arXiv subjects

Aleksei Tiulpin

Publications and source records attributed to Aleksei Tiulpin.

At least 19 recordsLinked to original sources

arXiv2026

Landmark-free Assessment of Lower-limb Alignment with Implicit Neural Shape Functions from Knee Radiographs

Radiographic assessment of lower-limb alignment (LLA) is important for predicting joint health and surgical outcomes in total knee arthroplasty. Traditional measurement methods are manual and time-consuming, while recent machine learning approaches typically rely on locating a fixed set of anatomical landmarks. This dependence limits flexibility and may require re-annotation when clinical definitions change. To address this, we propose an automated workflow using Implicit Neural Shape Functions (INSF). Rather than relying on explicit landmark coordinates, we encode the anatomy into a compact latent space and regress clinical alignment measurements directly from these latent codes. This architecture allows for rapid extendability to new tasks without altering the backbone representation. We trained our method on an internal dataset of 566 knee radiographs, each annotated with the outline of the femur and tibia. We evaluated it on both an internal test dataset of 50 patients and a separate external set of 402 preoperative cases from the MRKR dataset. Manual clinical measurements are available for these data, and the MRKR measurements will be made publicly accessible. Performance was comparable to state-of-the-art landmark-based methods and manual agreement, while offering a flexible shape representation that can be extended to additional measurement tasks.

cs.CV↗

arXiv2026

EchoPrune: Interpreting Redundancy as Temporal Echoes for Efficient VideoLLMs

Long-form video understanding remains challenging for Video Large Language Models (VideoLLMs), as the dense frame sampling introduces massive visual tokens while sparse sampling risks missing critical temporal evidence and leading to LLM hallucination. Existing training-free token reduction methods either treat videos equally as static images or rely on segment-level merging heuristics, which weaken fine-grained spatiotemporal modeling and introduce additional overhead. In this paper, we propose EchoPrune, a lightweight and training-free token pruning method that improves temporal resolution under a fixed LLM-side visual token budget. Our core idea is to interpret redundant video tokens as temporal echoes: if a token is well reconstructed from the previous frame, it is merely a temporally redundant echo; otherwise, it may capture new events, motion, or query-relevant visual evidence. Based on this insight, EchoPrune scores visual tokens by (i) query-guided crossmodal relevance and (ii) temporal reconstruction error, measured by correspondence matching and echo matching across consecutive frames. The selected tokens preserve task-relevant cues and temporal novelty while suppressing predictable redundancy, allowing VideoLLMs to observe more frames without increasing the decoding budget. Extensive experiments on LLaVA-OV, Qwen2.5VL, and Qwen3VL across six video understanding benchmarks show that EchoPrune enables VideoLLMs to process up to 20x frames under the same token budget, yielding improved performance (+8.6%) and inference speedup (5.6x for prefilling) on Qwen2.5VL-7B.

cs.CV↗

arXiv2026

MI-Pruner: Crossmodal Mutual Information-guided Token Pruner for Efficient MLLMs

For multimodal large language models (MLLMs), visual information is relatively sparse compared with text. As a result, research on visual pruning emerges for efficient inference. Current approaches typically measure token importance based on the attention scores in the visual encoder or in the LLM decoder, then select visual tokens with high attention scores while pruning others. In this paper, we pursue a different and more surgical approach. Instead of relying on mechanism-specific signals, we directly compute Mutual Information (MI) between visual and textual features themselves, prior to their interaction. This allows us to explicitly measure crossmodal dependency at the feature levels. Our MI-Pruner is simple, efficient and non-intrusive, requiring no access to internal attention maps or architectural modifications. Experimental results demonstrate that our approach outperforms previous attention-based pruning methods with minimal latency.

cs.CV↗

arXiv2025

The Role of Radiographic Knee Alignment in Total Knee Replacement Outcomes and Opportunities for Artificial Intelligence-Driven Assessment

