Linda G. Shapiro

Kalyani Marathe, Mahtab Bigverdi, Nishat Khan et al. · uw

Dense pixel-specific representation learning at scale has been bottlenecked due to the unavailability of large-scale multi-view datasets. Current methods for building effective pretraining datasets heavily rely on annotated 3D meshes, point clouds, and camera parameters from simulated environments, preventing them from building datasets from real-world data sources where such metadata is lacking. We propose a pretraining dataset-curation approach that does not require any additional annotations. Our method allows us to generate multi-view datasets from both real-world videos and simulated environments at scale. Specifically, we experiment with two scales: MIMIC-1M with 1.3M and MIMIC-3M with 3.1M multi-view image pairs. We train multiple models with different masked image modeling objectives to showcase the following findings: Representations trained on our automatically generated MIMIC-3M outperform those learned from expensive crowdsourced datasets (ImageNet-1K) and those learned from synthetic environments (MULTIVIEW-HABITAT) on two dense geometric tasks: depth estimation on NYUv2 (1.7%), and surface normals estimation on Taskonomy (2.05%). For dense tasks which also require object understanding, we outperform MULTIVIEW-HABITAT, on semantic segmentation on ADE20K (3.89%), pose estimation on MSCOCO (9.4%), and reduce the gap with models pre-trained on the object-centric expensive ImageNet-1K. We outperform even when the representations are frozen, and when downstream training data is limited to few-shot. Larger dataset (MIMIC-3M) significantly improves performance, which is promising since our curation method can arbitrarily scale to produce even larger datasets. MIMIC code, dataset, and pretrained models are open-sourced at https://github.com/RAIVNLab/MIMIC.

Wisdom Oluchi Ikezogwo, Mehmet Saygin Seyfioglu, Fatemeh Ghezloo et al. · uw

Recent accelerations in multi-modal applications have been made possible with the plethora of image and text data available online. However, the scarcity of analogous data in the medical field, specifically in histopathology, has slowed comparable progress. To enable similar representation learning for histopathology, we turn to YouTube, an untapped resource of videos, offering $1,087$ hours of valuable educational histopathology videos from expert clinicians. From YouTube, we curate QUILT: a large-scale vision-language dataset consisting of $802, 144$ image and text pairs. QUILT was automatically curated using a mixture of models, including large language models, handcrafted algorithms, human knowledge databases, and automatic speech recognition. In comparison, the most comprehensive datasets curated for histopathology amass only around $200$K samples. We combine QUILT with datasets from other sources, including Twitter, research papers, and the internet in general, to create an even larger dataset: QUILT-1M, with $1$M paired image-text samples, marking it as the largest vision-language histopathology dataset to date. We demonstrate the value of QUILT-1M by fine-tuning a pre-trained CLIP model. Our model outperforms state-of-the-art models on both zero-shot and linear probing tasks for classifying new histopathology images across $13$ diverse patch-level datasets of $8$ different sub-pathologies and cross-modal retrieval tasks.

Mehmet Saygın Seyfioğlu, Zixuan Liu, Pranav Kamath et al. · stanford

We propose a novel framework for Alzheimer's disease (AD) detection using brain MRIs. The framework starts with a data augmentation method called Brain-Aware Replacements (BAR), which leverages a standard brain parcellation to replace medically-relevant 3D brain regions in an anchor MRI from a randomly picked MRI to create synthetic samples. Ground truth "hard" labels are also linearly mixed depending on the replacement ratio in order to create "soft" labels. BAR produces a great variety of realistic-looking synthetic MRIs with higher local variability compared to other mix-based methods, such as CutMix. On top of BAR, we propose using a soft-label-capable supervised contrastive loss, aiming to learn the relative similarity of representations that reflect how mixed are the synthetic MRIs using our soft labels. This way, we do not fully exhaust the entropic capacity of our hard labels, since we only use them to create soft labels and synthetic MRIs through BAR. We show that a model pre-trained using our framework can be further fine-tuned with a cross-entropy loss using the hard labels that were used to create the synthetic samples. We validated the performance of our framework in a binary AD detection task against both from-scratch supervised training and state-of-the-art self-supervised training plus fine-tuning approaches. Then we evaluated BAR's individual performance compared to another mix-based method CutMix by integrating it within our framework. We show that our framework yields superior results in both precision and recall for the AD detection task.

