Babak Ehteshami Bejnordi

Mahdi S. Hosseini, Babak Ehteshami Bejnordi, Vincent Quoc-Huy Trinh et al.

Computational Pathology CPath is an interdisciplinary science that augments developments of computational approaches to analyze and model medical histopathology images. The main objective for CPath is to develop infrastructure and workflows of digital diagnostics as an assistive CAD system for clinical pathology, facilitating transformational changes in the diagnosis and treatment of cancer that are mainly address by CPath tools. With evergrowing developments in deep learning and computer vision algorithms, and the ease of the data flow from digital pathology, currently CPath is witnessing a paradigm shift. Despite the sheer volume of engineering and scientific works being introduced for cancer image analysis, there is still a considerable gap of adopting and integrating these algorithms in clinical practice. This raises a significant question regarding the direction and trends that are undertaken in CPath. In this article we provide a comprehensive review of more than 800 papers to address the challenges faced in problem design all-the-way to the application and implementation viewpoints. We have catalogued each paper into a model-card by examining the key works and challenges faced to layout the current landscape in CPath. We hope this helps the community to locate relevant works and facilitate understanding of the field's future directions. In a nutshell, we oversee the CPath developments in cycle of stages which are required to be cohesively linked together to address the challenges associated with such multidisciplinary science. We overview this cycle from different perspectives of data-centric, model-centric, and application-centric problems. We finally sketch remaining challenges and provide directions for future technical developments and clinical integration of CPath (https://github.com/AtlasAnalyticsLab/CPath_Survey).

Babak Ehteshami Bejnordi, Amirhossein Habibian, Fatih Porikli et al.

High-resolution images are widely adopted for high-performance object detection in videos. However, processing high-resolution inputs comes with high computation costs, and naive down-sampling of the input to reduce the computation costs quickly degrades the detection performance. In this paper, we propose SALISA, a novel non-uniform SALiency-based Input SAmpling technique for video object detection that allows for heavy down-sampling of unimportant background regions while preserving the fine-grained details of a high-resolution image. The resulting image is spatially smaller, leading to reduced computational costs while enabling a performance comparable to a high-resolution input. To achieve this, we propose a differentiable resampling module based on a thin plate spline spatial transformer network (TPS-STN). This module is regularized by a novel loss to provide an explicit supervision signal to learn to "magnify" salient regions. We report state-of-the-art results in the low compute regime on the ImageNet-VID and UA-DETRAC video object detection datasets. We demonstrate that on both datasets, the mAP of an EfficientDet-D1 (EfficientDet-D2) gets on par with EfficientDet-D2 (EfficientDet-D3) at a much lower computational cost. We also show that SALISA significantly improves the detection of small objects. In particular, SALISA with an EfficientDet-D1 detector improves the detection of small objects by $77\%$, and remarkably also outperforms EfficientDetD3 baseline.

Amelie Royer, Tijmen Blankevoort, Babak Ehteshami Bejnordi

Training a single model on multiple input domains and/or output tasks allows for compressing information from multiple sources into a unified backbone hence improves model efficiency. It also enables potential positive knowledge transfer across tasks/domains, leading to improved accuracy and data-efficient training. However, optimizing such networks is a challenge, in particular due to discrepancies between the different tasks or domains: Despite several hypotheses and solutions proposed over the years, recent work has shown that uniform scalarization training, i.e., simply minimizing the average of the task losses, yields on-par performance with more costly SotA optimization methods. This raises the issue of how well we understand the training dynamics of multi-task and multi-domain networks. In this work, we first devise a large-scale unified analysis of multi-domain and multi-task learning to better understand the dynamics of scalarization across varied task/domain combinations and model sizes. Following these insights, we then propose to leverage population-based training to efficiently search for the optimal scalarization weights when dealing with a large number of tasks or domains.

Jakob Drachmann Havtorn, Amelie Royer, Tijmen Blankevoort et al.

The input tokens to Vision Transformers carry little semantic meaning as they are defined as regular equal-sized patches of the input image, regardless of its content. However, processing uniform background areas of an image should not necessitate as much compute as dense, cluttered areas. To address this issue, we propose a dynamic mixed-scale tokenization scheme for ViT, MSViT. Our method introduces a conditional gating mechanism that selects the optimal token scale for every image region, such that the number of tokens is dynamically determined per input. In addition, to enhance the conditional behavior of the gate during training, we introduce a novel generalization of the batch-shaping loss. We show that our gating module is able to learn meaningful semantics despite operating locally at the coarse patch-level. The proposed gating module is lightweight, agnostic to the choice of transformer backbone, and trained within a few epochs with little training overhead. Furthermore, in contrast to token pruning, MSViT does not lose information about the input, thus can be readily applied for dense tasks. We validate MSViT on the tasks of classification and segmentation where it leads to improved accuracy-complexity trade-off.

