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The FAIR principles for scientific data (Findable, Accessible, Interoperable, Reusable) are also relevant to other digital objects such as research software and scientific workflows that operate on scientific data. The FAIR principles can be applied to the data being handled by a scientific workflow as well as the processes, software, and other infrastructure which are necessary to specify and execute a workflow. The FAIR principles were designed as guidelines, rather than rules, that would allow for differences in standards for different communities and for different degrees of compliance. There are many practical considerations which impact the level of FAIR-ness that can actually be achieved, including policies, traditions, and technologies. Because of these considerations, obstacles are often encountered during the workflow lifecycle that trace directly to shortcomings in the implementation of the FAIR principles. Here, we detail some cases, without naming names, in which data and workflows were Findable but otherwise lacking in areas commonly needed and expected by modern FAIR methods, tools, and users. We describe how some of these problems, all of which were overcome successfully, have motivated us to push on systems and approaches for fully FAIR workflows.

Most of the existing semantic segmentation approaches with image-level class labels as supervision, highly rely on the initial class activation map (CAM) generated from the standard classification network. In this paper, a novel "Progressive Patch Learning" approach is proposed to improve the local details extraction of the classification, producing the CAM better covering the whole object rather than only the most discriminative regions as in CAMs obtained in conventional classification models. "Patch Learning" destructs the feature maps into patches and independently processes each local patch in parallel before the final aggregation. Such a mechanism enforces the network to find weak information from the scattered discriminative local parts, achieving enhanced local details sensitivity. "Progressive Patch Learning" further extends the feature destruction and patch learning to multi-level granularities in a progressive manner. Cooperating with a multi-stage optimization strategy, such a "Progressive Patch Learning" mechanism implicitly provides the model with the feature extraction ability across different locality-granularities. As an alternative to the implicit multi-granularity progressive fusion approach, we additionally propose an explicit method to simultaneously fuse features from different granularities in a single model, further enhancing the CAM quality on the full object coverage. Our proposed method achieves outstanding performance on the PASCAL VOC 2012 dataset e.g., with 69.6$% mIoU on the test set), which surpasses most existing weakly supervised semantic segmentation methods. Code will be made publicly available here //github.com/TyroneLi/PPL_WSSS.

Reconstructing 3D objects from 2D images is both challenging for our brains and machine learning algorithms. To support this spatial reasoning task, contextual information about the overall shape of an object is critical. However, such information is not captured by established loss terms (e.g. Dice loss). We propose to complement geometrical shape information by including multi-scale topological features, such as connected components, cycles, and voids, in the reconstruction loss. Our method uses cubical complexes to calculate topological features of 3D volume data and employs an optimal transport distance to guide the reconstruction process. This topology-aware loss is fully differentiable, computationally efficient, and can be added to any neural network. We demonstrate the utility of our loss by incorporating it into SHAPR, a model for predicting the 3D cell shape of individual cells based on 2D microscopy images. Using a hybrid loss that leverages both geometrical and topological information of single objects to assess their shape, we find that topological information substantially improves the quality of reconstructions, thus highlighting its ability to extract more relevant features from image datasets.

Background: Testing and validation of the semantic correctness of patches provided by tools for Automated Program Repairs (APR) has received a lot of attention. Yet, the eventual acceptance or rejection of suggested patches for real world projects by humans patch reviewers has received a limited attention. Objective: To address this issue, we plan to investigate whether (possibly incorrect) security patches suggested by APR tools are recognized by human reviewers. We also want to investigate whether knowing that a patch was produced by an allegedly specialized tool does change the decision of human reviewers. Method: In the first phase, using a balanced design, we propose to human reviewers a combination of patches proposed by APR tools for different vulnerabilities and ask reviewers to adopt or reject the proposed patches. In the second phase, we tell participants that some of the proposed patches were generated by security specialized tools (even if the tool was actually a `normal' APR tool) and measure whether the human reviewers would change their decision to adopt or reject a patch. Limitations: The experiment will be conducted in an academic setting, and to maintain power, it will focus on a limited sample of popular APR tools and popular vulnerability types.

Forest fires may cause considerable damages both in ecosystems and lives. This proposal describes the application of Internet of Things and wireless sensor networks jointly with multi-hop routing through a real time and dynamic monitoring system for forest fire prevention. It is based on gathering and analyzing information related to meteorological conditions, concentrations of polluting gases and oxygen level around particular interesting forest areas. Unusual measurements of these environmental variables may help to prevent wildfire incidents and make their detection more efficient. A forest fire risk controller based on fuzzy logic has been implemented in order to activate environmental risk alerts through a Web service and a mobile application. For this purpose, security mechanisms have been proposed for ensuring integrity and confidentiality in the transmission of measured environmental information. Lamport's signature and a block cipher algorithm are used to achieve this objective.