Wisdom Oluchi Ikezogwo, Mehmet Saygin Seyfioglu, Linda Shapiro

Self-supervised learning (SSL) enables learning useful inductive biases through utilizing pretext tasks that require no labels. The unlabeled nature of SSL makes it especially important for whole slide histopathological images (WSIs), where patch-level human annotation is difficult. Masked Autoencoders (MAE) is a recent SSL method suitable for digital pathology as it does not require negative sampling and requires little to no data augmentations. However, the domain shift between natural images and digital pathology images requires further research in designing MAE for patch-level WSIs. In this paper, we investigate several design choices for MAE in histopathology. Furthermore, we introduce a multi-modal MAE (MMAE) that leverages the specific compositionality of Hematoxylin & Eosin (H&E) stained WSIs. We performed our experiments on the public patch-level dataset NCT-CRC-HE-100K. The results show that the MMAE architecture outperforms supervised baselines and other state-of-the-art SSL techniques for an eight-class tissue phenotyping task, utilizing only 100 labeled samples for fine-tuning. Our code is available at https://github.com/wisdomikezogwo/MMAE_Pathology

Mehmet Saygin Seyfioglu, Wisdom O. Ikezogwo, Fatemeh Ghezloo et al.

Diagnosis in histopathology requires a global whole slide images (WSIs) analysis, requiring pathologists to compound evidence from different WSI patches. The gigapixel scale of WSIs poses a challenge for histopathology multi-modal models. Training multi-model models for histopathology requires instruction tuning datasets, which currently contain information for individual image patches, without a spatial grounding of the concepts within each patch and without a wider view of the WSI. Therefore, they lack sufficient diagnostic capacity for histopathology. To bridge this gap, we introduce Quilt-Instruct, a large-scale dataset of 107,131 histopathology-specific instruction question/answer pairs, grounded within diagnostically relevant image patches that make up the WSI. Our dataset is collected by leveraging educational histopathology videos from YouTube, which provides spatial localization of narrations by automatically extracting the narrators' cursor positions. Quilt-Instruct supports contextual reasoning by extracting diagnosis and supporting facts from the entire WSI. Using Quilt-Instruct, we train Quilt-LLaVA, which can reason beyond the given single image patch, enabling diagnostic reasoning across patches. To evaluate Quilt-LLaVA, we propose a comprehensive evaluation dataset created from 985 images and 1283 human-generated question-answers. We also thoroughly evaluate Quilt-LLaVA using public histopathology datasets, where Quilt-LLaVA significantly outperforms SOTA by over 10% on relative GPT-4 score and 4% and 9% on open and closed set VQA. Our code, data, and model are publicly accessible at quilt-llava.github.io.

Zixuan Liu, Hanwen Xu, Addie Woicik et al.

We present OCTCube-M, a 3D OCT-based multi-modal foundation model for jointly analyzing OCT and en face images. OCTCube-M first developed OCTCube, a 3D foundation model pre-trained on 26,685 3D OCT volumes encompassing 1.62 million 2D OCT images. It then exploits a novel multi-modal contrastive learning framework COEP to integrate other retinal imaging modalities, such as fundus autofluorescence and infrared retinal imaging, into OCTCube, efficiently extending it into multi-modal foundation models. OCTCube achieves best performance on predicting 8 retinal diseases, demonstrating strong generalizability on cross-cohort, cross-device and cross-modality prediction. OCTCube can also predict cross-organ nodule malignancy (CT) and low cardiac ejection fraction as well as systemic diseases, such as diabetes and hypertension, revealing its wide applicability beyond retinal diseases. We further develop OCTCube-IR using COEP with 26,685 OCT and IR image pairs. OCTCube-IR can accurately retrieve between OCT and IR images, allowing joint analysis between 3D and 2D retinal imaging modalities. Finally, we trained a tri-modal foundation model OCTCube-EF from 4 million 2D OCT images and 400K en face retinal images. OCTCube-EF attains the best performance on predicting the growth rate of geographic atrophy (GA) across datasets collected from 6 multi-center global trials conducted in 23 countries. This improvement is statistically equivalent to running a clinical trial with more than double the size of the original study. Our analysis based on another retrospective case study reveals OCTCube-EF's ability to avoid false positive Phase-III results according to its accurate treatment effect estimation on the Phase-II results. In sum, OCTCube-M is a 3D multi-modal foundation model framework that integrates OCT and other retinal imaging modalities revealing substantial diagnostic and prognostic benefits.