Amelie Royer, Ilia Karmanov, Andrii Skliar et al.

Mixture of Experts (MoE) are rising in popularity as a means to train extremely large-scale models, yet allowing for a reasonable computational cost at inference time. Recent state-of-the-art approaches usually assume a large number of experts, and require training all experts jointly, which often lead to training instabilities such as the router collapsing In contrast, in this work, we propose to revisit the simple single-gate MoE, which allows for more practical training. Key to our work are (i) a base model branch acting both as an early-exit and an ensembling regularization scheme, (ii) a simple and efficient asynchronous training pipeline without router collapse issues, and finally (iii) a per-sample clustering-based initialization. We show experimentally that the proposed model obtains efficiency-to-accuracy trade-offs comparable with other more complex MoE, and outperforms non-mixture baselines. This showcases the merits of even a simple single-gate MoE, and motivates further exploration in this area.

Yelysei Bondarenko, Thomas Hehn, Rob Hesselink et al.

Large language models (LLMs) with chain-of-thought reasoning achieve state-of-the-art performance across complex problem-solving tasks, but their verbose reasoning traces and large context requirements make them impractical for edge deployment. These challenges include high token generation costs, large KV-cache footprints, and inefficiencies when distilling reasoning capabilities into smaller models for mobile devices. Existing approaches often rely on distilling reasoning traces from larger models into smaller models, which are verbose and stylistically redundant, undesirable for on-device inference. In this work, we propose a lightweight approach to enable reasoning in small LLMs using LoRA adapters combined with supervised fine-tuning. We further introduce budget forcing via reinforcement learning on these adapters, significantly reducing response length with minimal accuracy loss. To address memory-bound decoding, we exploit parallel test-time scaling, improving accuracy at minor latency increase. Finally, we present a dynamic adapter-switching mechanism that activates reasoning only when needed and a KV-cache sharing strategy during prompt encoding, reducing time-to-first-token for on-device inference. Experiments on Qwen2.5-7B demonstrate that our method achieves efficient, accurate reasoning under strict resource constraints, making LLM reasoning practical for mobile scenarios. Videos demonstrating our solution running on mobile devices are available on our project page.

Ruisi Cai, Yeonju Ro, Geon-Woo Kim et al.

The proliferation of large language models (LLMs) has led to the adoption of Mixture-of-Experts (MoE) architectures that dynamically leverage specialized subnetworks for improved efficiency and performance. Despite their benefits, MoE models face significant challenges during inference, including inefficient memory management and suboptimal batching, due to misaligned design choices between the model architecture and the system policies. Furthermore, the conventional approach of training MoEs from scratch is increasingly prohibitive in terms of cost. In this paper, we propose a novel framework Read-ME that transforms pre-trained dense LLMs into smaller MoE models (in contrast to "upcycling" generalist MoEs), avoiding the high costs of ground-up training. Our approach employs activation sparsity to extract experts. To compose experts, we examine the widely-adopted layer-wise router design and show its redundancy, and thus we introduce the pre-gating router decoupled from the MoE backbone that facilitates system-friendly pre-computing and lookahead scheduling, enhancing expert-aware batching and caching. Our codesign therefore addresses critical gaps on both the algorithmic and system fronts, establishing a scalable and efficient alternative for LLM inference in resource-constrained settings. Read-ME outperforms other popular open-source dense models of similar scales, achieving improvements of up to 10.1% on MMLU, and improving mean end-to-end latency up to 6.1%. Codes are available at: https://github.com/VITA-Group/READ-ME.

Benjamin Bergner, Andrii Skliar, Amelie Royer et al.

Large language models (LLMs) have become ubiquitous in practice and are widely used for generation tasks such as translation, summarization and instruction following. However, their enormous size and reliance on autoregressive decoding increase deployment costs and complicate their use in latency-critical applications. In this work, we propose a hybrid approach that combines language models of different sizes to increase the efficiency of autoregressive decoding while maintaining high performance. Our method utilizes a pretrained frozen LLM that encodes all prompt tokens once in parallel, and uses the resulting representations to condition and guide a small language model (SLM), which then generates the response more efficiently. We investigate the combination of encoder-decoder LLMs with both encoder-decoder and decoder-only SLMs from different model families and only require fine-tuning of the SLM. Experiments with various benchmarks show substantial speedups of up to $4\times$, with minor performance penalties of $1-2\%$ for translation and summarization tasks compared to the LLM.

