Could the generalized adoption of the COARA principles make administrative research evaluation socially desirable and solve all its problems? The answer to this question is no. To reach this conclusion, two main arguments are discussed. The first characterises COARA as a form of 'technocracy' perfectly consistent with a neo-liberal view of research. The second consists in the adoption of Philip Kitcher's idea of well-ordered science. It is argued that administrative evaluation of research, even if correct on the basis of COARA principles, is at odds with the principles of well-ordered science since it cannot escape neither the tyranny of expertise nor the tyranny of ignorance. These two arguments allow to suggest limiting administrative evaluation to the bare minimum (recruitment of researchers and funding of projects), and to focus attention mainly to the fairness of evaluation procedures.
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Despite that the segment anything model (SAM) achieved impressive results on general-purpose semantic segmentation with strong generalization ability on daily images, its demonstrated performance on medical image segmentation is less precise and not stable, especially when dealing with tumor segmentation tasks that involve objects of small sizes, irregular shapes, and low contrast. Notably, the original SAM architecture is designed for 2D natural images, therefore would not be able to extract the 3D spatial information from volumetric medical data effectively. In this paper, we propose a novel adaptation method for transferring SAM from 2D to 3D for promptable medical image segmentation. Through a holistically designed scheme for architecture modification, we transfer the SAM to support volumetric inputs while retaining the majority of its pre-trained parameters for reuse. The fine-tuning process is conducted in a parameter-efficient manner, wherein most of the pre-trained parameters remain frozen, and only a few lightweight spatial adapters are introduced and tuned. Regardless of the domain gap between natural and medical data and the disparity in the spatial arrangement between 2D and 3D, the transformer trained on natural images can effectively capture the spatial patterns present in volumetric medical images with only lightweight adaptations. We conduct experiments on four open-source tumor segmentation datasets, and with a single click prompt, our model can outperform domain state-of-the-art medical image segmentation models on 3 out of 4 tasks, specifically by 8.25%, 29.87%, and 10.11% for kidney tumor, pancreas tumor, colon cancer segmentation, and achieve similar performance for liver tumor segmentation. We also compare our adaptation method with existing popular adapters, and observed significant performance improvement on most datasets.
The study of associations between an individual's age and imaging and non-imaging data is an active research area that attempts to aid understanding of the effects and patterns of aging. In this work we have conducted a supervoxel-wise association study between both volumetric and tissue density features in coronary computed tomography angiograms and the chronological age of a subject, to understand the localized changes in morphology and tissue density with age. To enable a supervoxel-wise study of volume and tissue density, we developed a novel method based on image segmentation, inter-subject image registration, and robust supervoxel-based correlation analysis, to achieve a statistical association study between the images and age. We evaluate the registration methodology in terms of the Dice coefficient for the heart chambers and myocardium, and the inverse consistency of the transformations, showing that the method works well in most cases with high overlap and inverse consistency. In a sex-stratified study conducted on a subset of $n=1388$ images from the SCAPIS study, the supervoxel-wise analysis was able to find localized associations with age outside of the commonly segmented and analyzed sub-regions, and several substantial differences between the sexes in the association of age and volume.
We formalize a complete proof of the regular case of Fermat's Last Theorem in the Lean4 theorem prover. Our formalization includes a proof of Kummer's lemma, that is the main obstruction to Fermat's Last Theorem for regular primes. Rather than following the modern proof of Kummer's lemma via class field theory, we prove it by using Hilbert's Theorems 90-94 in a way that is more amenable to formalization.
Modern biological research is increasingly data-intensive, leading to a growing demand for effective training in biological data science. In this article, we provide an overview of key resources and best practices available within the Bioconductor project - an open-source software community focused on omics data analysis. This guide serves as a valuable reference for both learners and educators in the field.
Artificial intelligence models trained through loss minimization have demonstrated significant success, grounded in principles from fields like information theory and statistical physics. This work explores these established connections through the lens of statistical mechanics, starting from first-principles sample concentration behaviors that underpin AI and machine learning. Our development of statistical mechanics for modeling highlights the key role of exponential families, and quantities of statistics, physics, and information theory.
