A Lesion-aware Edge-based Graph Neural Network for Predicting Language Ability in Patients with Post-stroke Aphasia

We propose a lesion-aware graph neural network (LEGNet) to predict language ability from resting-state fMRI (rs-fMRI) connectivity in patients with post-stroke aphasia. Our model integrates three components: an edge-based learning module that encodes functional connectivity between brain regions, a lesion encoding module, and a subgraph learning module that leverages functional similarities for prediction. We use synthetic data derived from the Human Connectome Project (HCP) for hyperparameter tuning and model pretraining. We then evaluate the performance using repeated 10-fold cross-validation on an in-house neuroimaging dataset of post-stroke aphasia. Our results demonstrate that LEGNet outperforms baseline deep learning methods in predicting language ability. LEGNet also exhibits superior generalization ability when tested on a second in-house dataset that was acquired under a slightly different neuroimaging protocol. Taken together, the results of this study highlight the potential of LEGNet in effectively learning the relationships between rs-fMRI connectivity and language ability in a patient cohort with brain lesions for improved post-stroke aphasia evaluation.

Enhancing Emotion Prediction in News Headlines: Insights from ChatGPT and Seq2Seq Models for Free-Text Generation

Predicting emotions elicited by news headlines can be challenging as the task is largely influenced by the varying nature of people's interpretations and backgrounds. Previous works have explored classifying discrete emotions directly from news headlines. We provide a different approach to tackling this problem by utilizing people's explanations of their emotion, written in free-text, on how they feel after reading a news headline. Using the dataset BU-NEmo+ (Gao et al., 2022), we found that for emotion classification, the free-text explanations have a strong correlation with the dominant emotion elicited by the headlines. The free-text explanations also contain more sentimental context than the news headlines alone and can serve as a better input to emotion classification models. Therefore, in this work we explored generating emotion explanations from headlines by training a sequence-to-sequence transformer model and by using pretrained large language model, ChatGPT (GPT-4). We then used the generated emotion explanations for emotion classification. In addition, we also experimented with training the pretrained T5 model for the intermediate task of explanation generation before fine-tuning it for emotion classification. Using McNemar's significance test, methods that incorporate GPT-generated free-text emotion explanations demonstrated significant improvement (P-value < 0.05) in emotion classification from headlines, compared to methods that only use headlines. This underscores the value of using intermediate free-text explanations for emotion prediction tasks with headlines.

Detecting Frames in News Headlines and Lead Images in U.S. Gun Violence Coverage

News media structure their reporting of events or issues using certain perspectives. When describing an incident involving gun violence, for example, some journalists may focus on mental health or gun regulation, while others may emphasize the discussion of gun rights. Such perspectives are called \say{frames} in communication research. We study, for the first time, the value of combining lead images and their contextual information with text to identify the frame of a given news article. We observe that using multiple modes of information(article- and image-derived features) improves prediction of news frames over any single mode of information when the images are relevant to the frames of the headlines. We also observe that frame image relevance is related to the ease of conveying frames via images, which we call frame concreteness. Additionally, we release the first multimodal news framing dataset related to gun violence in the U.S., curated and annotated by communication researchers. The dataset will allow researchers to further examine the use of multiple information modalities for studying media framing.

BU-CVKit: Extendable Computer Vision Framework for Species Independent Tracking and Analysis

A major bottleneck of interdisciplinary computer vision (CV) research is the lack of a framework that eases the reuse and abstraction of state-of-the-art CV models by CV and non-CV researchers alike. We present here BU-CVKit, a computer vision framework that allows the creation of research pipelines with chainable Processors. The community can create plugins of their work for the framework, hence improving the re-usability, accessibility, and exposure of their work with minimal overhead. Furthermore, we provide MuSeqPose Kit, a user interface for the pose estimation package of BU-CVKit, which automatically scans for installed plugins and programmatically generates an interface for them based on the metadata provided by the user. It also provides software support for standard pose estimation features such as annotations, 3D reconstruction, reprojection, and camera calibration. Finally, we show examples of behavioral neuroscience pipelines created through the sample plugins created for our framework.

Exploring Consistency in Cross-Domain Transformer for Domain Adaptive Semantic Segmentation

While transformers have greatly boosted performance in semantic segmentation, domain adaptive transformers are not yet well explored. We identify that the domain gap can cause discrepancies in self-attention. Due to this gap, the transformer attends to spurious regions or pixels, which deteriorates accuracy on the target domain. We propose to perform adaptation on attention maps with cross-domain attention layers that share features between the source and the target domains. Specifically, we impose consistency between predictions from cross-domain attention and self-attention modules to encourage similar distribution in the attention and output of the model across domains, i.e., attention-level and output-level alignment. We also enforce consistency in attention maps between different augmented views to further strengthen the attention-based alignment. Combining these two components, our method mitigates the discrepancy in attention maps across domains and further boosts the performance of the transformer under unsupervised domain adaptation settings. Our model outperforms the existing state-of-the-art baseline model on three widely used benchmarks, including GTAV-to-Cityscapes by 1.3 percent point (pp), Synthia-to-Cityscapes by 0.6 pp, and Cityscapes-to-ACDC by 1.1 pp, on average. Additionally, we verify the effectiveness and generalizability of our method through extensive experiments. Our code will be publicly available.