Andrii Skliar, Ties van Rozendaal, Romain Lepert et al.

Mixture of Experts (MoE) LLMs have recently gained attention for their ability to enhance performance by selectively engaging specialized subnetworks or "experts" for each input. However, deploying MoEs on memory-constrained devices remains challenging, particularly when generating tokens sequentially with a batch size of one, as opposed to typical high-throughput settings involving long sequences or large batches. In this work, we optimize MoE on memory-constrained devices where only a subset of expert weights fit in DRAM. We introduce a novel cache-aware routing strategy that leverages expert reuse during token generation to improve cache locality. We evaluate our approach on language modeling, MMLU, and GSM8K benchmarks and present on-device results demonstrating 2$\times$ speedups on mobile devices, offering a flexible, training-free solution to extend MoE's applicability across real-world applications.

Anna Kuzina, Maciej Pioro, Paul N. Whatmough et al.

Large Language Models (LLMs) excel at multi-step reasoning problems with explicit chain-of-thought (CoT), but verbose traces incur significant computational costs and memory overhead, and often carry redundant, stylistic artifacts. Latent reasoning has emerged as an efficient alternative that internalizes the thought process, but it suffers from a critical lack of supervision, limiting its effectiveness on complex, natural-language reasoning traces. In this work, we propose KaVa, the first framework that bridges this gap by distilling knowledge directly from a compressed KV-cache of the teacher into a latent-reasoning student via self-distillation, leveraging the representational flexibility of continuous latent tokens to align stepwise KV trajectories. We show that the abstract, unstructured knowledge within compressed KV-cache, which lacks direct token correspondence, can serve as a rich supervisory signal for a latent reasoning student. Empirically, the approach consistently outperforms strong latent baselines, exhibits markedly smaller degradation from equation-only to natural-language traces, and scales to larger backbones while preserving efficiency. These results establish compressed KV-cache distillation as a scalable supervision signal for latent reasoning, combining the accuracy of CoT-trained teachers with the efficiency and deployability of latent inference.

Babak Ehteshami Bejnordi, Gaurav Kumar, Amelie Royer et al.

Jointly learning multiple tasks with a unified model can improve accuracy and data efficiency, but it faces the challenge of task interference, where optimizing one task objective may inadvertently compromise the performance of another. A solution to mitigate this issue is to allocate task-specific parameters, free from interference, on top of shared features. However, manually designing such architectures is cumbersome, as practitioners need to balance between the overall performance across all tasks and the higher computational cost induced by the newly added parameters. In this work, we propose \textit{InterroGate}, a novel multi-task learning (MTL) architecture designed to mitigate task interference while optimizing inference computational efficiency. We employ a learnable gating mechanism to automatically balance the shared and task-specific representations while preserving the performance of all tasks. Crucially, the patterns of parameter sharing and specialization dynamically learned during training, become fixed at inference, resulting in a static, optimized MTL architecture. Through extensive empirical evaluations, we demonstrate SoTA results on three MTL benchmarks using convolutional as well as transformer-based backbones on CelebA, NYUD-v2, and PASCAL-Context.

Leyla Mirvakhabova, Babak Ehteshami Bejnordi, Gaurav Kumar et al.

Upcycling pre-trained dense models into sparse Mixture-of-Experts (MoEs) efficiently increases model capacity but often suffers from poor expert specialization due to naive weight replication. Our analysis reveals that upcycled MoEs, even with conventional regularization, exhibit low-confidence, weakly differentiated routing, hindering performance. We introduce Dirichlet-Prior Shaping Loss (DPSL), a novel router regularization technique that directly shapes routing probability distributions by matching expert assignments to a target Dirichlet prior. DPSL offers fine-grained control over expert balance and specialization, and enables encoding of inductive biases such as encouraging experts to focus on specific modalities or tasks, without requiring manual intervention; notably, DPSL is a general tool applicable to any module that outputs categorical probability distributions, extending its utility beyond MoE training. Experiments on upcycled MoE vision-language models (with Qwen2, Phi3, Llama3.2 LLM backbones) show DPSL consistently outperforms upcycling strategies and regularization techniques across standard vision-language benchmarks, addressing the critical issue of poor specialization and fostering more adaptive, higher-performing models.

