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Alessandro Tibo

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3 papers

2 author rows

ICML Conference 2023 Conference Paper

Metagenomic Binning using Connectivity-constrained Variational Autoencoders

Andre Lamurias
Alessandro Tibo
Katja Hose
Mads Albertsen
Thomas D. Nielsen

Current state-of-the-art techniques for metagenomic binning only utilize local features for the individual DNA sequences (contigs), neglecting additional information such as the assembly graph, in which the contigs are connected according to overlapping reads, and gene markers identified in the contigs. In this paper, we propose the use of a Variational AutoEncoder (VAE) tailored to leverage auxiliary structural information about contig relations when learning contig representations for subsequent metagenomic binning. Our method, CCVAE, improves on previous work that used VAEs for learning latent representations of the individual contigs, by constraining these representations according to the connectivity information from the assembly graph. Additionally, we incorporate into the model additional information in the form of marker genes to better differentiate contigs from different genomes. Our experiments on both simulated and real-world datasets demonstrate that CCVAE outperforms current state-of-the-art techniques, thus providing a more effective method for metagenomic binning.

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IJCAI Conference 2021 Conference Paper

Learning Aggregation Functions

Giovanni Pellegrini
Alessandro Tibo
Paolo Frasconi
Andrea Passerini
Manfred Jaeger

Learning on sets is increasingly gaining attention in the machine learning community, due to its widespread applicability. Typically, representations over sets are computed by using fixed aggregation functions such as sum or maximum. However, recent results showed that universal function representation by sum- (or max-) decomposition requires either highly discontinuous (and thus poorly learnable) mappings, or a latent dimension equal to the maximum number of elements in the set. To mitigate this problem, we introduce LAF (Learning Aggregation Function), a learnable aggregator for sets of arbitrary cardinality. LAF can approximate several extensively used aggregators (such as average, sum, maximum) as well as more complex functions (e. g. variance and skewness). We report experiments on semi-synthetic and real data showing that LAF outperforms state-of-the-art sum- (max-) decomposition architectures such as DeepSets and library-based architectures like Principal Neighborhood Aggregation, and can be effectively combined with attention-based architectures.

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JMLR Journal 2020 Journal Article

Learning and Interpreting Multi-Multi-Instance Learning Networks

Alessandro Tibo
Manfred Jaeger
Paolo Frasconi

We introduce an extension of the multi-instance learning problem where examples are organized as nested bags of instances (e.g., a document could be represented as a bag of sentences, which in turn are bags of words). This framework can be useful in various scenarios, such as text and image classification, but also supervised learning over graphs. As a further advantage, multi-multi instance learning enables a particular way of interpreting predictions and the decision function. Our approach is based on a special neural network layer, called bag-layer, whose units aggregate bags of inputs of arbitrary size. We prove theoretically that the associated class of functions contains all Boolean functions over sets of sets of instances and we provide empirical evidence that functions of this kind can be actually learned on semi-synthetic datasets. We finally present experiments on text classification, on citation graphs, and social graph data, which show that our model obtains competitive results with respect to accuracy when compared to other approaches such as convolutional networks on graphs, while at the same time it supports a general approach to interpret the learnt model, as well as explain individual predictions. [abs] [ pdf ][ bib ] &copy JMLR 2020. ( edit, beta )

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