Rustin Soraki, Huayu Wang, Joann G. Elmore et al.

Cancer survival prediction from whole slide images (WSIs) is a challenging task in computational pathology due to the large size, irregular shape, and high granularity of the WSIs. These characteristics make it difficult to capture the full spectrum of patterns, from subtle cellular abnormalities to complex tissue interactions, which are crucial for accurate prognosis. To address this, we propose CrossFusion, a novel multi-scale feature integration framework that extracts and fuses information from patches across different magnification levels. By effectively modeling both scale-specific patterns and their interactions, CrossFusion generates a rich feature set that enhances survival prediction accuracy. We validate our approach across six cancer types from public datasets, demonstrating significant improvements over existing state-of-the-art methods. Moreover, when coupled with domain-specific feature extraction backbones, our method shows further gains in prognostic performance compared to general-purpose backbones. The source code is available at: https://github.com/RustinS/CrossFusion

Beibin Li, Nicholas Nuechterlein, Erin Barney et al.

Identifying oculomotor behaviors relevant for eye-tracking applications is a critical but often challenging task. Aiming to automatically learn and extract knowledge from existing eye-tracking data, we develop a novel method that creates rich representations of oculomotor scanpaths to facilitate the learning of downstream tasks. The proposed stimulus-agnostic Oculomotor Behavior Framework (OBF) model learns human oculomotor behaviors from unsupervised and semi-supervised tasks, including reconstruction, predictive coding, fixation identification, and contrastive learning tasks. The resultant pre-trained OBF model can be used in a variety of applications. Our pre-trained model outperforms baseline approaches and traditional scanpath methods in autism spectrum disorder and viewed-stimulus classification tasks. Ablation experiments further show our proposed method could achieve even better results with larger model sizes and more diverse eye-tracking training datasets, supporting the model's potential for future eye-tracking applications. Open source code: http://github.com/BeibinLi/OBF.

Sachin Mehta, Ximing Lu, Donald Weaver et al.

Training end-to-end networks for classifying gigapixel size histopathological images is computationally intractable. Most approaches are patch-based and first learn local representations (patch-wise) before combining these local representations to produce image-level decisions. However, dividing large tissue structures into patches limits the context available to these networks, which may reduce their ability to learn representations from clinically relevant structures. In this paper, we introduce a novel attention-based network, the Holistic ATtention Network (HATNet) to classify breast biopsy images. We streamline the histopathological image classification pipeline and show how to learn representations from gigapixel size images end-to-end. HATNet extends the bag-of-words approach and uses self-attention to encode global information, allowing it to learn representations from clinically relevant tissue structures without any explicit supervision. It outperforms the previous best network Y-Net, which uses supervision in the form of tissue-level segmentation masks, by 8%. Importantly, our analysis reveals that HATNet learns representations from clinically relevant structures, and it matches the classification accuracy of human pathologists for this challenging test set. Our source code is available at \url{https://github.com/sacmehta/HATNet}

Sachin Mehta, Mohammad Rastegari, Linda Shapiro et al.

We introduce a light-weight, power efficient, and general purpose convolutional neural network, ESPNetv2, for modeling visual and sequential data. Our network uses group point-wise and depth-wise dilated separable convolutions to learn representations from a large effective receptive field with fewer FLOPs and parameters. The performance of our network is evaluated on four different tasks: (1) object classification, (2) semantic segmentation, (3) object detection, and (4) language modeling. Experiments on these tasks, including image classification on the ImageNet and language modeling on the PenTree bank dataset, demonstrate the superior performance of our method over the state-of-the-art methods. Our network outperforms ESPNet by 4-5% and has 2-4x fewer FLOPs on the PASCAL VOC and the Cityscapes dataset. Compared to YOLOv2 on the MS-COCO object detection, ESPNetv2 delivers 4.4% higher accuracy with 6x fewer FLOPs. Our experiments show that ESPNetv2 is much more power efficient than existing state-of-the-art efficient methods including ShuffleNets and MobileNets. Our code is open-source and available at https://github.com/sacmehta/ESPNetv2

Sachin Mehta, Ezgi Mercan, Jamen Bartlett et al.