This paper presents a statistical model for stationary ergodic point processes, estimated from a single realization observed in a square window. With existing approaches in stochastic geometry, it is very difficult to model processes with complex geometries formed by a large number of particles. Inspired by recent works on gradient descent algorithms for sampling maximum-entropy models, we describe a model that allows for fast sampling of new configurations reproducing the statistics of the given observation. Starting from an initial random configuration, its particles are moved according to the gradient of an energy, in order to match a set of prescribed moments (functionals). Our moments are defined via a phase harmonic operator on the wavelet transform of point patterns. They allow one to capture multi-scale interactions between the particles, while controlling explicitly the number of moments by the scales of the structures to model. We present numerical experiments on point processes with various geometric structures, and assess the quality of the model by spectral and topological data analysis.

We study a patrolling game played on a network $Q$, considered as a metric space. The Attacker chooses a point of $Q$ (not necessarily a node) to attack during a chosen time interval of fixed duration. The Patroller chooses a unit speed path on $Q$ and intercepts the attack (and wins) if she visits the attacked point during the attack time interval. This zero-sum game models the problem of protecting roads or pipelines from an adversarial attack. The payoff to the maximizing Patroller is the probability that the attack is intercepted. Our results include the following: (i) a solution to the game for any network $Q$, as long as the time required to carry out the attack is sufficiently short, (ii) a solution to the game for all tree networks that satisfy a certain condition on their extremities, and (iii) a solution to the game for any attack duration for stars with one long arc and the remaining arcs equal in length. We present a conjecture on the solution of the game for arbitrary trees and establish it in certain cases.

I survey, for a general scientific audience, three decades of research into which sorts of problems admit exponential speedups via quantum computers -- from the classics (like the algorithms of Simon and Shor), to the breakthrough of Yamakawa and Zhandry from April 2022. I discuss both the quantum circuit model, which is what we ultimately care about in practice but where our knowledge is radically incomplete, and the so-called oracle or black-box or query complexity model, where we've managed to achieve a much more thorough understanding that then informs our conjectures about the circuit model. I discuss the strengths and weaknesses of switching attention to sampling tasks, as was done in the recent quantum supremacy experiments. I make some skeptical remarks about widely-repeated claims of exponential quantum speedups for practical machine learning and optimization problems. Through many examples, I try to convey the "law of conservation of weirdness," according to which every problem admitting an exponential quantum speedup must have some unusual property to allow the amplitude to be concentrated on the unknown right answer(s).

In the domain generalization literature, a common objective is to learn representations independent of the domain after conditioning on the class label. We show that this objective is not sufficient: there exist counter-examples where a model fails to generalize to unseen domains even after satisfying class-conditional domain invariance. We formalize this observation through a structural causal model and show the importance of modeling within-class variations for generalization. Specifically, classes contain objects that characterize specific causal features, and domains can be interpreted as interventions on these objects that change non-causal features. We highlight an alternative condition: inputs across domains should have the same representation if they are derived from the same object. Based on this objective, we propose matching-based algorithms when base objects are observed (e.g., through data augmentation) and approximate the objective when objects are not observed (MatchDG). Our simple matching-based algorithms are competitive to prior work on out-of-domain accuracy for rotated MNIST, Fashion-MNIST, PACS, and Chest-Xray datasets. Our method MatchDG also recovers ground-truth object matches: on MNIST and Fashion-MNIST, top-10 matches from MatchDG have over 50% overlap with ground-truth matches.

Clustering is one of the most fundamental and wide-spread techniques in exploratory data analysis. Yet, the basic approach to clustering has not really changed: a practitioner hand-picks a task-specific clustering loss to optimize and fit the given data to reveal the underlying cluster structure. Some types of losses---such as k-means, or its non-linear version: kernelized k-means (centroid based), and DBSCAN (density based)---are popular choices due to their good empirical performance on a range of applications. Although every so often the clustering output using these standard losses fails to reveal the underlying structure, and the practitioner has to custom-design their own variation. In this work we take an intrinsically different approach to clustering: rather than fitting a dataset to a specific clustering loss, we train a recurrent model that learns how to cluster. The model uses as training pairs examples of datasets (as input) and its corresponding cluster identities (as output). By providing multiple types of training datasets as inputs, our model has the ability to generalize well on unseen datasets (new clustering tasks). Our experiments reveal that by training on simple synthetically generated datasets or on existing real datasets, we can achieve better clustering performance on unseen real-world datasets when compared with standard benchmark clustering techniques. Our meta clustering model works well even for small datasets where the usual deep learning models tend to perform worse.