A graph-transformer for whole slide image classification

Deep learning is a powerful tool for whole slide image (WSI) analysis. Typically, when performing supervised deep learning, a WSI is divided into small patches, trained and the outcomes are aggregated to estimate disease grade. However, patch-based methods introduce label noise during training by assuming that each patch is independent with the same label as the WSI and neglect overall WSI-level information that is significant in disease grading. Here we present a Graph-Transformer (GT) that fuses a graph-based representation of an WSI and a vision transformer for processing pathology images, called GTP, to predict disease grade. We selected $4,818$ WSIs from the Clinical Proteomic Tumor Analysis Consortium (CPTAC), the National Lung Screening Trial (NLST), and The Cancer Genome Atlas (TCGA), and used GTP to distinguish adenocarcinoma (LUAD) and squamous cell carcinoma (LSCC) from adjacent non-cancerous tissue (normal). First, using NLST data, we developed a contrastive learning framework to generate a feature extractor. This allowed us to compute feature vectors of individual WSI patches, which were used to represent the nodes of the graph followed by construction of the GTP framework. Our model trained on the CPTAC data achieved consistently high performance on three-label classification (normal versus LUAD versus LSCC: mean accuracy$= 91.2$ $\pm$ $2.5\%$) based on five-fold cross-validation, and mean accuracy $= 82.3$ $\pm$ $1.0\%$ on external test data (TCGA). We also introduced a graph-based saliency mapping technique, called GraphCAM, that can identify regions that are highly associated with the class label. Our findings demonstrate GTP as an interpretable and effective deep learning framework for WSI-level classification.

A Unified Framework for Domain Adaptive Pose Estimation

While pose estimation is an important computer vision task, it requires expensive annotation and suffers from domain shift. In this paper, we investigate the problem of domain adaptive 2D pose estimation that transfers knowledge learned on a synthetic source domain to a target domain without supervision. While several domain adaptive pose estimation models have been proposed recently, they are not generic but only focus on either human pose or animal pose estimation, and thus their effectiveness is somewhat limited to specific scenarios. In this work, we propose a unified framework that generalizes well on various domain adaptive pose estimation problems. We propose to align representations using both input-level and output-level cues (pixels and pose labels, respectively), which facilitates the knowledge transfer from the source domain to the unlabeled target domain. Our experiments show that our method achieves state-of-the-art performance under various domain shifts. Our method outperforms existing baselines on human pose estimation by up to 4.5 percent points (pp), hand pose estimation by up to 7.4 pp, and animal pose estimation by up to 4.8 pp for dogs and 3.3 pp for sheep. These results suggest that our method is able to mitigate domain shift on diverse tasks and even unseen domains and objects (e.g., trained on horse and tested on dog).

Consistency Regularization with High-dimensional Non-adversarial Source-guided Perturbation for Unsupervised Domain Adaptation in Segmentation

Unsupervised domain adaptation for semantic segmentation has been intensively studied due to the low cost of the pixel-level annotation for synthetic data. The most common approaches try to generate images or features mimicking the distribution in the target domain while preserving the semantic contents in the source domain so that a model can be trained with annotations from the latter. However, such methods highly rely on an image translator or feature extractor trained in an elaborated mechanism including adversarial training, which brings in extra complexity and instability in the adaptation process. Furthermore, these methods mainly focus on taking advantage of the labeled source dataset, leaving the unlabeled target dataset not fully utilized. In this paper, we propose a bidirectional style-induced domain adaptation method, called BiSIDA, that employs consistency regularization to efficiently exploit information from the unlabeled target domain dataset, requiring only a simple neural style transfer model. BiSIDA aligns domains by not only transferring source images into the style of target images but also transferring target images into the style of source images to perform high-dimensional perturbation on the unlabeled target images, which is crucial to the success in applying consistency regularization in segmentation tasks. Extensive experiments show that our BiSIDA achieves new state-of-the-art on two commonly-used synthetic-to-real domain adaptation benchmarks: GTA5-to-CityScapes and SYNTHIA-to-CityScapes.

OpenFraming: We brought the ML; you bring the data. Interact with your data and discover its frames

When journalists cover a news story, they can cover the story from multiple angles or perspectives. A news article written about COVID-19 for example, might focus on personal preventative actions such as mask-wearing, while another might focus on COVID-19's impact on the economy. These perspectives are called "frames," which when used may influence public perception and opinion of the issue. We introduce a Web-based system for analyzing and classifying frames in text documents. Our goal is to make effective tools for automatic frame discovery and labeling based on topic modeling and deep learning widely accessible to researchers from a diverse array of disciplines. To this end, we provide both state-of-the-art pre-trained frame classification models on various issues as well as a user-friendly pipeline for training novel classification models on user-provided corpora. Researchers can submit their documents and obtain frames of the documents. The degree of user involvement is flexible: they can run models that have been pre-trained on select issues; submit labeled documents and train a new model for frame classification; or submit unlabeled documents and obtain potential frames of the documents. The code making up our system is also open-sourced and well-documented, making the system transparent and expandable. The system is available on-line at http://www.openframing.org and via our GitHub page https://github.com/davidatbu/openFraming .

SIDOD: A Synthetic Image Dataset for 3D Object Pose Recognition with Distractors

We present a new, publicly-available image dataset generated by the NVIDIA Deep Learning Data Synthesizer intended for use in object detection, pose estimation, and tracking applications. This dataset contains 144k stereo image pairs that synthetically combine 18 camera viewpoints of three photorealistic virtual environments with up to 10 objects (chosen randomly from the 21 object models of the YCB dataset [1]) and flying distractors. Object and camera pose, scene lighting, and quantity of objects and distractors were randomized. Each provided view includes RGB, depth, segmentation, and surface normal images, all pixel level. We describe our approach for domain randomization and provide insight into the decisions that produced the dataset.