Knee osteoarthritis (OA) is one of the most widespread and burdensome health problems [1-4]. Total knee replacement (TKR) may be offered as treatment for end-stage knee OA. Nevertheless, TKR is an invasive procedure involving prosthesis implantation at the knee joint, and around 10% of patients are dissatisfied following TKR [5,6]. Dissatisfaction is often assessed through patient-reported outcome measures (PROMs) [7], which are usually completed by patients and assessed by health professionals to evaluate the condition of TKR patients. In clinical practice, predicting poor TKR outcomes in advance could help optimise patient selection and improve management strategies. Radiographic knee alignment is an important biomarker for predicting TKR outcomes and long-term joint health. Abnormalities such as femoral or tibial deformities can directly influence surgical planning, implant selection, and postoperative recovery [8,9]. Traditional alignment measurement is manual, time-consuming, and requires long-leg radiographs, which are not always undertaken in clinical practice. Instead, standard anteroposterior (AP) knee radiographs are often the main imaging modality. Automated methods for alignment assessment in standard knee radiographs are potentially clinically valuable for improving efficiency in the knee OA treatment pathway.

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arXiv2025

SoftCFG: Uncertainty-guided Stable Guidance for Visual Autoregressive Model

Autoregressive (AR) models have emerged as powerful tools for image generation by modeling images as sequences of discrete tokens. While Classifier-Free Guidance (CFG) has been adopted to improve conditional generation, its application in AR models faces two key issues: guidance diminishing, where the conditional-unconditional gap quickly vanishes as decoding progresses, and over-guidance, where strong conditions distort visual coherence. To address these challenges, we propose SoftCFG, an uncertainty-guided inference method that distributes adaptive perturbations across all tokens in the sequence. The key idea behind SoftCFG is to let each generated token contribute certainty-weighted guidance, ensuring that the signal persists across steps while resolving conflicts between text guidance and visual context. To further stabilize long-sequence generation, we introduce Step Normalization, which bounds cumulative perturbations of SoftCFG. Our method is training-free, model-agnostic, and seamlessly integrates with existing AR pipelines. Experiments show that SoftCFG significantly improves image quality over standard CFG and achieves state-of-the-art FID on ImageNet 256*256 among autoregressive models.

cs.CV↗

arXiv2025

Deep Learning-based Alignment Measurement in Knee Radiographs

Radiographic knee alignment (KA) measurement is important for predicting joint health and surgical outcomes after total knee replacement. Traditional methods for KA measurements are manual, time-consuming and require long-leg radiographs. This study proposes a deep learning-based method to measure KA in anteroposterior knee radiographs via automatically localized knee anatomical landmarks. Our method builds on hourglass networks and incorporates an attention gate structure to enhance robustness and focus on key anatomical features. To our knowledge, this is the first deep learning-based method to localize over 100 knee anatomical landmarks to fully outline the knee shape while integrating KA measurements on both pre-operative and post-operative images. It provides highly accurate and reliable anatomical varus/valgus KA measurements using the anatomical tibiofemoral angle, achieving mean absolute differences ~1° when compared to clinical ground truth measurements. Agreement between automated and clinical measurements was excellent pre-operatively (intra-class correlation coefficient (ICC) = 0.97) and good post-operatively (ICC = 0.86). Our findings demonstrate that KA assessment can be automated with high accuracy, creating opportunities for digitally enhanced clinical workflows.

cs.CV↗

arXiv2025

Bayesian Optimization over Bounded Domains with the Beta Product Kernel

Bayesian optimization with Gaussian processes (GP) is commonly used to optimize black-box functions. The Matérn and the Radial Basis Function (RBF) covariance functions are used frequently, but they do not make any assumptions about the domain of the function, which may limit their applicability in bounded domains. To address the limitation, we introduce the Beta kernel, a non-stationary kernel induced by a product of Beta distribution density functions. Such a formulation allows our kernel to naturally model functions on bounded domains. We present statistical evidence supporting the hypothesis that the kernel exhibits an exponential eigendecay rate, based on empirical analyses of its spectral properties across different settings. Our experimental results demonstrate the robustness of the Beta kernel in modeling functions with optima located near the faces or vertices of the unit hypercube. The experiments show that our kernel consistently outperforms a wide range of kernels, including the well-known Matérn and RBF, in different problems, including synthetic function optimization and the compression of vision and language models.

