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May 13

Assessing Pancreatic Ductal Adenocarcinoma Vascular Invasion: the PDACVI Benchmark

Surgical resection remains the only potentially curative treatment for pancreatic ductal adenocarcinoma (PDAC), and eligibility depends on accurate assessment of vascular invasion (VI), i.e., tumor extension into adjacent critical vessels. Despite its importance for preoperative staging and surgical planning, computational VI assessment remains underexplored. Two major challenges are the lack of public datasets and the diagnostic ambiguity at the tumor-vessel interface, which leads to substantial inter-rater variability even among expert radiologists. To address these limitations, we introduce the CURVAS-PDACVI Dataset and Challenge, an open benchmark for uncertainty-aware AI in PDAC staging based on a densely annotated dataset with five independent expert annotations per scan. We also propose a multi-metric evaluation framework that extends beyond spatial overlap to include probabilistic calibration and VI assessment. Evaluation of six state-of-the-art methods shows that strong global volumetric overlap does not necessarily translate into reliable performance at clinically critical tumor-vessel interfaces. In particular, methods optimized for binary segmentation perform competitively on average overlap metrics, but often degrade in high-complexity cases with low expert consensus, either collapsing in volume or overextending at uncertain boundaries. In contrast, methods that model inter-rater disagreement produce better calibrated probabilistic maps and show greater robustness in these ambiguous cases. The benchmark highlights the limitations of volumetric accuracy as a proxy for localized surgical utility, motivating uncertainty-aware probabilistic models for preoperative decision-making.

  • 26 authors
·
Apr 29 2

Can large language models provide useful feedback on research papers? A large-scale empirical analysis

Expert feedback lays the foundation of rigorous research. However, the rapid growth of scholarly production and intricate knowledge specialization challenge the conventional scientific feedback mechanisms. High-quality peer reviews are increasingly difficult to obtain. Researchers who are more junior or from under-resourced settings have especially hard times getting timely feedback. With the breakthrough of large language models (LLM) such as GPT-4, there is growing interest in using LLMs to generate scientific feedback on research manuscripts. However, the utility of LLM-generated feedback has not been systematically studied. To address this gap, we created an automated pipeline using GPT-4 to provide comments on the full PDFs of scientific papers. We evaluated the quality of GPT-4's feedback through two large-scale studies. We first quantitatively compared GPT-4's generated feedback with human peer reviewer feedback in 15 Nature family journals (3,096 papers in total) and the ICLR machine learning conference (1,709 papers). The overlap in the points raised by GPT-4 and by human reviewers (average overlap 30.85% for Nature journals, 39.23% for ICLR) is comparable to the overlap between two human reviewers (average overlap 28.58% for Nature journals, 35.25% for ICLR). The overlap between GPT-4 and human reviewers is larger for the weaker papers. We then conducted a prospective user study with 308 researchers from 110 US institutions in the field of AI and computational biology to understand how researchers perceive feedback generated by our GPT-4 system on their own papers. Overall, more than half (57.4%) of the users found GPT-4 generated feedback helpful/very helpful and 82.4% found it more beneficial than feedback from at least some human reviewers. While our findings show that LLM-generated feedback can help researchers, we also identify several limitations.

  • 12 authors
·
Oct 3, 2023

AUPIMO: Redefining Visual Anomaly Detection Benchmarks with High Speed and Low Tolerance

Recent advances in visual anomaly detection research have seen AUROC and AUPRO scores on public benchmark datasets such as MVTec and VisA converge towards perfect recall, giving the impression that these benchmarks are near-solved. However, high AUROC and AUPRO scores do not always reflect qualitative performance, which limits the validity of these metrics in real-world applications. We argue that the artificial ceiling imposed by the lack of an adequate evaluation metric restrains progression of the field, and it is crucial that we revisit the evaluation metrics used to rate our algorithms. In response, we introduce Per-IMage Overlap (PIMO), a novel metric that addresses the shortcomings of AUROC and AUPRO. PIMO retains the recall-based nature of the existing metrics but introduces two distinctions: the assignment of curves (and respective area under the curve) is per-image, and its X-axis relies solely on normal images. Measuring recall per image simplifies instance score indexing and is more robust to noisy annotations. As we show, it also accelerates computation and enables the usage of statistical tests to compare models. By imposing low tolerance for false positives on normal images, PIMO provides an enhanced model validation procedure and highlights performance variations across datasets. Our experiments demonstrate that PIMO offers practical advantages and nuanced performance insights that redefine anomaly detection benchmarks -- notably challenging the perception that MVTec AD and VisA datasets have been solved by contemporary models. Available on GitHub: https://github.com/jpcbertoldo/aupimo.

