Spatial transcriptomics (ST) technologies have revolutionized the study of gene expression patterns in tissues by providing multimodality data in transcriptomic, spatial, and morphological, offering opportunities for understanding tissue biology beyond transcriptomics. However, we identify the modality bias phenomenon in ST data species, i.e., the inconsistent contribution of different modalities to the labels leads to a tendency for the analysis methods to retain the information of the dominant modality. How to mitigate the adverse effects of modality bias to satisfy various downstream tasks remains a fundamental challenge. This paper introduces Multiple-modality Structure Transformation, named MuST, a novel methodology to tackle the challenge. MuST integrates the multi-modality information contained in the ST data effectively into a uniform latent space to provide a foundation for all the downstream tasks. It learns intrinsic local structures by topology discovery strategy and topology fusion loss function to solve the inconsistencies among different modalities. Thus, these topology-based and deep learning techniques provide a solid foundation for a variety of analytical tasks while coordinating different modalities. The effectiveness of MuST is assessed by performance metrics and biological significance. The results show that it outperforms existing state-of-the-art methods with clear advantages in the precision of identifying and preserving structures of tissues and biomarkers. MuST offers a versatile toolkit for the intricate analysis of complex biological systems.
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In the field of robotics and automation, conventional object recognition and instance segmentation methods face a formidable challenge when it comes to perceiving Deformable Linear Objects (DLOs) like wires, cables, and flexible tubes. This challenge arises primarily from the lack of distinct attributes such as shape, color, and texture, which calls for tailored solutions to achieve precise identification. In this work, we propose a foundation model-based DLO instance segmentation technique that is text-promptable and user-friendly. Specifically, our approach combines the text-conditioned semantic segmentation capabilities of CLIPSeg model with the zero-shot generalization capabilities of Segment Anything Model (SAM). We show that our method exceeds SOTA performance on DLO instance segmentation, achieving a mIoU of $91.21\%$. We also introduce a rich and diverse DLO-specific dataset for instance segmentation.
Generative Pre-trained Transformer (GPT) models have exhibited exciting progress in their capabilities, capturing the interest of practitioners and the public alike. Yet, while the literature on the trustworthiness of GPT models remains limited, practitioners have proposed employing capable GPT models for sensitive applications such as healthcare and finance -- where mistakes can be costly. To this end, this work proposes a comprehensive trustworthiness evaluation for large language models with a focus on GPT-4 and GPT-3.5, considering diverse perspectives -- including toxicity, stereotype bias, adversarial robustness, out-of-distribution robustness, robustness on adversarial demonstrations, privacy, machine ethics, and fairness. Based on our evaluations, we discover previously unpublished vulnerabilities to trustworthiness threats. For instance, we find that GPT models can be easily misled to generate toxic and biased outputs and leak private information in both training data and conversation history. We also find that although GPT-4 is usually more trustworthy than GPT-3.5 on standard benchmarks, GPT-4 is more vulnerable given jailbreaking system or user prompts, potentially because GPT-4 follows (misleading) instructions more precisely. Our work illustrates a comprehensive trustworthiness evaluation of GPT models and sheds light on the trustworthiness gaps. Our benchmark is publicly available at //decodingtrust.github.io/ ; our dataset can be previewed at //huggingface.co/datasets/AI-Secure/DecodingTrust ; a concise version of this work is at //openreview.net/pdf?id=kaHpo8OZw2 .
Image enhancement algorithms are very useful for real world computer vision tasks where image resolution is often physically limited by the sensor size. While state-of-the-art deep neural networks show impressive results for image enhancement, they often struggle to enhance real-world images. In this work, we tackle a real-world setting: inpainting of images from Dunhuang caves. The Dunhuang dataset consists of murals, half of which suffer from corrosion and aging. These murals feature a range of rich content, such as Buddha statues, bodhisattvas, sponsors, architecture, dance, music, and decorative patterns designed by different artists spanning ten centuries, which makes manual restoration challenging. We modify two different existing methods (CAR, HINet) that are based upon state-of-the-art (SOTA) super resolution and deblurring networks. We show that those can successfully inpaint and enhance these deteriorated cave paintings. We further show that a novel combination of CAR and HINet, resulting in our proposed inpainting network (ARIN), is very robust to external noise, especially Gaussian noise. To this end, we present a quantitative and qualitative comparison of our proposed approach with existing SOTA networks and winners of the Dunhuang challenge. One of the proposed methods HINet) represents the new state of the art and outperforms the 1st place of the Dunhuang Challenge, while our combination ARIN, which is robust to noise, is comparable to the 1st place. We also present and discuss qualitative results showing the impact of our method for inpainting on Dunhuang cave images.
Recent embedding-based methods have achieved great successes in exploiting entity alignment from knowledge graph (KG) embeddings of multiple modalities. In this paper, we study embedding-based entity alignment (EEA) from a perspective of generative models. We show that EEA shares similarities with typical generative models and prove the effectiveness of the recently developed generative adversarial network (GAN)-based EEA methods theoretically. We then reveal that their incomplete objective limits the capacity on both entity alignment and entity synthesis (i.e., generating new entities). We mitigate this problem by introducing a generative EEA (GEEA) framework with the proposed mutual variational autoencoder (M-VAE) as the generative model. M-VAE enables entity conversion between KGs and generation of new entities from random noise vectors. We demonstrate the power of GEEA with theoretical analysis and empirical experiments on both entity alignment and entity synthesis tasks.
