Leveraging Computational Pathology AI for Noninvasive Optical Imaging Analysis Without Retraining

Noninvasive optical imaging modalities can probe patient's tissue in 3D and over time generate gigabytes of clinically relevant data per sample. There is a need for AI models to analyze this data and assist clinical workflow. The lack of expert labelers and the large dataset required (>100,000 images) for model training and tuning are the main hurdles in creating foundation models. In this paper we introduce FoundationShift, a method to apply any AI model from computational pathology without retraining. We show our method is more accurate than state of the art models (SAM, MedSAM, SAM-Med2D, CellProfiler, Hover-Net, PLIP, UNI and ChatGPT), with multiple imaging modalities (OCT and RCM). This is achieved without the need for model retraining or fine-tuning. Applying our method to noninvasive in vivo images could enable physicians to readily incorporate optical imaging modalities into their clinical practice, providing real time tissue analysis and improving patient care.

SpaceJAM: a Lightweight and Regularization-free Method for Fast Joint Alignment of Images

The unsupervised task of Joint Alignment (JA) of images is beset by challenges such as high complexity, geometric distortions, and convergence to poor local or even global optima. Although Vision Transformers (ViT) have recently provided valuable features for JA, they fall short of fully addressing these issues. Consequently, researchers frequently depend on expensive models and numerous regularization terms, resulting in long training times and challenging hyperparameter tuning. We introduce the Spatial Joint Alignment Model (SpaceJAM), a novel approach that addresses the JA task with efficiency and simplicity. SpaceJAM leverages a compact architecture with only 16K trainable parameters and uniquely operates without the need for regularization or atlas maintenance. Evaluations on SPair-71K and CUB datasets demonstrate that SpaceJAM matches the alignment capabilities of existing methods while significantly reducing computational demands and achieving at least a 10x speedup. SpaceJAM sets a new standard for rapid and effective image alignment, making the process more accessible and efficient. Our code is available at: https://bgu-cs-vil.github.io/SpaceJAM/.

Trainable Highly-expressive Activation Functions

Nonlinear activation functions are pivotal to the success of deep neural nets, and choosing the appropriate activation function can significantly affect their performance. Most networks use fixed activation functions (e.g., ReLU, GELU, etc.), and this choice might limit their expressiveness. Furthermore, different layers may benefit from diverse activation functions. Consequently, there has been a growing interest in trainable activation functions. In this paper, we introduce DiTAC, a trainable highly-expressive activation function based on an efficient diffeomorphic transformation (called CPAB). Despite introducing only a negligible number of trainable parameters, DiTAC enhances model expressiveness and performance, often yielding substantial improvements. It also outperforms existing activation functions (regardless whether the latter are fixed or trainable) in tasks such as semantic segmentation, image generation, regression problems, and image classification. Our code is available at https://github.com/BGU-CS-VIL/DiTAC.

Wavelet Convolutions for Large Receptive Fields

In recent years, there have been attempts to increase the kernel size of Convolutional Neural Nets (CNNs) to mimic the global receptive field of Vision Transformers' (ViTs) self-attention blocks. That approach, however, quickly hit an upper bound and saturated way before achieving a global receptive field. In this work, we demonstrate that by leveraging the Wavelet Transform (WT), it is, in fact, possible to obtain very large receptive fields without suffering from over-parameterization, e.g., for a $k \times k$ receptive field, the number of trainable parameters in the proposed method grows only logarithmically with $k$. The proposed layer, named WTConv, can be used as a drop-in replacement in existing architectures, results in an effective multi-frequency response, and scales gracefully with the size of the receptive field. We demonstrate the effectiveness of the WTConv layer within ConvNeXt and MobileNetV2 architectures for image classification, as well as backbones for downstream tasks, and show it yields additional properties such as robustness to image corruption and an increased response to shapes over textures. Our code is available at https://github.com/BGU-CS-VIL/WTConv.

A Deep Moving-camera Background Model

In video analysis, background models have many applications such as background/foreground separation, change detection, anomaly detection, tracking, and more. However, while learning such a model in a video captured by a static camera is a fairly-solved task, in the case of a Moving-camera Background Model (MCBM), the success has been far more modest due to algorithmic and scalability challenges that arise due to the camera motion. Thus, existing MCBMs are limited in their scope and their supported camera-motion types. These hurdles also impeded the employment, in this unsupervised task, of end-to-end solutions based on deep learning (DL). Moreover, existing MCBMs usually model the background either on the domain of a typically-large panoramic image or in an online fashion. Unfortunately, the former creates several problems, including poor scalability, while the latter prevents the recognition and leveraging of cases where the camera revisits previously-seen parts of the scene. This paper proposes a new method, called DeepMCBM, that eliminates all the aforementioned issues and achieves state-of-the-art results. Concretely, first we identify the difficulties associated with joint alignment of video frames in general and in a DL setting in particular. Next, we propose a new strategy for joint alignment that lets us use a spatial transformer net with neither a regularization nor any form of specialized (and non-differentiable) initialization. Coupled with an autoencoder conditioned on unwarped robust central moments (obtained from the joint alignment), this yields an end-to-end regularization-free MCBM that supports a broad range of camera motions and scales gracefully. We demonstrate DeepMCBM's utility on a variety of videos, including ones beyond the scope of other methods. Our code is available at https://github.com/BGU-CS-VIL/DeepMCBM .

