Publications

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.

Continual Learning has inspired a plethora of approaches and evaluation settings; however, the majority of them overlooks the properties of a practical scenario, where the data stream cannot be shaped as a sequence of tasks and offline training is not viable. We work towards General Continual Learning (GCL), where task boundaries blur and the domain and class distributions shift either gradually or suddenly. We address it through mixing rehearsal with knowledge distillation and regularization; our simple baseline, Dark Experience Replay, matches the network's logits sampled throughout the optimization trajectory, thus promoting consistency with its past. By conducting an extensive analysis on both standard benchmarks and a novel GCL evaluation setting (MNIST-360), we show that such a seemingly simple baseline outperforms consolidated approaches and leverages limited resources. We further explore the generalization capabilities of our objective, showing its regularization being beneficial beyond mere performance.

Nowadays, robots are heavily used in factories for different tasks, most of them including grasping and manipulation of generic objects in unstructured scenarios. In order to better mimic a human operator involved in a grasping action, where he/she needs to identify the object and detect an optimal grasp by means of visual information, a widely adopted sensing solution is Artificial Vision. Nonetheless, state-of-art applications need long training and fine-tuning for manually build the object's model that is used at run-time during the normal operations, which reduce the overall operational throughput of the robotic system. To overcome such limits, the paper presents a framework based on Deep Convolutional Neural Networks (DCNN) to predict both single and multiple grasp poses for multiple objects all at once, using a single RGB image as input. Thanks to a novel loss function, our framework is trained in an end-to-end fashion and matches state-of-art accuracy with a substantially smaller architecture, which gives unprecedented real-time performances during experimental tests, and makes the application reliable for working on real robots. The system has been implemented using the ROS framework and tested on a Baxter collaborative robot.

Summary: In the last decade, increasing attention has been paid to the study of gene fusions. However, the problem of determining whether a gene fusion is a cancer driver or just a passenger mutation is still an open issue. Here we present DEEPrior, an inherently flexible deep learning tool with two modes (Inference and Retraining). Inference mode predicts the probability of a gene fusion being involved in an oncogenic process, by directly exploiting the amino acid sequence of the fused protein. Retraining mode allows to obtain a custom prediction model including new data provided by the user. Availability and implementation: Both DEEPrior and the protein fusions dataset are freely available from GitHub at (https://github.com/bioinformatics-polito/DEEPrior). The tool was designed to operate in Python 3.7, with minimal additional libraries. Supplementary information: Supplementary data are available at Bioinformatics online.

We address the problem of unsupervised gaze correction in the wild, presenting a solution that works without the need of precise annotations of the gaze angle and the head pose. We created a new dataset called CelebAGaze consisting of two domains X, Y, where the eyes are either staring at the camera or somewhere else. Our method consists of three novel modules: the Gaze Correction module(GCM), the Gaze Animation module(GAM), and the Pretrained Autoencoder module (PAM). Specifically, GCM and GAM separately train a dual in-painting network using data from the domain X for gaze correction and data from the domain Y for gaze animation. Additionally, a Synthesis-As-Training method is proposed when training GAM to encourage the features encoded from the eye region to be correlated with the angle information, resulting in gaze animation achieved by interpolation in the latent space. To further preserve the identity information e.g., eye shape, iris color, we propose the PAM with an Autoencoder, which is based on Self-Supervised mirror learning where the bottleneck features are angle-invariant and which works as an extra input to the dual in-painting models. Extensive experiments validate the effectiveness of the proposed method for gaze correction and gaze animation in the wild and demonstrate the superiority of our approach in producing more compelling results than state-of-the-art baselines. Our code, the pretrained models and supplementary results are available at:https://github.com/zhangqianhui/GazeAnimation.

Clustering methods are increasingly applied to single-cell DNA sequencing (scDNAseq) data to infer the subclonal structure of cancer. However, the complexity of these data exacerbates some data-science issues and affects clustering results. Additionally, determining whether such inferences are accurate and clusters recapitulate the real cell phylogeny is not trivial, mainly because ground truth information is not available for most experimental settings. Here, by exploiting simulated sequencing data representing known phylogenies of cancer cells, we propose a formal and systematic assessment of well-known clustering methods to study their performance and identify the approach providing the most accurate reconstruction of phylogenetic relationships.

Background and objectives: Immunohistopathology is an essential technique in the diagnostic workflow of a kidney biopsy. Deep learning is an effective tool in the elaboration of medical imaging. We wanted to evaluate the role of a convolutional neural network as a support tool for kidney immunofluorescence reporting. Design, setting, participants, & measurements: High-magnification (×400) immunofluorescence images of kidney biopsies performed from the year 2001 to 2018 were collected. The report, adopted at the Division of Nephrology of the AOU Policlinico di Modena, describes the specimen in terms of “appearance,” “distribution,” “location,” and “intensity” of the glomerular deposits identified with fluorescent antibodies against IgG, IgA, IgM, C1q and C3 complement fractions, fibrinogen, and κ- and λ-light chains. The report was used as ground truth for the training of the convolutional neural networks. Results: In total, 12,259 immunofluorescence images of 2542 subjects undergoing kidney biopsy were collected. The test set analysis showed accuracy values between 0.79 (“irregular capillary wall” feature) and 0.94 (“fine granular” feature). The agreement test of the results obtained by the convolutional neural networks with respect to the ground truth showed similar values to three pathologists of our center. Convolutional neural networks were 117 times faster than human evaluators in analyzing 180 test images. A web platform, where it is possible to upload digitized images of immunofluorescence specimens, is available to evaluate the potential of our approach. Conclusions: The data showed that the accuracy of convolutional neural networks is comparable with that of pathologists experienced in the field.

Replicating the human ability to connect Vision and Language has recently been gaining a lot of attention in the Computer Vision and the Natural Language Processing communities. This research effort has resulted in algorithms that can retrieve images from textual descriptions and vice versa, when realistic images and sentences with simple semantics are employed and when paired training data is provided. In this paper, we go beyond these limitations and tackle the design of visual-semantic algorithms in the domain of the Digital Humanities. This setting not only advertises more complex visual and semantic structures but also features a significant lack of training data which makes the use of fully-supervised approaches infeasible. With this aim, we propose a joint visual-semantic embedding that can automatically align illustrations and textual elements without paired supervision. This is achieved by transferring the knowledge learned on ordinary visual-semantic datasets to the artistic domain. Experiments, performed on two datasets specifically designed for this domain, validate the proposed strategies and quantify the domain shift between natural images and artworks.

Depth cameras allow to set up reliable solutions for people monitoring and behavior understanding, especially when unstable or poor illumination conditions make unusable common RGB sensors. Therefore, we propose a complete framework for the estimation of the head and shoulder pose based on depth images only. A head detection and localization module is also included, in order to develop a complete end-to-end system. The core element of the framework is a Convolutional Neural Network, called POSEidon+, that receives as input three types of images and provides the 3D angles of the pose as output. Moreover, a Face-from-Depth component based on a Deterministic Conditional GAN model is able to hallucinate a face from the corresponding depth image. We empirically demonstrate that this positively impacts the system performances. We test the proposed framework on two public datasets, namely Biwi Kinect Head Pose and ICT-3DHP, and on Pandora, a new challenging dataset mainly inspired by the automotive setup. Experimental results show that our method overcomes several recent state-of-art works based on both intensity and depth input data, running in real-time at more than 30 frames per second.