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arXiv2025

CARE: Confidence-aware Ratio Estimation for Medical Biomarkers

Ratio-based biomarkers (RBBs), such as the proportion of necrotic tissue within a tumor, are widely used in clinical practice to support diagnosis, prognosis, and treatment planning. These biomarkers are typically estimated from segmentation outputs by computing region-wise ratios. Despite the high-stakes nature of clinical decision making, existing methods provide only point estimates, offering no measure of uncertainty. In this work, we propose a unified confidence-aware framework for estimating ratio-based biomarkers. Our uncertainty analysis stems from two observations: (1) the probability ratio estimator inherently admits a statistical confidence interval regarding local randomness (bias and variance); (2) the segmentation network is not perfectly calibrated (calibration error).We perform a systematic analysis of error propagation in the segmentation-to-biomarker pipeline and identify model miscalibration as the dominant source of uncertainty. Extensive experiments show that our method produces statistically sound confidence intervals, with tunable confidence levels, enabling more trustworthy application of segmentation-derived RBBs in clinical workflows.

cs.CV↗

arXiv2025

Toward Cost-efficient Adaptive Clinical Trials in Knee Osteoarthritis with Reinforcement Learning

Osteoarthritis (OA) is the most common musculoskeletal disease, with knee OA (KOA) being one of the leading causes of disability and a significant economic burden. Predicting KOA progression is crucial for improving patient outcomes, optimizing healthcare resources, studying the disease, and developing new treatments. The latter application particularly requires one to understand the disease progression in order to collect the most informative data at the right time. Existing methods, however, are limited by their static nature and their focus on individual joints, leading to suboptimal predictive performance and downstream utility. Our study proposes a new method that allows to dynamically monitor patients rather than individual joints with KOA using a novel Active Sensing (AS) approach powered by Reinforcement Learning (RL). Our key idea is to directly optimize for the downstream task by training an agent that maximizes informative data collection while minimizing overall costs. Our RL-based method leverages a specially designed reward function to monitor disease progression across multiple body parts, employs multimodal deep learning, and requires no human input during testing. Extensive numerical experiments demonstrate that our approach outperforms current state-of-the-art models, paving the way for the next generation of KOA trials.

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arXiv2024

LoG-VMamba: Local-Global Vision Mamba for Medical Image Segmentation

Mamba, a State Space Model (SSM), has recently shown competitive performance to Convolutional Neural Networks (CNNs) and Transformers in Natural Language Processing and general sequence modeling. Various attempts have been made to adapt Mamba to Computer Vision tasks, including medical image segmentation (MIS). Vision Mamba (VM)-based networks are particularly attractive due to their ability to achieve global receptive fields, similar to Vision Transformers, while also maintaining linear complexity in the number of tokens. However, the existing VM models still struggle to maintain both spatially local and global dependencies of tokens in high dimensional arrays due to their sequential nature. Employing multiple and/or complicated scanning strategies is computationally costly, which hinders applications of SSMs to high-dimensional 2D and 3D images that are common in MIS problems. In this work, we propose Local-Global Vision Mamba, LoG-VMamba, that explicitly enforces spatially adjacent tokens to remain nearby on the channel axis, and retains the global context in a compressed form. Our method allows the SSMs to access the local and global contexts even before reaching the last token while requiring only a simple scanning strategy. Our segmentation models are computationally efficient and substantially outperform both CNN and Transformers-based baselines on a diverse set of 2D and 3D MIS tasks. The implementation of LoG-VMamba is available at \url{https://github.com/Oulu-IMEDS/LoG-VMamba}.

