In this work, we present a meta-imitation learning method that enables a robot to learn how to learn more efficiently, allowing it to acquire new skills from just a single demonstration. Unlike prior methods for one-shot imitation, our method can scale to raw pixel inputs and requires data from significantly fewer prior tasks for effective learning of new skills. Our experiments on both simulated and real robot platforms demonstrate the ability to learn new tasks, end-to-end, from a single visual demonstration., Comment: Conference on Robot Learning, 2017 (to appear). First two authors contributed equally. Video available at https://sites.google.com/view/one-shot-imitation

Model predictive control (MPC) is a popular control method that has proved effective for robotics, among other fields. MPC performs re-planning at every time step. Re-planning is done with a limited horizon per computational and real-time constraints and often also for robustness to potential model errors. However, the limited horizon leads to suboptimal performance. In this work, we consider the iterative learning setting, where the same task can be repeated several times, and propose a policy improvement scheme for MPC. The main idea is that between executions we can, offline, run MPC with a longer horizon, resulting in a hindsight plan. To bring the next real-world execution closer to the hindsight plan, our approach learns to re-shape the original cost function with the goal of satisfying the following property: short horizon planning (as realistic during real executions) with respect to the shaped cost should result in mimicking the hindsight plan. This effectively consolidates long-term reasoning into the short-horizon planning. We empirically evaluate our approach in contact-rich manipulation tasks both in simulated and real environments, such as peg insertion by a real PR2 robot., Comment: Additional experiments for neural network generalization and for varying the planning horizon. Paper accepted to ICRA 2017

Policy search can in principle acquire complex strategies for control of robots and other autonomous systems. When the policy is trained to process raw sensory inputs, such as images and depth maps, it can also acquire a strategy that combines perception and control. However, effectively processing such complex inputs requires an expressive policy class, such as a large neural network. These high-dimensional policies are difficult to train, especially when learning to control safety-critical systems. We propose PLATO, an algorithm that trains complex control policies with supervised learning, using model-predictive control (MPC) to generate the supervision, hence never in need of running a partially trained and potentially unsafe policy. PLATO uses an adaptive training method to modify the behavior of MPC to gradually match the learned policy in order to generate training samples at states that are likely to be visited by the learned policy. PLATO also maintains the MPC cost as an objective to avoid highly undesirable actions that would result from strictly following the learned policy before it has been fully trained. We prove that this type of adaptive MPC expert produces supervision that leads to good long-horizon performance of the resulting policy. We also empirically demonstrate that MPC can still avoid dangerous on-policy actions in unexpected situations during training. Our empirical results on a set of challenging simulated aerial vehicle tasks demonstrate that, compared to prior methods, PLATO learns faster, experiences substantially fewer catastrophic failures (crashes) during training, and often converges to a better policy.

Model predictive control (MPC) is an effective method for controlling robotic systems, particularly autonomous aerial vehicles such as quadcopters. However, application of MPC can be computationally demanding, and typically requires estimating the state of the system, which can be challenging in complex, unstructured environments. Reinforcement learning can in principle forego the need for explicit state estimation and acquire a policy that directly maps sensor readings to actions, but is difficult to apply to unstable systems that are liable to fail catastrophically during training before an effective policy has been found. We propose to combine MPC with reinforcement learning in the framework of guided policy search, where MPC is used to generate data at training time, under full state observations provided by an instrumented training environment. This data is used to train a deep neural network policy, which is allowed to access only the raw observations from the vehicle's onboard sensors. After training, the neural network policy can successfully control the robot without knowledge of the full state, and at a fraction of the computational cost of MPC. We evaluate our method by learning obstacle avoidance policies for a simulated quadrotor, using simulated onboard sensors and no explicit state estimation at test time.