  • 4 authors
·
Jan 3, 2024

Synthesizing Consistent Novel Views via 3D Epipolar Attention without Re-Training

Large diffusion models demonstrate remarkable zero-shot capabilities in novel view synthesis from a single image. However, these models often face challenges in maintaining consistency across novel and reference views. A crucial factor leading to this issue is the limited utilization of contextual information from reference views. Specifically, when there is an overlap in the viewing frustum between two views, it is essential to ensure that the corresponding regions maintain consistency in both geometry and appearance. This observation leads to a simple yet effective approach, where we propose to use epipolar geometry to locate and retrieve overlapping information from the input view. This information is then incorporated into the generation of target views, eliminating the need for training or fine-tuning, as the process requires no learnable parameters. Furthermore, to enhance the overall consistency of generated views, we extend the utilization of epipolar attention to a multi-view setting, allowing retrieval of overlapping information from the input view and other target views. Qualitative and quantitative experimental results demonstrate the effectiveness of our method in significantly improving the consistency of synthesized views without the need for any fine-tuning. Moreover, This enhancement also boosts the performance of downstream applications such as 3D reconstruction. The code is available at https://github.com/botaoye/ConsisSyn.

  • 5 authors
·
Feb 25, 2025

Don't Think It Twice: Exploit Shift Invariance for Efficient Online Streaming Inference of CNNs

Deep learning time-series processing often relies on convolutional neural networks with overlapping windows. This overlap allows the network to produce an output faster than the window length. However, it introduces additional computations. This work explores the potential to optimize computational efficiency during inference by exploiting convolution's shift-invariance properties to skip the calculation of layer activations between successive overlapping windows. Although convolutions are shift-invariant, zero-padding and pooling operations, widely used in such networks, are not efficient and complicate efficient streaming inference. We introduce StreamiNNC, a strategy to deploy Convolutional Neural Networks for online streaming inference. We explore the adverse effects of zero padding and pooling on the accuracy of streaming inference, deriving theoretical error upper bounds for pooling during streaming. We address these limitations by proposing signal padding and pooling alignment and provide guidelines for designing and deploying models for StreamiNNC. We validate our method in simulated data and on three real-world biomedical signal processing applications. StreamiNNC achieves a low deviation between streaming output and normal inference for all three networks (2.03 - 3.55% NRMSE). This work demonstrates that it is possible to linearly speed up the inference of streaming CNNs processing overlapping windows, negating the additional computation typically incurred by overlapping windows.

  • 4 authors
·
Aug 6, 2024

On composition and decomposition operations for vector spaces, graphs and matroids

In this paper, we study the ideas of composition and decomposition in the context of vector spaces, graphs and matroids. For vector spaces V_{AB}, treated as collection of row vectors, with specified column set Auplus B, we define V_{SP}lrarv V_{PQ}, Scap Q= emptyset, to be the collection of all vectors (f_S,f_Q) such that (f_S,f_P)in V_{SP}, (f_P,f_Q)in V_{PQ}. An analogous operation G_{SP}lrarg G_{PQ}equivd G_{PQ} can be defined in relation to graphs G_{SP}, G_{PQ}, on edge sets Suplus P, Puplus Q, respectively in terms of an overlapping subgraph G_P which gets deleted in the right side graph (see for instance the notion of k-sum oxley). For matroids we define the `linking' M_{SP}lrarm M_{PQ} equivd (M_{SP}vee M_{PQ})times (Suplus Q), denoting the contraction operation by 'times'. In each case, we examine how to minimize the size of the `overlap' set P, without affecting the right side entity. In the case of vector spaces, there is a polynomial time algorithm for achieving the minimum, which we present. Similar ideas work for graphs and for matroids under appropriate conditions. Next we consider the problem of decomposition. Here, in the case of vector spaces, the problem is to decompose V_{SQ} as V_{SP}lrarv V_{PQ}, with minimum size P. We give a polynomial time algorithm for this purpose. In the case of graphs and matroids we give a solution to this problem under certain restrictions.