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arXiv2024

SiNGR: Brain Tumor Segmentation via Signed Normalized Geodesic Transform Regression

One of the primary challenges in brain tumor segmentation arises from the uncertainty of voxels close to tumor boundaries. However, the conventional process of generating ground truth segmentation masks fails to treat such uncertainties properly. Those "hard labels" with 0s and 1s conceptually influenced the majority of prior studies on brain image segmentation. As a result, tumor segmentation is often solved through voxel classification. In this work, we instead view this problem as a voxel-level regression, where the ground truth represents a certainty mapping from any pixel to the border of the tumor. We propose a novel ground truth label transformation, which is based on a signed geodesic transform, to capture the uncertainty in brain tumors' vicinity. We combine this idea with a Focal-like regression L1-loss that enables effective regression learning in high-dimensional output space by appropriately weighting voxels according to their difficulty. We thoroughly conduct an experimental evaluation to validate the components of our proposed method, compare it to a diverse array of state-of-the-art segmentation models, and show that it is architecture-agnostic. The code of our method is made publicly available (\url{https://github.com/Oulu-IMEDS/SiNGR/}).

cs.CV↗

arXiv2024

Image-level Regression for Uncertainty-aware Retinal Image Segmentation

Accurate retinal vessel (RV) segmentation is a crucial step in the quantitative assessment of retinal vasculature, which is needed for the early detection of retinal diseases and other conditions. Numerous studies have been conducted to tackle the problem of segmenting vessels automatically using a pixel-wise classification approach. The common practice of creating ground truth labels is to categorize pixels as foreground and background. This approach is, however, biased, and it ignores the uncertainty of a human annotator when it comes to annotating e.g. thin vessels. In this work, we propose a simple and effective method that casts the RV segmentation task as an image-level regression. For this purpose, we first introduce a novel Segmentation Annotation Uncertainty-Aware (SAUNA) transform, which adds pixel uncertainty to the ground truth using the pixel's closeness to the annotation boundary and vessel thickness. To train our model with soft labels, we generalize the earlier proposed Jaccard metric loss to arbitrary hypercubes for soft Jaccard index (Intersection-over-Union) optimization. Additionally, we employ a stable version of the Focal-L1 loss for pixel-wise regression. We conduct thorough experiments and compare our method to a diverse set of baselines across 5 retinal image datasets. Our empirical results indicate that the integration of the SAUNA transform and these segmentation losses led to significant performance boosts for different segmentation models. Particularly, our methodology enables UNet-like architectures to substantially outperform computational-intensive baselines. Our implementation is available at \url{https://github.com/Oulu-IMEDS/SAUNA}.

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arXiv2024

Understanding metric-related pitfalls in image analysis validation

Validation metrics are key for the reliable tracking of scientific progress and for bridging the current chasm between artificial intelligence (AI) research and its translation into practice. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately in relation to the underlying research problem. This could be attributed to a lack of accessibility of metric-related knowledge: While taking into account the individual strengths, weaknesses, and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. Focusing on biomedical image analysis but with the potential of transfer to other fields, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. To facilitate comprehension, illustrations and specific examples accompany each pitfall. As a structured body of information accessible to researchers of all levels of expertise, this work enhances global comprehension of a key topic in image analysis validation.

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arXiv2024

Metrics reloaded: Recommendations for image analysis validation

Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. Particularly in automatic biomedical image analysis, chosen performance metrics often do not reflect the domain interest, thus failing to adequately measure scientific progress and hindering translation of ML techniques into practice. To overcome this, our large international expert consortium created Metrics Reloaded, a comprehensive framework guiding researchers in the problem-aware selection of metrics. Following the convergence of ML methodology across application domains, Metrics Reloaded fosters the convergence of validation methodology. The framework was developed in a multi-stage Delphi process and is based on the novel concept of a problem fingerprint - a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), data set and algorithm output. Based on the problem fingerprint, users are guided through the process of choosing and applying appropriate validation metrics while being made aware of potential pitfalls. Metrics Reloaded targets image analysis problems that can be interpreted as a classification task at image, object or pixel level, namely image-level classification, object detection, semantic segmentation, and instance segmentation tasks. To improve the user experience, we implemented the framework in the Metrics Reloaded online tool, which also provides a point of access to explore weaknesses, strengths and specific recommendations for the most common validation metrics. The broad applicability of our framework across domains is demonstrated by an instantiation for various biological and medical image analysis use cases.

