Publications

In this paper, we address the problem of generating person images conditioned on both pose and appearance information. Specifically, given an image xa of a person and a target pose P(xb), extracted from an image xb, we synthesize a new image of that person in pose P(xb), while preserving the visual details in xa. In order to deal with pixel-to-pixel misalignments caused by the pose differences between P(xa) and P(xb), we introduce deformable skip connections in the generator of our Generative Adversarial Network. Moreover, a nearest-neighbour loss is proposed instead of the common L1 and L2 losses in order to match the details of the generated image with the target image. Quantitative and qualitative results, using common datasets and protocols recently proposed for this task, show that our approach is competitive with respect to the state of the art. Moreover, we conduct an extensive evaluation using off-the-shell person re-identification (Re-ID) systems trained with person-generation based augmented data, which is one of themain important applications for this task. Our experiments show that our Deformable GANs can significantly boost the Re-ID accuracy and are even better than data-augmentation methods specifically trained using Re-ID losses.

Background: Tumors are composed by a number of cancer cell subpopulations (subclones), characterized by a distinguishable set of mutations. This phenomenon, known as intra-tumor heterogeneity (ITH), may be studied using Copy Number Aberrations (CNAs). Nowadays ITH can be assessed at the highest possible resolution using single-cell DNA (scDNA) sequencing technology. Additionally, single-cell CNA (scCNA) profiles from multiple samples of the same tumor can in principle be exploited to study the spatial distribution of subclones within a tumor mass. However, since the technology required to generate large scDNA sequencing datasets is relatively recent, dedicated analytical approaches are still lacking. Results: We present PhyliCS, the first tool which exploits scCNA data from multiple samples from the same tumor to estimate whether the different clones of a tumor are well mixed or spatially separated. Starting from the CNA data produced with third party instruments, it computes a score, the Spatial Heterogeneity score, aimed at distinguishing spatially intermixed cell populations from spatially segregated ones. Additionally, it provides functionalities to facilitate scDNA analysis, such as feature selection and dimensionality reduction methods, visualization tools and a flexible clustering module. Conclusions: PhyliCS represents a valuable instrument to explore the extent of spatial heterogeneity in multi-regional tumour sampling, exploiting the potential of scCNA data.

Hashing methods have recently been shown to be very effective in the retrieval of remote sensing (RS) images due to their computational efficiency and fast search speed. Common hashing methods in RS are based on hand-crafted features on top of which they learn a hash function, which provides the final binary codes. However, these features are not optimized for the final task (i.e., retrieval using binary codes). On the other hand, modern deep neural networks (DNNs) have shown an impressive success in learning optimized features for a specific task in an end-to-end fashion. Unfortunately, typical RS data sets are composed of only a small number of labeled samples, which make the training (or fine-tuning) of big DNNs problematic and prone to overfitting. To address this problem, in this letter, we introduce a metric-learning-based hashing network, which: 1) implicitly uses a big, pretrained DNN as an intermediate representation step without the need of retraining or fine-tuning; 2) learns a semantic-based metric space where the features are optimized for the target retrieval task; and 3) computes compact binary hash codes for fast search. Experiments carried out on two RS benchmarks highlight that the proposed network significantly improves the retrieval performance under the same retrieval time when compared to the state-of-the-art hashing methods in RS.

Recurrent Neural Networks with Long Short-Term Memory (LSTM) make use of gating mechanisms to mitigate exploding and vanishing gradients when learning long-term dependencies. For this reason, LSTMs and other gated RNNs are widely adopted, being the standard de facto for many sequence modeling tasks. Although the memory cell inside the LSTM contains essential information, it is not allowed to influence the gating mechanism directly. In this work, we improve the gate potential by including information coming from the internal cell state. The proposed modification, named Working Memory Connection, consists in adding a learnable nonlinear projection of the cell content into the network gates. This modification can fit into the classical LSTM gates without any assumption on the underlying task, being particularly effective when dealing with longer sequences. Previous research effort in this direction, which goes back to the early 2000s, could not bring a consistent improvement over vanilla LSTM. As part of this paper, we identify a key issue tied to previous connections that heavily limits their effectiveness, hence preventing a successful integration of the knowledge coming from the internal cell state. We show through extensive experimental evaluation that Working Memory Connections constantly improve the performance of LSTMs on a variety of tasks. Numerical results suggest that the cell state contains useful information that is worth including in the gate structure.