Recent advances in the theory of Neural Operators (NOs) have enabled fast and accurate computation of the solutions to complex systems described by partial differential equations (PDEs). Despite their great success, current NO-based solutions face important challenges when dealing with spatio-temporal PDEs over long time scales. Specifically, the current theory of NOs does not present a systematic framework to perform data assimilation and efficiently correct the evolution of PDE solutions over time based on sparsely sampled noisy measurements. In this paper, we propose a learning-based state-space approach to compute the solution operators to infinite-dimensional semilinear PDEs. Exploiting the structure of semilinear PDEs and the theory of nonlinear observers in function spaces, we develop a flexible recursive method that allows for both prediction and data assimilation by combining prediction and correction operations. The proposed framework is capable of producing fast and accurate predictions over long time horizons, dealing with irregularly sampled noisy measurements to correct the solution, and benefits from the decoupling between the spatial and temporal dynamics of this class of PDEs. We show through experiments on the Kuramoto-Sivashinsky, Navier-Stokes and Korteweg-de Vries equations that the proposed model is robust to noise and can leverage arbitrary amounts of measurements to correct its prediction over a long time horizon with little computational overhead.
We combine standard persistent homology with image persistent homology to define a novel way of characterizing shapes and interactions between them. In particular, we introduce: (1) a mixup barcode, which captures geometric-topological interactions (mixup) between two point sets in arbitrary dimension; (2) simple summary statistics, total mixup and total percentage mixup, which quantify the complexity of the interactions as a single number; (3) a software tool for playing with the above. As a proof of concept, we apply this tool to a problem arising from machine learning. In particular, we study the disentanglement in embeddings of different classes. The results suggest that topological mixup is a useful method for characterizing interactions for low and high-dimensional data. Compared to the typical usage of persistent homology, the new tool is sensitive to the geometric locations of the topological features, which is often desirable.
One promising approach towards effective robot decision making in complex, long-horizon tasks is to sequence together parameterized skills. We consider a setting where a robot is initially equipped with (1) a library of parameterized skills, (2) an AI planner for sequencing together the skills given a goal, and (3) a very general prior distribution for selecting skill parameters. Once deployed, the robot should rapidly and autonomously learn to improve its performance by specializing its skill parameter selection policy to the particular objects, goals, and constraints in its environment. In this work, we focus on the active learning problem of choosing which skills to practice to maximize expected future task success. We propose that the robot should estimate the competence of each skill, extrapolate the competence (asking: "how much would the competence improve through practice?"), and situate the skill in the task distribution through competence-aware planning. This approach is implemented within a fully autonomous system where the robot repeatedly plans, practices, and learns without any environment resets. Through experiments in simulation, we find that our approach learns effective parameter policies more sample-efficiently than several baselines. Experiments in the real-world demonstrate our approach's ability to handle noise from perception and control and improve the robot's ability to solve two long-horizon mobile-manipulation tasks after a few hours of autonomous practice.
The ability to understand visual concepts and replicate and compose these concepts from images is a central goal for computer vision. Recent advances in text-to-image (T2I) models have lead to high definition and realistic image quality generation by learning from large databases of images and their descriptions. However, the evaluation of T2I models has focused on photorealism and limited qualitative measures of visual understanding. To quantify the ability of T2I models in learning and synthesizing novel visual concepts (a.k.a. personalized T2I), we introduce ConceptBed, a large-scale dataset that consists of 284 unique visual concepts, and 33K composite text prompts. Along with the dataset, we propose an evaluation metric, Concept Confidence Deviation (CCD), that uses the confidence of oracle concept classifiers to measure the alignment between concepts generated by T2I generators and concepts contained in target images. We evaluate visual concepts that are either objects, attributes, or styles, and also evaluate four dimensions of compositionality: counting, attributes, relations, and actions. Our human study shows that CCD is highly correlated with human understanding of concepts. Our results point to a trade-off between learning the concepts and preserving the compositionality which existing approaches struggle to overcome. The data, code, and interactive demo is available at: //conceptbed.github.io/
Causal Machine Learning (CausalML) is an umbrella term for machine learning methods that formalize the data-generation process as a structural causal model (SCM). This allows one to reason about the effects of changes to this process (i.e., interventions) and what would have happened in hindsight (i.e., counterfactuals). We categorize work in \causalml into five groups according to the problems they tackle: (1) causal supervised learning, (2) causal generative modeling, (3) causal explanations, (4) causal fairness, (5) causal reinforcement learning. For each category, we systematically compare its methods and point out open problems. Further, we review modality-specific applications in computer vision, natural language processing, and graph representation learning. Finally, we provide an overview of causal benchmarks and a critical discussion of the state of this nascent field, including recommendations for future work.
With the capability of modeling bidirectional contexts, denoising autoencoding based pretraining like BERT achieves better performance than pretraining approaches based on autoregressive language modeling. However, relying on corrupting the input with masks, BERT neglects dependency between the masked positions and suffers from a pretrain-finetune discrepancy. In light of these pros and cons, we propose XLNet, a generalized autoregressive pretraining method that (1) enables learning bidirectional contexts by maximizing the expected likelihood over all permutations of the factorization order and (2) overcomes the limitations of BERT thanks to its autoregressive formulation. Furthermore, XLNet integrates ideas from Transformer-XL, the state-of-the-art autoregressive model, into pretraining. Empirically, XLNet outperforms BERT on 20 tasks, often by a large margin, and achieves state-of-the-art results on 18 tasks including question answering, natural language inference, sentiment analysis, and document ranking.
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