CPU- and GPU-based Distributed Sampling in Dirichlet Process Mixtures for Large-scale Analysis

In the realm of unsupervised learning, Bayesian nonparametric mixture models, exemplified by the Dirichlet Process Mixture Model (DPMM), provide a principled approach for adapting the complexity of the model to the data. Such models are particularly useful in clustering tasks where the number of clusters is unknown. Despite their potential and mathematical elegance, however, DPMMs have yet to become a mainstream tool widely adopted by practitioners. This is arguably due to a misconception that these models scale poorly as well as the lack of high-performance (and user-friendly) software tools that can handle large datasets efficiently. In this paper we bridge this practical gap by proposing a new, easy-to-use, statistical software package for scalable DPMM inference. More concretely, we provide efficient and easily-modifiable implementations for high-performance distributed sampling-based inference in DPMMs where the user is free to choose between either a multiple-machine, multiple-core, CPU implementation (written in Julia) and a multiple-stream GPU implementation (written in CUDA/C++). Both the CPU and GPU implementations come with a common (and optional) python wrapper, providing the user with a single point of entry with the same interface. On the algorithmic side, our implementations leverage a leading DPMM sampler from (Chang and Fisher III, 2013). While Chang and Fisher III's implementation (written in MATLAB/C++) used only CPU and was designed for a single multi-core machine, the packages we proposed here distribute the computations efficiently across either multiple multi-core machines or across mutiple GPU streams. This leads to speedups, alleviates memory and storage limitations, and lets us fit DPMMs to significantly larger datasets and of higher dimensionality than was possible previously by either (Chang and Fisher III, 2013) or other DPMM methods.

DeepDPM: Deep Clustering With an Unknown Number of Clusters

Deep Learning (DL) has shown great promise in the unsupervised task of clustering. That said, while in classical (i.e., non-deep) clustering the benefits of the nonparametric approach are well known, most deep-clustering methods are parametric: namely, they require a predefined and fixed number of clusters, denoted by K. When K is unknown, however, using model-selection criteria to choose its optimal value might become computationally expensive, especially in DL as the training process would have to be repeated numerous times. In this work, we bridge this gap by introducing an effective deep-clustering method that does not require knowing the value of K as it infers it during the learning. Using a split/merge framework, a dynamic architecture that adapts to the changing K, and a novel loss, our proposed method outperforms existing nonparametric methods (both classical and deep ones). While the very few existing deep nonparametric methods lack scalability, we demonstrate ours by being the first to report the performance of such a method on ImageNet. We also demonstrate the importance of inferring K by showing how methods that fix it deteriorate in performance when their assumed K value gets further from the ground-truth one, especially on imbalanced datasets. Our code is available at https://github.com/BGU-CS-VIL/DeepDPM.

Common Failure Modes of Subcluster-based Sampling in Dirichlet Process Gaussian Mixture Models -- and a Deep-learning Solution

The Dirichlet Process Gaussian Mixture Model (DPGMM) is often used to cluster data when the number of clusters is unknown. One main DPGMM inference paradigm relies on sampling. Here we consider a known state-of-art sampler (proposed by Chang and Fisher III (2013) and improved by Dinari et al. (2019)), analyze its failure modes, and show how to improve it, often drastically. Concretely, in that sampler, whenever a new cluster is formed it is augmented with two subclusters whose labels are initialized at random. Upon their evolution, the subclusters serve to propose a split of the parent cluster. We show that the random initialization is often problematic and hurts the otherwise-effective sampler. Specifically, we demonstrate that this initialization tends to lead to poor split proposals and/or too many iterations before a desired split is accepted. This slows convergence and can damage the clustering. As a remedy, we propose two drop-in-replacement options for the subcluster-initialization subroutine. The first is an intuitive heuristic while the second is based on deep learning. We show that the proposed approach yields better splits, which in turn translate to substantial improvements in performance, results, and stability.

Sampling in Dirichlet Process Mixture Models for Clustering Streaming Data

Practical tools for clustering streaming data must be fast enough to handle the arrival rate of the observations. Typically, they also must adapt on the fly to possible lack of stationarity; i.e., the data statistics may be time-dependent due to various forms of drifts, changes in the number of clusters, etc. The Dirichlet Process Mixture Model (DPMM), whose Bayesian nonparametric nature allows it to adapt its complexity to the data, seems a natural choice for the streaming-data case. In its classical formulation, however, the DPMM cannot capture common types of drifts in the data statistics. Moreover, and regardless of that limitation, existing methods for online DPMM inference are too slow to handle rapid data streams. In this work we propose adapting both the DPMM and a known DPMM sampling-based non-streaming inference method for streaming-data clustering. We demonstrate the utility of the proposed method on several challenging settings, where it obtains state-of-the-art results while being on par with other methods in terms of speed.

Effective Learning of a GMRF Mixture Model

Learning a Gaussian Mixture Model (GMM) is hard when the number of parameters is too large given the amount of available data. As a remedy, we propose restricting the GMM to a Gaussian Markov Random Field Mixture Model (GMRF-MM), as well as a new method for estimating the latter's sparse precision (i.e., inverse covariance) matrices. When the sparsity pattern of each matrix is known, we propose an efficient optimization method for the Maximum Likelihood Estimate (MLE) of that matrix. When it is unknown, we utilize the popular Graphical LASSO (GLASSO) to estimate that pattern. However, we show that even for a single Gaussian, when GLASSO is tuned to successfully estimate the sparsity pattern, it does so at the price of a substantial bias of the values of the nonzero entries of the matrix, and we show that this problem only worsens in a mixture setting. To overcome this, we discard the non-zero values estimated by GLASSO, keep only its pattern estimate and use it within the proposed MLE method. This yields an effective two-step procedure that removes the bias. We show that our "debiasing" approach outperforms GLASSO in both the single-GMRF and the GMRF-MM cases. We also show that when learning priors for image patches, our method outperforms GLASSO even if we merely use an educated guess about the sparsity pattern, and that our GMRF-MM outperforms the baseline GMM on real and synthetic high-dimensional datasets. Our code is available at \url{https://github.com/shahaffind/GMRF-MM}.