The problem of labeling the connected components of a binary image is well-defined and several proposals have been presented in the past. Since an exact solution to the problem exists, algorithms mainly differ on their execution speed. In this paper, we propose and describe YACCLAB, Yet Another Connected Components Labeling Benchmark. Together with a rich and varied dataset, YACCLAB contains an open source platform to test new proposals and to compare them with publicly available competitors. Textual and graphical outputs are automatically generated for many kinds of tests, which analyze the methods from different perspectives. An extensive set of experiments among state-of-the-art techniques is reported and discussed.

Dorsal root ganglia (DRGs) host the somata of sensory neurons which convey information from the periphery to the central nervous system. These neurons have heterogeneous size and neurochemistry, and those of small-to-medium size, which play an important role in nociception, form two distinct subpopulations based on the presence (peptidergic) or absence (non-peptidergic) of transmitter neuropeptides. Few investigations have so far addressed the spatial relationship between neurochemically different subpopulations of DRG neurons and glia. We used a whole-mount mouse lumbar DRG preparation, confocal microscopy and computer-aided 3D analysis to unveil that IB4+ non-peptidergic neurons form small clusters of 4.7 ± 0.26 cells, differently from CGRP+ peptidergic neurons that are, for the most, isolated (1.89 ± 0.11 cells). Both subpopulations of neurons are ensheathed by a thin layer of satellite glial cells (SGCs) that can be observed after immunolabeling with the specific marker glutamine synthetase (GS). Notably, at the ultrastructural level we observed that this glial layer was discontinuous, as there were patches of direct contact between the membranes of two adjacent IB4+ neurons. To test whether this cytoarchitectonic organization was modified in the diabetic neuropathy, one of the most devastating sensory pathologies, mice were made diabetic by streptozotocin (STZ). In diabetic animals, cluster organization of the IB4+ non-peptidergic neurons was maintained, but the neuro-glial relationship was altered, as STZ treatment caused a statistically significant increase of GS staining around CGRP+ neurons but a reduction around IB4+ neurons. Ultrastructural analysis unveiled that SGC coverage was increased at the interface between IB4+ cluster-forming neurons in diabetic mice, with a 50% reduction in the points of direct contacts between cells. These observations demonstrate the existence of a structural plasticity of the DRG cytoarchitecture in response to STZ.

This paper presents a novel strategy that employs Generative Adversarial Networks (GANs) to augment data in the skin lesion segmentation task, which is a fundamental first step in the automated melanoma detection process. The proposed framework generates both skin lesion images and their segmentation masks, making the data augmentation process extremely straightforward. In order to thoroughly analyze how the quality and diversity of synthetic images impact the efficiency of the method, we remodel two different well known GANs: a Deep Convolutional GAN (DCGAN) and a Laplacian GAN (LAPGAN). Experimental results reveal that, by introducing such kind of synthetic data into the training process, the overall accuracy of a state-of-the-art Convolutional/Deconvolutional Neural Network for melanoma skin lesion segmentation is increased.

West Nile Disease (WND) is one of the most spread zoonosis in Italy and Europe caused by a vector-borne virus. Its transmission cycle is well understood, with birds acting as the primary hosts and mosquito vectors transmitting the virus to other birds, while humans and horses are occasional dead-end hosts. Identifying suitable environmental conditions across large areas containing multiple species of potential hosts and vectors can be difficult. The recent and massive availability of Earth Observation data and the continuous development of innovative Machine Learning methods can contribute to automatically identify patterns in big datasets and to make highly accurate identification of areas at risk. In this paper, we investigated the West Nile Virus (WNV) circulation in relation to Land Surface Temperature, Normalized Difference Vegetation Index and Surface Soil Moisture collected during the 160 days before the infection took place, with the aim of evaluating the predictive capacity of lagged remotely sensed variables in the identification of areas at risk for WNV circulation. WNV detection in mosquitoes, birds and horses in 2017, 2018 and 2019, has been collected from the National Information System for Animal Disease Notification. An Extreme Gradient Boosting model was trained with data from 2017 and 2018 and tested for the 2019 epidemic, predicting the spatio-temporal WNV circulation two weeks in advance with an overall accuracy of 0.84. This work lays the basis for a future early warning system that could alert public authorities when climatic and environmental conditions become favourable to the onset and spread of WNV.