Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks

We participated in three of the protein-protein interaction subtasks of the Second BioCreative Challenge: classification of abstracts relevant for protein-protein interaction (IAS), discovery of protein pairs (IPS) and text passages characterizing protein interaction (ISS) in full text documents. We approached the abstract classification task with a novel, lightweight linear model inspired by spam-detection techniques, as well as an uncertainty-based integration scheme. We also used a Support Vector Machine and the Singular Value Decomposition on the same features for comparison purposes. Our approach to the full text subtasks (protein pair and passage identification) includes a feature expansion method based on word-proximity networks. Our approach to the abstract classification task (IAS) was among the top submissions for this task in terms of the measures of performance used in the challenge evaluation (accuracy, F-score and AUC). We also report on a web-tool we produced using our approach: the Protein Interaction Abstract Relevance Evaluator (PIARE). Our approach to the full text tasks resulted in one of the highest recall rates as well as mean reciprocal rank of correct passages. Our approach to abstract classification shows that a simple linear model, using relatively few features, is capable of generalizing and uncovering the conceptual nature of protein-protein interaction from the bibliome. Since the novel approach is based on a very lightweight linear model, it can be easily ported and applied to similar problems. In full text problems, the expansion of word features with word-proximity networks is shown to be useful, though the need for some improvements is discussed

Revisiting Unsupervised Relation Extraction

Unsupervised relation extraction (URE) extracts relations between named entities from raw text without manually-labelled data and existing knowledge bases (KBs). URE methods can be categorised into generative and discriminative approaches, which rely either on hand-crafted features or surface form. However, we demonstrate that by using only named entities to induce relation types, we can outperform existing methods on two popular datasets. We conduct a comparison and evaluation of our findings with other URE techniques, to ascertain the important features in URE. We conclude that entity types provide a strong inductive bias for URE.Comment: 8 pages, 1 figure, 2 tables. Accepted in ACL 202

Electron-phonon Interaction close to a Mott transition

The effect of Holstein electron-phonon interaction on a Hubbard model close to a Mott-Hubbard transition at half-filling is investigated by means of Dynamical Mean-Field Theory. We observe a reduction of the effective mass that we interpret in terms of a reduced effective repulsion. When the repulsion is rescaled to take into account this effect, the quasiparticle low-energy features are unaffected by the electron-phonon interaction. Phonon features are only observed within the high-energy Hubbard bands. The lack of electron-phonon fingerprints in the quasiparticle physics can be explained interpreting the quasiparticle motion in terms of rare fast processes.Comment: 4 pages, 3 color figures. Slightly revised text and references. Kondo effect result added in Fig. 2 for comparison with DMFT dat

Bi-class classification of humpback whale sound units against complex background noise with Deep Convolution Neural Network

Automatically detecting sound units of humpback whales in complex time-varying background noises is a current challenge for scientists. In this paper, we explore the applicability of Convolution Neural Network (CNN) method for this task. In the evaluation stage, we present 6 bi-class classification experimentations of whale sound detection against different background noise types (e.g., rain, wind). In comparison to classical FFT-based representation like spectrograms, we showed that the use of image-based pretrained CNN features brought higher performance to classify whale sounds and background noise.Comment: arXiv admin note: text overlap with arXiv:1702.02741 by other author