In this paper, we introduce a conceptually simple network for generating discriminative tissue-level segmentation masks for the purpose of breast cancer diagnosis. Our method efficiently segments different types of tissues in breast biopsy images while simultaneously predicting a discriminative map for identifying important areas in an image. Our network, Y-Net, extends and generalizes U-Net by adding a parallel branch for discriminative map generation and by supporting convolutional block modularity, which allows the user to adjust network efficiency without altering the network topology. Y-Net delivers state-of-the-art segmentation accuracy while learning 6.6x fewer parameters than its closest competitors. The addition of descriptive power from Y-Net's discriminative segmentation masks improve diagnostic classification accuracy by 7% over state-of-the-art methods for diagnostic classification. Source code is available at: https://sacmehta.github.io/YNet.

Mahtab Bigverdi, Zelun Luo, Cheng-Yu Hsieh et al. · uw

Multimodal language models (MLMs) still face challenges in fundamental visual perception tasks where specialized models excel. Tasks requiring reasoning about 3D structures benefit from depth estimation, and reasoning about 2D object instances benefits from object detection. Yet, MLMs can not produce intermediate depth or boxes to reason over. Finetuning MLMs on relevant data doesn't generalize well and outsourcing computation to specialized vision tools is too compute-intensive and memory-inefficient. To address this, we introduce Perception Tokens, intrinsic image representations designed to assist reasoning tasks where language is insufficient. Perception tokens act as auxiliary reasoning tokens, akin to chain-of-thought prompts in language models. For example, in a depth-related task, an MLM augmented with perception tokens can reason by generating a depth map as tokens, enabling it to solve the problem effectively. We propose AURORA, a training method that augments MLMs with perception tokens for improved reasoning over visual inputs. AURORA leverages a VQVAE to transform intermediate image representations, such as depth maps into a tokenized format and bounding box tokens, which is then used in a multi-task training framework. AURORA achieves notable improvements across counting benchmarks: +10.8% on BLINK, +11.3% on CVBench, and +8.3% on SEED-Bench, outperforming finetuning approaches in generalization across datasets. It also improves on relative depth: over +6% on BLINK. With perception tokens, AURORA expands the scope of MLMs beyond language-based reasoning, paving the way for more effective visual reasoning capabilities.

Fatemeh Ghezloo, Mehmet Saygin Seyfioglu, Rustin Soraki et al.

Diagnosing diseases through histopathology whole slide images (WSIs) is fundamental in modern pathology but is challenged by the gigapixel scale and complexity of WSIs. Trained histopathologists overcome this challenge by navigating the WSI, looking for relevant patches, taking notes, and compiling them to produce a final holistic diagnostic. Traditional AI approaches, such as multiple instance learning and transformer-based models, fail short of such a holistic, iterative, multi-scale diagnostic procedure, limiting their adoption in the real-world. We introduce PathFinder, a multi-modal, multi-agent framework that emulates the decision-making process of expert pathologists. PathFinder integrates four AI agents, the Triage Agent, Navigation Agent, Description Agent, and Diagnosis Agent, that collaboratively navigate WSIs, gather evidence, and provide comprehensive diagnoses with natural language explanations. The Triage Agent classifies the WSI as benign or risky; if risky, the Navigation and Description Agents iteratively focus on significant regions, generating importance maps and descriptive insights of sampled patches. Finally, the Diagnosis Agent synthesizes the findings to determine the patient's diagnostic classification. Our Experiments show that PathFinder outperforms state-of-the-art methods in skin melanoma diagnosis by 8% while offering inherent explainability through natural language descriptions of diagnostically relevant patches. Qualitative analysis by pathologists shows that the Description Agent's outputs are of high quality and comparable to GPT-4o. PathFinder is also the first AI-based system to surpass the average performance of pathologists in this challenging melanoma classification task by 9%, setting a new record for efficient, accurate, and interpretable AI-assisted diagnostics in pathology. Data, code and models available at https://pathfinder-dx.github.io/

Kechun Liu, Wenjun Wu, Joann G. Elmore et al.

