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The 2021 Data Fusion Contest, organized by the Image Analysis and Data Fusion Technical Committee (IADF TC) of the IEEE Geoscience and Remote Sensing Society (GRSS), promotes research on geospatial artificial intelligence (AI) for social good. The global objective is to build models for understanding the state of and changes in artificial and natural environments from remote sensing data toward sustainable development.

Biodiversity conservation depends on accurate, up-to-date information about wildlife population distributions. Motion-activated cameras, also known as camera traps, are a critical tool for population surveys, as they are cheap and non-intrusive. However, extracting useful information from camera trap images is a cumbersome process: a typical camera trap survey may produce millions of images that require slow, expensive manual review. Consequently, critical information is often lost due to resource limitations, and critical conservation questions may be answered too slowly to support decision-making. Computer vision is poised to dramatically increase efficiency in image-based biodiversity surveys, and recent studies have harnessed deep learning techniques for automatic information extraction from camera trap images. However, the accuracy of results depends on the amount, quality, and diversity of the data available to train models, and the literature has focused on projects with millions of relevant, labeled training images. Many camera trap projects do not have a large set of labeled images and hence cannot benefit from existing machine learning techniques. Furthermore, even projects that do have labeled data from similar ecosystems have struggled to adopt deep learning methods because image classification models overfit to specific image backgrounds (i.e., camera locations). In this paper, we focus not on automating the labeling of camera trap images, but on accelerating this process. We combine the power of machine intelligence and human intelligence to build a scalable, fast, and accurate active learning system to minimize the manual work required to identify and count animals in camera trap images. Our proposed scheme can match the state of the art accuracy on a 3.2 million image dataset with as few as 14,100 manual labels, which means decreasing manual labeling effort by over 99.5%., 15 pages, 5 figures

The introduction of exome sequencing in the clinic has sparked tremendous optimism for the future of rare disease diagnosis, and there is exciting opportunity to further leverage these advances. To provide diagnostic clarity to all of these patients, however, there is a critical need for the field to develop and implement strategies to understand the mechanisms underlying all rare diseases and translate these to clinical care.

Predicting defects in RNA splicing Most eukaryotic messenger RNAs (mRNAs) are spliced to remove introns. Splicing generates uninterrupted open reading frames that can be translated into proteins. Splicing is often highly regulated, generating alternative spliced forms that code for variant proteins in different tissues. RNA-binding proteins that bind specific sequences in the mRNA regulate splicing. Xiong et al. develop a computational model that predicts splicing regulation for any mRNA sequence (see the Perspective by Guigó and Valcárcel). They use this to analyze more than half a million mRNA splicing sequence variants in the human genome. They are able to identify thousands of known disease-causing mutations, as well as many new disease candidates, including 17 new autism-linked genes. Science , this issue 10.1126/science.1254806 ; see also p. 124

In this paper a novel feature selection scheme is proposed, which exploits the potentialities of a recent probabilistic generative model, the Counting Grid. This model is able to cluster together similar observations, highlighting the compactness of a class and its underlying structure. The proposed feature selection scheme is applied to the expression microarray scenario, a peculiar context with very few patterns and a huge number of features. Experiments on benchmark datasets show that the proposed approach is effective and stable, assessing state-of-the-art classification accuracies.

A score function induced by a generative model of the data can provide a feature vector of a fixed dimension for each data sample. Data samples themselves may be of differing lengths (e.g., speech segments or other sequential data), but as a score function is based on the properties of the data generation process, it produces a fixed-length vector in a highly informative space, typically referred to as "score space." Discriminative classifiers have been shown to achieve higher performances in appropriately chosen score spaces with respect to what is achievable by either the corresponding generative likelihood-based classifiers or the discriminative classifiers using standard feature extractors. In this paper, we present a novel score space that exploits the free energy associated with a generative model. The resulting free energy score space (FESS) takes into account the latent structure of the data at various levels and can be shown to lead to classification performance that at least matches the performance of the free energy classifier based on the same generative model and the same factorization of the posterior. We also show that in several typical computer vision and computational biology applications the classifiers optimized in FESS outperform the corresponding pure generative approaches, as well as a number of previous approaches combining discriminating and generative models.

We propose a new generative model, and a new image similarity kernel based on a linked hierarchy of probabilistic segmentations. The model is used to efficiently segment multiple images into a consistent set of image regions. The segmentations are provided at several levels of granularity and links among them are automatically provided. Model training and inference in it is faster than most local feature extraction algorithms, and yet the provided image segmentation, and the segment matching among images provide a rich backdrop for image recognition, segmentation and registration tasks.