Amir Ghodrati, Babak Ehteshami Bejnordi, Amirhossein Habibian

In this paper, we propose a conditional early exiting framework for efficient video recognition. While existing works focus on selecting a subset of salient frames to reduce the computation costs, we propose to use a simple sampling strategy combined with conditional early exiting to enable efficient recognition. Our model automatically learns to process fewer frames for simpler videos and more frames for complex ones. To achieve this, we employ a cascade of gating modules to automatically determine the earliest point in processing where an inference is sufficiently reliable. We generate on-the-fly supervision signals to the gates to provide a dynamic trade-off between accuracy and computational cost. Our proposed model outperforms competing methods on three large-scale video benchmarks. In particular, on ActivityNet1.3 and mini-kinetics, we outperform the state-of-the-art efficient video recognition methods with 1.3$\times$ and 2.1$\times$ less GFLOPs, respectively. Additionally, our method sets a new state of the art for efficient video understanding on the HVU benchmark.

Amirhossein Habibian, Davide Abati, Taco S. Cohen et al.

We propose Skip-Convolutions to leverage the large amount of redundancies in video streams and save computations. Each video is represented as a series of changes across frames and network activations, denoted as residuals. We reformulate standard convolution to be efficiently computed on residual frames: each layer is coupled with a binary gate deciding whether a residual is important to the model prediction,~\eg foreground regions, or it can be safely skipped, e.g. background regions. These gates can either be implemented as an efficient network trained jointly with convolution kernels, or can simply skip the residuals based on their magnitude. Gating functions can also incorporate block-wise sparsity structures, as required for efficient implementation on hardware platforms. By replacing all convolutions with Skip-Convolutions in two state-of-the-art architectures, namely EfficientDet and HRNet, we reduce their computational cost consistently by a factor of 3~4x for two different tasks, without any accuracy drop. Extensive comparisons with existing model compression, as well as image and video efficiency methods demonstrate that Skip-Convolutions set a new state-of-the-art by effectively exploiting the temporal redundancies in videos.

Noureldien Hussein, Mihir Jain, Babak Ehteshami Bejnordi

When recognizing a long-range activity, exploring the entire video is exhaustive and computationally expensive, as it can span up to a few minutes. Thus, it is of great importance to sample only the salient parts of the video. We propose TimeGate, along with a novel conditional gating module, for sampling the most representative segments from the long-range activity. TimeGate has two novelties that address the shortcomings of previous sampling methods, as SCSampler. First, it enables a differentiable sampling of segments. Thus, TimeGate can be fitted with modern CNNs and trained end-to-end as a single and unified model.Second, the sampling is conditioned on both the segments and their context. Consequently, TimeGate is better suited for long-range activities, where the importance of a segment heavily depends on the video context.TimeGate reduces the computation of existing CNNs on three benchmarks for long-range activities: Charades, Breakfast and MultiThumos. In particular, TimeGate reduces the computation of I3D by 50% while maintaining the classification accuracy.

Davide Abati, Jakub Tomczak, Tijmen Blankevoort et al.

Convolutional Neural Networks experience catastrophic forgetting when optimized on a sequence of learning problems: as they meet the objective of the current training examples, their performance on previous tasks drops drastically. In this work, we introduce a novel framework to tackle this problem with conditional computation. We equip each convolutional layer with task-specific gating modules, selecting which filters to apply on the given input. This way, we achieve two appealing properties. Firstly, the execution patterns of the gates allow to identify and protect important filters, ensuring no loss in the performance of the model for previously learned tasks. Secondly, by using a sparsity objective, we can promote the selection of a limited set of kernels, allowing to retain sufficient model capacity to digest new tasks.Existing solutions require, at test time, awareness of the task to which each example belongs to. This knowledge, however, may not be available in many practical scenarios. Therefore, we additionally introduce a task classifier that predicts the task label of each example, to deal with settings in which a task oracle is not available. We validate our proposal on four continual learning datasets. Results show that our model consistently outperforms existing methods both in the presence and the absence of a task oracle. Notably, on Split SVHN and Imagenet-50 datasets, our model yields up to 23.98% and 17.42% improvement in accuracy w.r.t. competing methods.

Babak Ehteshami Bejnordi, Tijmen Blankevoort, Max Welling

We present a method that trains large capacity neural networks with significantly improved accuracy and lower dynamic computational cost. We achieve this by gating the deep-learning architecture on a fine-grained-level. Individual convolutional maps are turned on/off conditionally on features in the network. To achieve this, we introduce a new residual block architecture that gates convolutional channels in a fine-grained manner. We also introduce a generally applicable tool $batch$-$shaping$ that matches the marginal aggregate posteriors of features in a neural network to a pre-specified prior distribution. We use this novel technique to force gates to be more conditional on the data. We present results on CIFAR-10 and ImageNet datasets for image classification, and Cityscapes for semantic segmentation. Our results show that our method can slim down large architectures conditionally, such that the average computational cost on the data is on par with a smaller architecture, but with higher accuracy. In particular, on ImageNet, our ResNet50 and ResNet34 gated networks obtain 74.60% and 72.55% top-1 accuracy compared to the 69.76% accuracy of the baseline ResNet18 model, for similar complexity. We also show that the resulting networks automatically learn to use more features for difficult examples and fewer features for simple examples.