  • 1 authors
·
Jul 13, 2023

Personalized Denoising Implicit Feedback for Robust Recommender System

While implicit feedback is foundational to modern recommender systems, factors such as human error, uncertainty, and ambiguity in user behavior inevitably introduce significant noise into this feedback, adversely affecting the accuracy and robustness of recommendations. To address this issue, existing methods typically aim to reduce the training weight of noisy feedback or discard it entirely, based on the observation that noisy interactions often exhibit higher losses in the overall loss distribution. However, we identify two key issues: (1) there is a significant overlap between normal and noisy interactions in the overall loss distribution, and (2) this overlap becomes even more pronounced when transitioning from pointwise loss functions (e.g., BCE loss) to pairwise loss functions (e.g., BPR loss). This overlap leads traditional methods to misclassify noisy interactions as normal, and vice versa. To tackle these challenges, we further investigate the loss overlap and find that for a given user, there is a clear distinction between normal and noisy interactions in the user's personal loss distribution. Based on this insight, we propose a resampling strategy to Denoise using the user's Personal Loss distribution, named PLD, which reduces the probability of noisy interactions being optimized. Specifically, during each optimization iteration, we create a candidate item pool for each user and resample the items from this pool based on the user's personal loss distribution, prioritizing normal interactions. Additionally, we conduct a theoretical analysis to validate PLD's effectiveness and suggest ways to further enhance its performance. Extensive experiments conducted on three datasets with varying noise ratios demonstrate PLD's efficacy and robustness.

  • 6 authors
·
Feb 1, 2025

RankSEG-RMA: An Efficient Segmentation Algorithm via Reciprocal Moment Approximation

Semantic segmentation labels each pixel in an image with its corresponding class, and is typically evaluated using the Intersection over Union (IoU) and Dice metrics to quantify the overlap between predicted and ground-truth segmentation masks. In the literature, most existing methods estimate pixel-wise class probabilities, then apply argmax or thresholding to obtain the final prediction. These methods have been shown to generally lead to inconsistent or suboptimal results, as they do not directly maximize segmentation metrics. To address this issue, a novel consistent segmentation framework, RankSEG, has been proposed, which includes RankDice and RankIoU specifically designed to optimize the Dice and IoU metrics, respectively. Although RankSEG almost guarantees improved performance, it suffers from two major drawbacks. First, it is its computational expense-RankDice has a complexity of O(d log d) with a substantial constant factor (where d represents the number of pixels), while RankIoU exhibits even higher complexity O(d^2), thus limiting its practical application. For instance, in LiTS, prediction with RankSEG takes 16.33 seconds compared to just 0.01 seconds with the argmax rule. Second, RankSEG is only applicable to overlapping segmentation settings, where multiple classes can occupy the same pixel, which contrasts with standard benchmarks that typically assume non-overlapping segmentation. In this paper, we overcome these two drawbacks via a reciprocal moment approximation (RMA) of RankSEG with the following contributions: (i) we improve RankSEG using RMA, namely RankSEG-RMA, reduces the complexity of both algorithms to O(d) while maintaining comparable performance; (ii) inspired by RMA, we develop a pixel-wise score function that allows efficient implementation for non-overlapping segmentation settings.