Accurate cancer diagnosis remains a critical challenge in digital pathology, largely due to the gigapixel size and complex spatial relationships present in whole slide images. Traditional multiple instance learning (MIL) methods often struggle with these intricacies, especially in preserving the necessary context for accurate diagnosis. In response, we introduce a novel framework named Semantics-Aware Attention Guidance (SAG), which includes 1) a technique for converting diagnostically relevant entities into attention signals, and 2) a flexible attention loss that efficiently integrates various semantically significant information, such as tissue anatomy and cancerous regions. Our experiments on two distinct cancer datasets demonstrate consistent improvements in accuracy, precision, and recall with two state-of-the-art baseline models. Qualitative analysis further reveals that the incorporation of heuristic guidance enables the model to focus on regions critical for diagnosis. SAG is not only effective for the models discussed here, but its adaptability extends to any attention-based diagnostic model. This opens up exciting possibilities for further improving the accuracy and efficiency of cancer diagnostics.

Wisdom O. Ikezogwo, Kevin Zhang, Mehmet Saygin Seyfioglu et al.

We propose MedicalNarratives, a dataset curated from medical pedagogical videos similar in nature to data collected in Think-Aloud studies and inspired by Localized Narratives, which collects grounded image-text data by curating instructors' speech and mouse cursor movements synchronized in time. MedicalNarratives enables pretraining of both semantic and dense objectives, alleviating the need to train medical semantic and dense tasks disparately due to the lack of reasonably sized datasets. Our dataset contains 4.7M image-text pairs from videos and articles, with 1M samples containing dense annotations in the form of traces and bounding boxes. To evaluate the utility of MedicalNarratives, we train GenMedClip based on the CLIP architecture using our dataset spanning 12 medical domains and demonstrate that it outperforms previous state-of-the-art models on a newly constructed medical imaging benchmark that comprehensively evaluates performance across all modalities. Data, demo, code and models available at https://medical-narratives.github.io

Xin Wang, Yin Guo, Kaiyu Zhang et al.

This work presents a novel Bayesian framework for unsupervised domain adaptation (UDA) in medical image segmentation. While prior works have explored this clinically significant task using various strategies of domain alignment, they often lack an explicit and explainable mechanism to ensure that target image features capture meaningful structural information. Besides, these methods are prone to the curse of dimensionality, inevitably leading to challenges in interpretability and computational efficiency. To address these limitations, we propose RemInD, a framework inspired by human adaptation. RemInD learns a domain-agnostic latent manifold, characterized by several anchors, to memorize anatomical variations. By mapping images onto this manifold as weighted anchor averages, our approach ensures realistic and reliable predictions. This design mirrors how humans develop representative components to understand images and then retrieve component combinations from memory to guide segmentation. Notably, model prediction is determined by two explainable factors: a low-dimensional anchor weight vector, and a spatial deformation. This design facilitates computationally efficient and geometry-adherent adaptation by aligning weight vectors between domains on a probability simplex. Experiments on two public datasets, encompassing cardiac and abdominal imaging, demonstrate the superiority of RemInD, which achieves state-of-the-art performance using a single alignment approach, outperforming existing methods that often rely on multiple complex alignment strategies.

Xinzhe Luo, Xin Wang, Linda Shapiro et al.