cs.CV↗

arXiv2023

Consistent and Asymptotically Unbiased Estimation of Proper Calibration Errors

Proper scoring rules evaluate the quality of probabilistic predictions, playing an essential role in the pursuit of accurate and well-calibrated models. Every proper score decomposes into two fundamental components -- proper calibration error and refinement -- utilizing a Bregman divergence. While uncertainty calibration has gained significant attention, current literature lacks a general estimator for these quantities with known statistical properties. To address this gap, we propose a method that allows consistent, and asymptotically unbiased estimation of all proper calibration errors and refinement terms. In particular, we introduce Kullback--Leibler calibration error, induced by the commonly used cross-entropy loss. As part of our results, we prove the relation between refinement and f-divergences, which implies information monotonicity in neural networks, regardless of which proper scoring rule is optimized. Our experiments validate empirically the claimed properties of the proposed estimator and suggest that the selection of a post-hoc calibration method should be determined by the particular calibration error of interest.

cs.LG↗

arXiv2023

Beyond Classification: Definition and Density-based Estimation of Calibration in Object Detection

Despite their impressive predictive performance in various computer vision tasks, deep neural networks (DNNs) tend to make overly confident predictions, which hinders their widespread use in safety-critical applications. While there have been recent attempts to calibrate DNNs, most of these efforts have primarily been focused on classification tasks, thus neglecting DNN-based object detectors. Although several recent works addressed calibration for object detection and proposed differentiable penalties, none of them are consistent estimators of established concepts in calibration. In this work, we tackle the challenge of defining and estimating calibration error specifically for this task. In particular, we adapt the definition of classification calibration error to handle the nuances associated with object detection, and predictions in structured output spaces more generally. Furthermore, we propose a consistent and differentiable estimator of the detection calibration error, utilizing kernel density estimation. Our experiments demonstrate the effectiveness of our estimator against competing train-time and post-hoc calibration methods, while maintaining similar detection performance.

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arXiv2023

Common Limitations of Image Processing Metrics: A Picture Story

While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation. Performance metrics are particularly key for meaningful, objective, and transparent performance assessment and validation of the used automatic algorithms, but relatively little attention has been given to the practical pitfalls when using specific metrics for a given image analysis task. These are typically related to (1) the disregard of inherent metric properties, such as the behaviour in the presence of class imbalance or small target structures, (2) the disregard of inherent data set properties, such as the non-independence of the test cases, and (3) the disregard of the actual biomedical domain interest that the metrics should reflect. This living dynamically document has the purpose to illustrate important limitations of performance metrics commonly applied in the field of image analysis. In this context, it focuses on biomedical image analysis problems that can be phrased as image-level classification, semantic segmentation, instance segmentation, or object detection task. The current version is based on a Delphi process on metrics conducted by an international consortium of image analysis experts from more than 60 institutions worldwide.

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arXiv2023

Clinically-Inspired Multi-Agent Transformers for Disease Trajectory Forecasting from Multimodal Data

Deep neural networks are often applied to medical images to automate the problem of medical diagnosis. However, a more clinically relevant question that practitioners usually face is how to predict the future trajectory of a disease. Current methods for prognosis or disease trajectory forecasting often require domain knowledge and are complicated to apply. In this paper, we formulate the prognosis prediction problem as a one-to-many prediction problem. Inspired by a clinical decision-making process with two agents -- a radiologist and a general practitioner -- we predict prognosis with two transformer-based components that share information with each other. The first transformer in this framework aims to analyze the imaging data, and the second one leverages its internal states as inputs, also fusing them with auxiliary clinical data. The temporal nature of the problem is modeled within the transformer states, allowing us to treat the forecasting problem as a multi-task classification, for which we propose a novel loss. We show the effectiveness of our approach in predicting the development of structural knee osteoarthritis changes and forecasting Alzheimer's disease clinical status directly from raw multi-modal data. The proposed method outperforms multiple state-of-the-art baselines with respect to performance and calibration, both of which are needed for real-world applications. An open-source implementation of our method is made publicly available at \url{https://github.com/Oulu-IMEDS/CLIMATv2}.

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