  • 2 authors
·
Oct 17, 2025

Excision Score: Evaluating Edits with Surgical Precision

Many tasks revolve around editing a document, whether code or text. We formulate the revision similarity problem to unify a wide range of machine learning evaluation problems whose goal is to assess a revision to an existing document. We observe that revisions usually change only a small portion of an existing document, so the existing document and its immediate revisions share a majority of their content. We formulate five adequacy criteria for revision similarity measures, designed to align them with human judgement. We show that popular pairwise measures, like BLEU, fail to meet these criteria, because their scores are dominated by the shared content. They report high similarity between two revisions when humans would assess them as quite different. This is a fundamental flaw we address. We propose a novel static measure, Excision Score (ES), which computes longest common subsequence (LCS) to remove content shared by an existing document with the ground truth and predicted revisions, before comparing only the remaining divergent regions. This is analogous to a surgeon creating a sterile field to focus on the work area. We use approximation to speed the standard cubic LCS computation to quadratic. In code-editing evaluation, where static measures are often used as a cheap proxy for passing tests, we demonstrate that ES surpasses existing measures. When aligned with test execution on HumanEvalFix, ES improves over its nearest competitor, SARI, by 12% Pearson correlation and by >21% over standard measures like BLEU. The key criterion is invariance to shared context; when we perturb HumanEvalFix with increased shared context, ES' improvement over SARI increases to 20% and >30% over standard measures. ES also handles other corner cases that other measures do not, such as correctly aligning moved code blocks, and appropriately rewarding matching insertions or deletions.

  • 4 authors
·
Oct 24, 2025

Joint Evaluation of Fairness and Relevance in Recommender Systems with Pareto Frontier

Fairness and relevance are two important aspects of recommender systems (RSs). Typically, they are evaluated either (i) separately by individual measures of fairness and relevance, or (ii) jointly using a single measure that accounts for fairness with respect to relevance. However, approach (i) often does not provide a reliable joint estimate of the goodness of the models, as it has two different best models: one for fairness and another for relevance. Approach (ii) is also problematic because these measures tend to be ad-hoc and do not relate well to traditional relevance measures, like NDCG. Motivated by this, we present a new approach for jointly evaluating fairness and relevance in RSs: Distance to Pareto Frontier (DPFR). Given some user-item interaction data, we compute their Pareto frontier for a pair of existing relevance and fairness measures, and then use the distance from the frontier as a measure of the jointly achievable fairness and relevance. Our approach is modular and intuitive as it can be computed with existing measures. Experiments with 4 RS models, 3 re-ranking strategies, and 6 datasets show that existing metrics have inconsistent associations with our Pareto-optimal solution, making DPFR a more robust and theoretically well-founded joint measure for assessing fairness and relevance. Our code: https://github.com/theresiavr/DPFR-recsys-evaluation

  • 4 authors
·
Feb 17, 2025

LABIIUM: AI-Enhanced Zero-configuration Measurement Automation System

The complexity of laboratory environments requires solutions that simplify instrument interaction and enhance measurement automation. Traditional tools often require configuration, software, and programming skills, creating barriers to productivity. Previous approaches, including dedicated software suites and custom scripts, frequently fall short in providing user-friendly solutions that align with programming practices. We present LABIIUM, an AI-enhanced, zero-configuration measurement automation system designed to streamline experimental workflows and improve user productivity. LABIIUM integrates an AI assistant powered by Large Language Models (LLMs) to generate code. LABIIUM's Lab-Automation-Measurement Bridges (LAMBs) enable seamless instrument connectivity using standard tools such as VSCode and Python, eliminating setup overhead. To demonstrate its capabilities, we conducted experiments involving the measurement of the parametric transfer curve of a simple two-transistor inverting amplifier with a current source load. The AI assistant was evaluated using different prompt scenarios and compared with multiple models, including Claude Sonnet 3.5, Gemini Pro 1.5, and GPT-4o. An expert solution implementing the Gradient-Weighted Adaptive Stochastic Sampling (GWASS) method was used as a baseline. The solutions generated by the AI assistant were compared with the expert solution and a uniform linear sweep baseline with 10,000 points. The graph results show that the LLMs were able to successfully complete the most basic uniform sweep, but LLMs were unable to develop adaptive sweeping algorithms to compete with GWASS. The evaluation underscores LABIIUM's ability to enhance laboratory productivity and support digital transformation in research and industry, and emphasizes the future work required to improve LLM performance in Electronic Measurement Science Tasks.

