Pretraining the Vision Transformer using self-supervised methods for vision based Deep Reinforcement Learning

The Vision Transformer architecture has shown to be competitive in the computer vision (CV) space where it has dethroned convolution-based networks in several benchmarks. Nevertheless, Convolutional Neural Networks (CNN) remain the preferential architecture for the representation module in Reinforcement Learning. In this work, we study pretraining a Vision Transformer using several state-of-the-art self-supervised methods and assess data-efficiency gains from this training framework. We propose a new self-supervised learning method called TOV-VICReg that extends VICReg to better capture temporal relations between observations by adding a temporal order verification task. Furthermore, we evaluate the resultant encoders with Atari games in a sample-efficiency regime. Our results show that the vision transformer, when pretrained with TOV-VICReg, outperforms the other self-supervised methods but still struggles to overcome a CNN. Nevertheless, we were able to outperform a CNN in two of the ten games where we perform a 100k steps evaluation. Ultimately, we believe that such approaches in Deep Reinforcement Learning (DRL) might be the key to achieving new levels of performance as seen in natural language processing and computer vision. Source code will be available at: https://github.com/mgoulao/TOV-VICRe

BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data

<p>Abstract</p> <p>Background</p> <p>The ability to monitor changes in expression patterns over time, and to observe the emergence of coherent temporal responses using expression time series, is critical to advance our understanding of complex biological processes. Biclustering has been recognized as an effective method for discovering local temporal expression patterns and unraveling potential regulatory mechanisms. The general biclustering problem is NP-hard. In the case of time series this problem is tractable, and efficient algorithms can be used. However, there is still a need for specialized applications able to take advantage of the temporal properties inherent to expression time series, both from a computational and a biological perspective.</p> <p>Findings</p> <p>BiGGEsTS makes available state-of-the-art biclustering algorithms for analyzing expression time series. Gene Ontology (GO) annotations are used to assess the biological relevance of the biclusters. Methods for preprocessing expression time series and post-processing results are also included. The analysis is additionally supported by a visualization module capable of displaying informative representations of the data, including heatmaps, dendrograms, expression charts and graphs of enriched GO terms.</p> <p>Conclusion</p> <p>BiGGEsTS is a free open source graphical software tool for revealing local coexpression of genes in specific intervals of time, while integrating meaningful information on gene annotations. It is freely available at: <url>http://kdbio.inesc-id.pt/software/biggests</url>. We present a case study on the discovery of transcriptional regulatory modules in the response of <it>Saccharomyces cerevisiae </it>to heat stress.</p

DeepThought: An Architecture for Autonomous Self-motivated Systems

The ability of large language models (LLMs) to engage in credible dialogues with humans, taking into account the training data and the context of the conversation, has raised discussions about their ability to exhibit intrinsic motivations, agency, or even some degree of consciousness. We argue that the internal architecture of LLMs and their finite and volatile state cannot support any of these properties. By combining insights from complementary learning systems, global neuronal workspace, and attention schema theories, we propose to integrate LLMs and other deep learning systems into an architecture for cognitive language agents able to exhibit properties akin to agency, self-motivation, even some features of meta-cognition

Discriminative learning of Bayesian networks via factorized conditional log-likelihood

We propose an efficient and parameter-free scoring criterion, the factorized conditional log-likelihood (ˆfCLL), for learning Bayesian network classifiers. The proposed score is an approximation of the conditional log-likelihood criterion. The approximation is devised in order to guarantee decomposability over the network structure, as well as efficient estimation of the optimal parameters, achieving the same time and space complexity as the traditional log-likelihood scoring criterion. The resulting criterion has an information-theoretic interpretation based on interaction information, which exhibits its discriminative nature. To evaluate the performance of the proposed criterion, we present an empirical comparison with state-of-the-art classifiers. Results on a large suite of benchmark data sets from the UCI repository show that ˆfCLL-trained classifiers achieve at least as good accuracy as the best compared classifiers, using significantly less computational resources.Peer reviewe

An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance

BACKGROUND: Motif finding algorithms have developed in their ability to use computationally efficient methods to detect patterns in biological sequences. However the posterior classification of the output still suffers from some limitations, which makes it difficult to assess the biological significance of the motifs found. Previous work has highlighted the existence of positional bias of motifs in the DNA sequences, which might indicate not only that the pattern is important, but also provide hints of the positions where these patterns occur preferentially.RESULTS: We propose to integrate position uniformity tests and over-representation tests to improve the accuracy of the classification of motifs. Using artificial data, we have compared three different statistical tests (Chi-Square, Kolmogorov-Smirnov and a Chi-Square bootstrap) to assess whether a given motif occurs uniformly in the promoter region of a gene. Using the test that performed better in this dataset, we proceeded to study the positional distribution of several well known cis-regulatory elements, in the promoter sequences of different organisms (S. cerevisiae, H. sapiens, D. melanogaster, E. coli and several Dicotyledons plants). The results show that position conservation is relevant for the transcriptional machinery.CONCLUSION: We conclude that many biologically relevant motifs appear heterogeneously distributed in the promoter region of genes, and therefore, that non-uniformity is a good indicator of biological relevance and can be used to complement over-representation tests commonly used. In this article we present the results obtained for the S. cerevisiae data sets.publishersversionpublishe

Potential and limitations of computed tomography images as predictors of the outcome of ischemic stroke events: a review

The prediction of functional outcome after a stroke remains a relevant, open problem. In this article, we present a systematic review of approaches that have been proposed to predict the most likely functional outcome of ischemic stroke patients, as measured by the modified Rankin scale. Different methods use a variety of clinical information and features extracted from brain computed tomography (CT) scans, usually obtained at the time of hospital admission. Most studies have concluded that CT data contains useful information, but the use of this information by models does not always translate into statistically significant improvements in the quality of the predictions