Mitko Veta, Yujing J. Heng, Nikolas Stathonikos et al.

Tumor proliferation is an important biomarker indicative of the prognosis of breast cancer patients. Assessment of tumor proliferation in a clinical setting is highly subjective and labor-intensive task. Previous efforts to automate tumor proliferation assessment by image analysis only focused on mitosis detection in predefined tumor regions. However, in a real-world scenario, automatic mitosis detection should be performed in whole-slide images (WSIs) and an automatic method should be able to produce a tumor proliferation score given a WSI as input. To address this, we organized the TUmor Proliferation Assessment Challenge 2016 (TUPAC16) on prediction of tumor proliferation scores from WSIs. The challenge dataset consisted of 500 training and 321 testing breast cancer histopathology WSIs. In order to ensure fair and independent evaluation, only the ground truth for the training dataset was provided to the challenge participants. The first task of the challenge was to predict mitotic scores, i.e., to reproduce the manual method of assessing tumor proliferation by a pathologist. The second task was to predict the gene expression based PAM50 proliferation scores from the WSI. The best performing automatic method for the first task achieved a quadratic-weighted Cohen's kappa score of $κ$ = 0.567, 95% CI [0.464, 0.671] between the predicted scores and the ground truth. For the second task, the predictions of the top method had a Spearman's correlation coefficient of r = 0.617, 95% CI [0.581 0.651] with the ground truth. This was the first study that investigated tumor proliferation assessment from WSIs. The achieved results are promising given the difficulty of the tasks and weakly-labelled nature of the ground truth. However, further research is needed to improve the practical utility of image analysis methods for this task.

Babak Ehteshami Bejnordi, Guido Zuidhof, Maschenka Balkenhol et al.

Automated classification of histopathological whole-slide images (WSI) of breast tissue requires analysis at very high resolutions with a large contextual area. In this paper, we present context-aware stacked convolutional neural networks (CNN) for classification of breast WSIs into normal/benign, ductal carcinoma in situ (DCIS), and invasive ductal carcinoma (IDC). We first train a CNN using high pixel resolution patches to capture cellular level information. The feature responses generated by this model are then fed as input to a second CNN, stacked on top of the first. Training of this stacked architecture with large input patches enables learning of fine-grained (cellular) details and global interdependence of tissue structures. Our system is trained and evaluated on a dataset containing 221 WSIs of H&E stained breast tissue specimens. The system achieves an AUC of 0.962 for the binary classification of non-malignant and malignant slides and obtains a three class accuracy of 81.3% for classification of WSIs into normal/benign, DCIS, and IDC, demonstrating its potentials for routine diagnostics.

Francesco Ciompi, Oscar Geessink, Babak Ehteshami Bejnordi et al.

The development of reliable imaging biomarkers for the analysis of colorectal cancer (CRC) in hematoxylin and eosin (H&E) stained histopathology images requires an accurate and reproducible classification of the main tissue components in the image. In this paper, we propose a system for CRC tissue classification based on convolutional networks (ConvNets). We investigate the importance of stain normalization in tissue classification of CRC tissue samples in H&E-stained images. Furthermore, we report the performance of ConvNets on a cohort of rectal cancer samples and on an independent publicly available dataset of colorectal H&E images.

Babak Ehteshami Bejnordi, Jimmy Linz, Ben Glass et al.

Diagnosis of breast carcinomas has so far been limited to the morphological interpretation of epithelial cells and the assessment of epithelial tissue architecture. Consequently, most of the automated systems have focused on characterizing the epithelial regions of the breast to detect cancer. In this paper, we propose a system for classification of hematoxylin and eosin (H&E) stained breast specimens based on convolutional neural networks that primarily targets the assessment of tumor-associated stroma to diagnose breast cancer patients. We evaluate the performance of our proposed system using a large cohort containing 646 breast tissue biopsies. Our evaluations show that the proposed system achieves an area under ROC of 0.92, demonstrating the discriminative power of previously neglected tumor-associated stroma as a diagnostic biomarker.

Geert Litjens, Thijs Kooi, Babak Ehteshami Bejnordi et al.

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.