Recent advancements in feature representation and dimension reduction have highlighted their crucial role in enhancing the efficacy of predictive modeling. This work introduces TemporalPaD, a novel end-to-end deep learning framework designed for temporal pattern datasets. TemporalPaD integrates reinforcement learning (RL) with neural networks to achieve concurrent feature representation and feature reduction. The framework consists of three cooperative modules: a Policy Module, a Representation Module, and a Classification Module, structured based on the Actor-Critic (AC) framework. The Policy Module, responsible for dimensionality reduction through RL, functions as the actor, while the Representation Module for feature extraction and the Classification Module collectively serve as the critic. We comprehensively evaluate TemporalPaD using 29 UCI datasets, a well-known benchmark for validating feature reduction algorithms, through 10 independent tests and 10-fold cross-validation. Additionally, given that TemporalPaD is specifically designed for time series data, we apply it to a real-world DNA classification problem involving enhancer category and enhancer strength. The results demonstrate that TemporalPaD is an efficient and effective framework for achieving feature reduction, applicable to both structured data and sequence datasets. The source code of the proposed TemporalPaD is freely available as supplementary material to this article and at //www.healthinformaticslab.org/supp/.
This paper studies offline policy learning, which aims at utilizing observations collected a priori (from either fixed or adaptively evolving behavior policies) to learn an optimal individualized decision rule that achieves the best overall outcomes for a given population. Existing policy learning methods rely on a uniform overlap assumption, i.e., the propensities of exploring all actions for all individual characteristics must be lower bounded. As one has no control over the data collection process, this assumption can be unrealistic in many situations, especially when the behavior policies are allowed to evolve over time with diminishing propensities for certain actions. In this paper, we propose Pessimistic Policy Learning (PPL), a new algorithm that optimizes lower confidence bounds (LCBs) -- instead of point estimates -- of the policy values. The LCBs are constructed using knowledge of the behavior policies for collecting the offline data. Without assuming any uniform overlap condition, we establish a data-dependent upper bound for the suboptimality of our algorithm, which only depends on (i) the overlap for the optimal policy, and (ii) the complexity of the policy class we optimize over. As an implication, for adaptively collected data, we ensure efficient policy learning as long as the propensities for optimal actions are lower bounded over time, while those for suboptimal ones are allowed to diminish arbitrarily fast. In our theoretical analysis, we develop a new self-normalized type concentration inequality for inverse-propensity-weighting estimators, generalizing the well-known empirical Bernstein's inequality to unbounded and non-i.i.d. data. We complement our theory with an efficient optimization algorithm via Majorization-Minimization and policy tree search, as well as extensive simulation studies and real-world applications that demonstrate the efficacy of PPL.
We study the decidability and complexity of non-cooperative rational synthesis problem (abbreviated as NCRSP) for some classes of probabilistic strategies. We show that NCRSP for stationary strategies and Muller objectives is in 3-EXPTIME, and if we restrict the strategies of environment players to be positional, NCRSP becomes NEXPSPACE solvable. On the other hand, NCRSP_>, which is a variant of NCRSP, is shown to be undecidable even for pure finite-state strategies and terminal reachability objectives. Finally, we show that NCRSP becomes EXPTIME solvable if we restrict the memory of a strategy to be the most recently visited t vertices where t is linear in the size of the game.
Artificial neural networks thrive in solving the classification problem for a particular rigid task, acquiring knowledge through generalized learning behaviour from a distinct training phase. The resulting network resembles a static entity of knowledge, with endeavours to extend this knowledge without targeting the original task resulting in a catastrophic forgetting. Continual learning shifts this paradigm towards networks that can continually accumulate knowledge over different tasks without the need to retrain from scratch. We focus on task incremental classification, where tasks arrive sequentially and are delineated by clear boundaries. Our main contributions concern 1) a taxonomy and extensive overview of the state-of-the-art, 2) a novel framework to continually determine the stability-plasticity trade-off of the continual learner, 3) a comprehensive experimental comparison of 11 state-of-the-art continual learning methods and 4 baselines. We empirically scrutinize method strengths and weaknesses on three benchmarks, considering Tiny Imagenet and large-scale unbalanced iNaturalist and a sequence of recognition datasets. We study the influence of model capacity, weight decay and dropout regularization, and the order in which the tasks are presented, and qualitatively compare methods in terms of required memory, computation time, and storage.
When and why can a neural network be successfully trained? This article provides an overview of optimization algorithms and theory for training neural networks. First, we discuss the issue of gradient explosion/vanishing and the more general issue of undesirable spectrum, and then discuss practical solutions including careful initialization and normalization methods. Second, we review generic optimization methods used in training neural networks, such as SGD, adaptive gradient methods and distributed methods, and theoretical results for these algorithms. Third, we review existing research on the global issues of neural network training, including results on bad local minima, mode connectivity, lottery ticket hypothesis and infinite-width analysis.
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