This article presents a general Bayesian learning framework for multi-modal groupwise image registration. The method builds on probabilistic modelling of the image generative process, where the underlying common anatomy and geometric variations of the observed images are explicitly disentangled as latent variables. Therefore, groupwise image registration is achieved via hierarchical Bayesian inference. We propose a novel hierarchical variational auto-encoding architecture to realise the inference procedure of the latent variables, where the registration parameters can be explicitly estimated in a mathematically interpretable fashion. Remarkably, this new paradigm learns groupwise image registration in an unsupervised closed-loop self-reconstruction process, sparing the burden of designing complex image-based similarity measures. The computationally efficient disentangled network architecture is also inherently scalable and flexible, allowing for groupwise registration on large-scale image groups with variable sizes. Furthermore, the inferred structural representations from multi-modal images via disentanglement learning are capable of capturing the latent anatomy of the observations with visual semantics. Extensive experiments were conducted to validate the proposed framework, including four different datasets from cardiac, brain, and abdominal medical images. The results have demonstrated the superiority of our method over conventional similarity-based approaches in terms of accuracy, efficiency, scalability, and interpretability.

Xin Wang, Yin Guo, Jiamin Xia et al.

Most prior unsupervised domain adaptation approaches for medical image segmentation are narrowly tailored to either the source-accessible setting, where adaptation is guided by source-target alignment, or the source-free setting, which typically resorts to implicit supervision mechanisms such as pseudo-labeling and model distillation. This substantial divergence in methodological designs between the two settings reveals an inherent flaw: the lack of an explicit, structured construction of anatomical knowledge that naturally generalizes across domains and settings. To bridge this longstanding divide, we introduce a unified, semantically grounded framework that supports both source-accessible and source-free adaptation. Fundamentally distinct from all prior works, our framework's adaptability emerges naturally as a direct consequence of the model architecture, without the need for any handcrafted adaptation strategies. Specifically, our model learns a domain-agnostic probabilistic manifold as a global space of anatomical regularities, mirroring how humans establish visual understanding. Thus, the structural content in each image can be interpreted as a canonical anatomy retrieved from the manifold and a spatial transformation capturing individual-specific geometry. This disentangled, interpretable formulation enables semantically meaningful prediction with intrinsic adaptability. Extensive experiments on challenging cardiac and abdominal datasets show that our framework achieves state-of-the-art results in both settings, with source-free performance closely approaching its source-accessible counterpart, a level of consistency rarely observed in prior works. Beyond quantitative improvement, we demonstrate strong interpretability of the proposed framework via manifold traversal for smooth shape manipulation.

Bindita Chaudhuri, Nikolaos Sarafianos, Linda Shapiro et al.

We introduce a novel approach to generate diverse high fidelity texture maps for 3D human meshes in a semi-supervised setup. Given a segmentation mask defining the layout of the semantic regions in the texture map, our network generates high-resolution textures with a variety of styles, that are then used for rendering purposes. To accomplish this task, we propose a Region-adaptive Adversarial Variational AutoEncoder (ReAVAE) that learns the probability distribution of the style of each region individually so that the style of the generated texture can be controlled by sampling from the region-specific distributions. In addition, we introduce a data generation technique to augment our training set with data lifted from single-view RGB inputs. Our training strategy allows the mixing of reference image styles with arbitrary styles for different regions, a property which can be valuable for virtual try-on AR/VR applications. Experimental results show that our method synthesizes better texture maps compared to prior work while enabling independent layout and style controllability.

Beibin Li, Ezgi Mercan, Sachin Mehta et al.

In this study, we propose the Ductal Instance-Oriented Pipeline (DIOP) that contains a duct-level instance segmentation model, a tissue-level semantic segmentation model, and three-levels of features for diagnostic classification. Based on recent advancements in instance segmentation and the Mask R-CNN model, our duct-level segmenter tries to identify each ductal individual inside a microscopic image; then, it extracts tissue-level information from the identified ductal instances. Leveraging three levels of information obtained from these ductal instances and also the histopathology image, the proposed DIOP outperforms previous approaches (both feature-based and CNN-based) in all diagnostic tasks; for the four-way classification task, the DIOP achieves comparable performance to general pathologists in this unique dataset. The proposed DIOP only takes a few seconds to run in the inference time, which could be used interactively on most modern computers. More clinical explorations are needed to study the robustness and generalizability of this system in the future.

Bindita Chaudhuri, Noranart Vesdapunt, Linda Shapiro et al.