As a useful concept in the study of the low level image class structure, we introduce the notion of a structure element - `stel.' The notion is related to the notions of a pixel, superpixel, segment or a part, but instead of referring to an element or a region of a single image, stel is a probabilistic element of an entire image class. Stels often define clear object or scene parts as a consequence of the modeling constraint which forces the regions belonging to a single stel to have a tight distribution over local measurements, such as color or texture. This self-similarity within a region in a single image is typical of most meaningful image parts, even when in different images of similar objects the corresponding parts may not have similar local measurements. The stel itself is expected to be consistent within a class, yet flexible, which we accomplish using a novel approach we dubbed stel component analysis. Experimental results show how stel component analysis can assist in image/video segmentation and object recognition where, in particular, it can be used as an alternative of, or in conjunction with, bag-of-features and related classifiers, where stel inference provides a meaningful spatial partition of features.

Hybrid, generative-discriminative, techniques have proven to be valuable approaches in tackling difficult object or scene recognition problems. In general, a generative model over the available data for each image class is first learned providing a relatively comprehensive statistical multi-level representation. In this way, new meaningful image features become available, which encode the degree of fitness of the data with respect to the model at different representation levels. Such features are then fed into a discriminative classifier which can exploit the intrinsic data separability. In this paper, we propose the use of variational free energy terms as feature vectors, so that the degree of fitness of the data and the uncertainty over the generative process are explicitly included in the data description. The proposed method is automatically superior to a pure generative classification, and we also experimentally validate it on a wide selection of generative models applied to challenging benchmarks in hard computer vision tasks such as scene, object, and shape recognition. In several instances, the proposed approach outperforms the current state-of-the-art techniques as for classification results, while also showing to be computationally inexpensive.

The ability of human immunodeficiency virus type 1 (HIV-1) to develop high levels of genetic diversity, and thereby acquire mutations to escape immune pressures, contributes to the difficulties in producing a vaccine. Possibly no single HIV-1 sequence can induce sufficiently broad immunity to protect against a wide variety of infectious strains, or block mutational escape pathways available to the virus after infection. The authors describe the generation of HIV-1 immunogens that minimizes the phylogenetic distance of viral strains throughout the known viral population (the center of tree [COT]) and then extend the COT immunogen by addition of a composite sequence that includes high-frequency variable sites preserved in their native contexts. The resulting COT+ antigens compress the variation found in many independent HIV-1 isolates into lengths suitable for vaccine immunogens. It is possible to capture 62% of the variation found in the Nef protein and 82% of the variation in the Gag protein into immunogens of three gene lengths. The authors put forward immunogen designs that maximize representation of the diverse antigenic features present in a spectrum of HIV-1 strains. These immunogens should elicit immune responses against high-frequency viral strains as well as against most mutant forms of the virus., Author Summary The ability of human immunodeficiency virus type 1 (HIV-1) to acquire mutations that preserve virus viability yet evade immune responses contributes to the current failure in producing a vaccine. We describe the generation of candidate HIV-1 immunogens that include multiple forms of variable elements of the virus including some that retain colinearity with the virus and thus are expected to retain protein function. These antigens compress the variation found in many viral strains into lengths suitable for vaccine immunogens. For example, we can capture 62% of the variation found in the Nef protein and 82% of the variation in the Gag protein into immunogens of three gene lengths. We put forward immunogen designs that maximize representation of the diverse antigenic features present in a spectrum of HIV-1 strains. These immunogens should elicit immune responses against high frequency viral strains as well as against most mutant forms of the virus.

Transcript quantification is a long-standing problem in genomics and estimating the relative abundance of alternatively-spliced isoforms from the same transcript is an important special case. Both problems have recently been illuminated by high-throughput RNA sequencing experiments which are quickly generating large amounts of data. However, much of the signal present in this data is corrupted or obscured by biases resulting in non-uniform and non-proportional representation of sequences from different transcripts. Many existing analyses attempt to deal with these and other biases with various task-specific approaches, which makes direct comparison between them difficult. However, two popular tools for isoform quantification, MISO and Cufflinks, have adopted a general probabilistic framework to model and mitigate these biases in a more general fashion. These advances motivate the need to investigate the effects of RNA-seq biases on the accuracy of different approaches for isoform quantification. We conduct the investigation by building models of increasing sophistication to account for noise introduced by the biases and compare their accuracy to the established approaches. We focus on methods that estimate the expression of alternatively-spliced isoforms with the percent-spliced-in (PSI) metric for each exon skipping event. To improve their estimates, many methods use evidence from RNA-seq reads that align to exon bodies. However, the methods we propose focus on reads that span only exon-exon junctions. As a result, our approaches are simpler and less sensitive to exon definitions than existing methods, which enables us to distinguish their strengths and weaknesses more easily. We present several probabilistic models of of position-specific read counts with increasing complexity and compare them to each other and to the current state-of-the-art methods in isoform quantification, MISO and Cufflinks. On a validation set with RT-PCR measurements for 26 cassette events, some of our methods are more accurate and some are significantly more consistent than these two popular tools. This comparison demonstrates the challenges in estimating the percent inclusion of alternatively spliced junctions and illuminates the tradeoffs between different approaches.