  • 2 authors
·
Dec 6, 2024

SuPRA: Surgical Phase Recognition and Anticipation for Intra-Operative Planning

Intra-operative recognition of surgical phases holds significant potential for enhancing real-time contextual awareness in the operating room. However, we argue that online recognition, while beneficial, primarily lends itself to post-operative video analysis due to its limited direct impact on the actual surgical decisions and actions during ongoing procedures. In contrast, we contend that the prediction and anticipation of surgical phases are inherently more valuable for intra-operative assistance, as they can meaningfully influence a surgeon's immediate and long-term planning by providing foresight into future steps. To address this gap, we propose a dual approach that simultaneously recognises the current surgical phase and predicts upcoming ones, thus offering comprehensive intra-operative assistance and guidance on the expected remaining workflow. Our novel method, Surgical Phase Recognition and Anticipation (SuPRA), leverages past and current information for accurate intra-operative phase recognition while using future segments for phase prediction. This unified approach challenges conventional frameworks that treat these objectives separately. We have validated SuPRA on two reputed datasets, Cholec80 and AutoLaparo21, where it demonstrated state-of-the-art performance with recognition accuracies of 91.8% and 79.3%, respectively. Additionally, we introduce and evaluate our model using new segment-level evaluation metrics, namely Edit and F1 Overlap scores, for a more temporal assessment of segment classification. In conclusion, SuPRA presents a new multi-task approach that paves the way for improved intra-operative assistance through surgical phase recognition and prediction of future events.

  • 5 authors
·
Mar 10, 2024

Red Blood Cell Segmentation with Overlapping Cell Separation and Classification on Imbalanced Dataset

Automated red blood cell (RBC) classification on blood smear images helps hematologists to analyze RBC lab results in a reduced time and cost. However, overlapping cells can cause incorrect predicted results, and so they have to be separated into multiple single RBCs before classifying. To classify multiple classes with deep learning, imbalance problems are common in medical imaging because normal samples are always higher than rare disease samples. This paper presents a new method to segment and classify RBCs from blood smear images, specifically to tackle cell overlapping and data imbalance problems. Focusing on overlapping cell separation, our segmentation process first estimates ellipses to represent RBCs. The method detects the concave points and then finds the ellipses using directed ellipse fitting. The accuracy from 20 blood smear images was 0.889. Classification requires balanced training datasets. However, some RBC types are rare. The imbalance ratio of this dataset was 34.538 for 12 RBC classes from 20,875 individual RBC samples. The use of machine learning for RBC classification with an imbalanced dataset is hence more challenging than many other applications. We analyzed techniques to deal with this problem. The best accuracy and F1-score were 0.921 and 0.8679, respectively, using EfficientNet-B1 with augmentation. Experimental results showed that the weight balancing technique with augmentation had the potential to deal with imbalance problems by improving the F1-score on minority classes, while data augmentation significantly improved the overall classification performance.

  • 5 authors
·
Dec 2, 2020

Machine Translation Meta Evaluation through Translation Accuracy Challenge Sets

Recent machine translation (MT) metrics calibrate their effectiveness by correlating with human judgement but without any insights about their behaviour across different error types. Challenge sets are used to probe specific dimensions of metric behaviour but there are very few such datasets and they either focus on a limited number of phenomena or a limited number of language pairs. We introduce ACES, a contrastive challenge set spanning 146 language pairs, aimed at discovering whether metrics can identify 68 translation accuracy errors. These phenomena range from simple alterations at the word/character level to more complex errors based on discourse and real-world knowledge. We conduct a large-scale study by benchmarking ACES on 50 metrics submitted to the WMT 2022 and 2023 metrics shared tasks. We benchmark metric performance, assess their incremental performance over successive campaigns, and measure their sensitivity to a range of linguistic phenomena. We also investigate claims that Large Language Models (LLMs) are effective as MT evaluators by evaluating on ACES. Our results demonstrate that different metric families struggle with different phenomena and that LLM-based methods fail to demonstrate reliable performance. Our analyses indicate that most metrics ignore the source sentence, tend to prefer surface-level overlap and end up incorporating properties of base models which are not always beneficial. We expand ACES to include error span annotations, denoted as SPAN-ACES and we use this dataset to evaluate span-based error metrics showing these metrics also need considerable improvement. Finally, we provide a set of recommendations for building better MT metrics, including focusing on error labels instead of scores, ensembling, designing strategies to explicitly focus on the source sentence, focusing on semantic content and choosing the right base model for representations.

  • 8 authors
·
Jan 29, 2024