Traditional methods for image-based 3D face reconstruction and facial motion retargeting fit a 3D morphable model (3DMM) to the face, which has limited modeling capacity and fail to generalize well to in-the-wild data. Use of deformation transfer or multilinear tensor as a personalized 3DMM for blendshape interpolation does not address the fact that facial expressions result in different local and global skin deformations in different persons. Moreover, existing methods learn a single albedo per user which is not enough to capture the expression-specific skin reflectance variations. We propose an end-to-end framework that jointly learns a personalized face model per user and per-frame facial motion parameters from a large corpus of in-the-wild videos of user expressions. Specifically, we learn user-specific expression blendshapes and dynamic (expression-specific) albedo maps by predicting personalized corrections on top of a 3DMM prior. We introduce novel constraints to ensure that the corrected blendshapes retain their semantic meanings and the reconstructed geometry is disentangled from the albedo. Experimental results show that our personalization accurately captures fine-grained facial dynamics in a wide range of conditions and efficiently decouples the learned face model from facial motion, resulting in more accurate face reconstruction and facial motion retargeting compared to state-of-the-art methods.

Beibin Li, Nicholas Nuechterlein, Erin Barney et al.

In genomic analysis, biomarker discovery, image recognition, and other systems involving machine learning, input variables can often be organized into different groups by their source or semantic category. Eliminating some groups of variables can expedite the process of data acquisition and avoid over-fitting. Researchers have used the group lasso to ensure group sparsity in linear models and have extended it to create compact neural networks in meta-learning. Different from previous studies, we use multi-layer non-linear neural networks to find sparse groups for input variables. We propose a new loss function to regularize parameters for grouped input variables, design a new optimization algorithm for this loss function, and test these methods in three real-world settings. We achieve group sparsity for three datasets, maintaining satisfying results while excluding one nucleotide position from an RNA splicing experiment, excluding 89.9% of stimuli from an eye-tracking experiment, and excluding 60% of image rows from an experiment on the MNIST dataset.

Deepali Aneja, Alex Colburn, Gary Faigin et al.

We present DeepExpr, a novel expression transfer system from humans to multiple stylized characters via deep learning. We developed : 1) a data-driven perceptual model of facial expressions, 2) a novel stylized character data set with cardinal expression annotations : FERG (Facial Expression Research Group) - DB (added two new characters), and 3) . We evaluated our method on a set of retrieval tasks on our collected stylized character dataset of expressions. We have also shown that the ranking order predicted by the proposed features is highly correlated with the ranking order provided by a facial expression expert and Mechanical Turk (MT) experiments.

Beibin Li, Sachin Mehta, Deepali Aneja et al.

In this paper, we introduce an end-to-end machine learning-based system for classifying autism spectrum disorder (ASD) using facial attributes such as expressions, action units, arousal, and valence. Our system classifies ASD using representations of different facial attributes from convolutional neural networks, which are trained on images in the wild. Our experimental results show that different facial attributes used in our system are statistically significant and improve sensitivity, specificity, and F1 score of ASD classification by a large margin. In particular, the addition of different facial attributes improves the performance of ASD classification by about 7% which achieves a F1 score of 76%.

Shu Liang, Xiufeng Huang, Xianyu Meng et al.

Imagine taking a selfie video with your mobile phone and getting as output a 3D model of your head (face and 3D hair strands) that can be later used in VR, AR, and any other domain. State of the art hair reconstruction methods allow either a single photo (thus compromising 3D quality) or multiple views, but they require manual user interaction (manual hair segmentation and capture of fixed camera views that span full 360 degree). In this paper, we describe a system that can completely automatically create a reconstruction from any video (even a selfie video), and we don't require specific views, since taking your -90 degree, 90 degree, and full back views is not feasible in a selfie capture. In the core of our system, in addition to the automatization components, hair strands are estimated and deformed in 3D (rather than 2D as in state of the art) thus enabling superior results. We provide qualitative, quantitative, and Mechanical Turk human studies that support the proposed system, and show results on a diverse variety of videos (8 different celebrity videos, 9 selfie mobile videos, spanning age, gender, hair length, type, and styling).

Shu Liang, Ira Kemelmacher-Shlizerman, Linda G. Shapiro

We present an algorithm that takes a single frame of a person's face from a depth camera, e.g., Kinect, and produces a high-resolution 3D mesh of the input face. We leverage a dataset of 3D face meshes of 1204 distinct individuals ranging from age 3 to 40, captured in a neutral expression. We divide the input depth frame into semantically significant regions (eyes, nose, mouth, cheeks) and search the database for the best matching shape per region. We further combine the input depth frame with the matched database shapes into a single mesh that results in a high-resolution shape of the input person. Our system is fully automatic and uses only depth data for matching, making it invariant to imaging conditions. We evaluate our results using ground truth shapes, as well as compare to state-of-the-art shape estimation methods. We demonstrate the robustness of our local matching approach with high-quality reconstruction of faces that fall outside of the dataset span, e.g., faces older than 40 years old, facial expressions, and different ethnicities.

Shu Liang, Linda G. Shapiro, Ira Kemelmacher-Shlizerman

3D face reconstruction from Internet photos has recently produced exciting results. A person's face, e.g., Tom Hanks, can be modeled and animated in 3D from a completely uncalibrated photo collection. Most methods, however, focus solely on face area and mask out the rest of the head. This paper proposes that head modeling from the Internet is a problem we can solve. We target reconstruction of the rough shape of the head. Our method is to gradually "grow" the head mesh starting from the frontal face and extending to the rest of views using photometric stereo constraints. We call our method boundary-value growing algorithm. Results on photos of celebrities downloaded from the Internet are presented.

Sachin Mehta, Mohammad Rastegari, Anat Caspi et al.

We introduce a fast and efficient convolutional neural network, ESPNet, for semantic segmentation of high resolution images under resource constraints. ESPNet is based on a new convolutional module, efficient spatial pyramid (ESP), which is efficient in terms of computation, memory, and power. ESPNet is 22 times faster (on a standard GPU) and 180 times smaller than the state-of-the-art semantic segmentation network PSPNet, while its category-wise accuracy is only 8% less. We evaluated ESPNet on a variety of semantic segmentation datasets including Cityscapes, PASCAL VOC, and a breast biopsy whole slide image dataset. Under the same constraints on memory and computation, ESPNet outperforms all the current efficient CNN networks such as MobileNet, ShuffleNet, and ENet on both standard metrics and our newly introduced performance metrics that measure efficiency on edge devices. Our network can process high resolution images at a rate of 112 and 9 frames per second on a standard GPU and edge device, respectively.

Sachin Mehta, Hannaneh Hajishirzi, Linda Shapiro

We present an approach for identifying the most walkable direction for navigation using a hand-held camera. Our approach extracts semantically rich contextual information from the scene using a custom encoder-decoder architecture for semantic segmentation and models the spatial and temporal behavior of objects in the scene using a spatio-temporal graph. The system learns to minimize a cost function over the spatial and temporal object attributes to identify the most walkable direction. We construct a new annotated navigation dataset collected using a hand-held mobile camera in an unconstrained outdoor environment, which includes challenging settings such as highly dynamic scenes, occlusion between objects, and distortions. Our system achieves an accuracy of 84% on predicting a safe direction. We also show that our custom segmentation network is both fast and accurate, achieving mIOU (mean intersection over union) scores of 81 and 44.7 on the PASCAL VOC and the PASCAL Context datasets, respectively, while running at about 21 frames per second.

Sachin Mehta, Ezgi Mercan, Jamen Bartlett et al.

We trained and applied an encoder-decoder model to semantically segment breast biopsy images into biologically meaningful tissue labels. Since conventional encoder-decoder networks cannot be applied directly on large biopsy images and the different sized structures in biopsies present novel challenges, we propose four modifications: (1) an input-aware encoding block to compensate for information loss, (2) a new dense connection pattern between encoder and decoder, (3) dense and sparse decoders to combine multi-level features, (4) a multi-resolution network that fuses the results of encoder-decoders run on different resolutions. Our model outperforms a feature-based approach and conventional encoder-decoders from the literature. We use semantic segmentations produced with our model in an automated diagnosis task and obtain higher accuracies than a baseline approach that employs an SVM for feature-based segmentation, both using the same segmentation-based diagnostic features.