Cancer is increasingly a global health issue. Seconding cardiovascular diseases, cancers are the second biggest cause of death in the world with millions of people succumbing to the disease every year. According to the World Health Organization (WHO) report, by the end of 2020, more than 7.8 million women have been diagnosed with breast cancer, making it the world's most prevalent cancer. In this paper, using the Nightingale Open Science dataset of digital pathology (breast biopsy) images, we leverage the capabilities of pre-trained computer vision models for the breast cancer stage prediction task. While individual models achieve decent performances, we find out that the predictions of an ensemble model are more efficient, and offer a winning solution\footnote{https://www.nightingalescience.org/updates/hbc1-results}. We also provide analyses of the results and explore pathways for better interpretability and generalization. Our code is open-source at \url{https://github.com/bonaventuredossou/nightingale_winning_solution}
In recent years, multilingual pre-trained language models have gained prominence due to their remarkable performance on numerous downstream Natural Language Processing tasks (NLP). However, pre-training these large multilingual language models requires a lot of training data, which is not available for African Languages. Active learning is a semi-supervised learning algorithm, in which a model consistently and dynamically learns to identify the most beneficial samples to train itself on, in order to achieve better optimization and performance on downstream tasks. Furthermore, active learning effectively and practically addresses real-world data scarcity. Despite all its benefits, active learning, in the context of NLP and especially multilingual language models pretraining, has received little consideration. In this paper, we present AfroLM, a multilingual language model pretrained from scratch on 23 African languages (the largest effort to date) using our novel self-active learning framework. Pretrained on a dataset significantly (14x) smaller than existing baselines, AfroLM outperforms many multilingual pretrained language models (AfriBERTa, XLMR-base, mBERT) on various NLP downstream tasks (NER, text classification, and sentiment analysis). Additional out-of-domain sentiment analysis experiments show that \textbf{AfroLM} is able to generalize well across various domains. We release the code source, and our datasets used in our framework at https://github.com/bonaventuredossou/MLM_AL.
As antibiotic-resistant bacterial strains are rapidly spreading worldwide, infections caused by these strains are emerging as a global crisis causing the death of millions of people every year. Antimicrobial Peptides (AMPs) are one of the candidates to tackle this problem because of their potential diversity, and ability to favorably modulate the host immune response. However, large-scale screening of new AMP candidates is expensive, time-consuming, and now affordable in developing countries, which need the treatments the most. In this work, we propose a novel active machine learning-based framework that statistically minimizes the number of wet-lab experiments needed to design new AMPs, while ensuring a high diversity and novelty of generated AMPs sequences, in multi-rounds of wet-lab AMP screening settings. Combining recurrent neural network models and a graph-based filter (GraphCC), our proposed approach delivers novel and diverse candidates and demonstrates better performances according to our defined metrics.
Recent advances in the pre-training of language models leverage large-scale datasets to create multilingual models. However, low-resource languages are mostly left out in these datasets. This is primarily because many widely spoken languages are not well represented on the web and therefore excluded from the large-scale crawls used to create datasets. Furthermore, downstream users of these models are restricted to the selection of languages originally chosen for pre-training. This work investigates how to optimally leverage existing pre-trained models to create low-resource translation systems for 16 African languages. We focus on two questions: 1) How can pre-trained models be used for languages not included in the initial pre-training? and 2) How can the resulting translation models effectively transfer to new domains? To answer these questions, we create a new African news corpus covering 16 languages, of which eight languages are not part of any existing evaluation dataset. We demonstrate that the most effective strategy for transferring both to additional languages and to additional domains is to fine-tune large pre-trained models on small quantities of high-quality translation data.
In this paper, we focus on the task of multilingual machine translation for African languages and describe our contribution in the 2021 WMT Shared Task: Large-Scale Multilingual Machine Translation. We introduce MMTAfrica, the first many-to-many multilingual translation system for six African languages: Fon (fon), Igbo (ibo), Kinyarwanda (kin), Swahili/Kiswahili (swa), Xhosa (xho), and Yoruba (yor) and two non-African languages: English (eng) and French (fra). For multilingual translation concerning African languages, we introduce a novel backtranslation and reconstruction objective, BT\&REC, inspired by the random online back translation and T5 modeling framework respectively, to effectively leverage monolingual data. Additionally, we report improvements from MMTAfrica over the FLORES 101 benchmarks (spBLEU gains ranging from $+0.58$ in Swahili to French to $+19.46$ in French to Xhosa). We release our dataset and code source at https://github.com/edaiofficial/mmtafrica.
Design of de novo biological sequences with desired properties, like protein and DNA sequences, often involves an active loop with several rounds of molecule ideation and expensive wet-lab evaluations. These experiments can consist of multiple stages, with increasing levels of precision and cost of evaluation, where candidates are filtered. This makes the diversity of proposed candidates a key consideration in the ideation phase. In this work, we propose an active learning algorithm leveraging epistemic uncertainty estimation and the recently proposed GFlowNets as a generator of diverse candidate solutions, with the objective to obtain a diverse batch of useful (as defined by some utility function, for example, the predicted anti-microbial activity of a peptide) and informative candidates after each round. We also propose a scheme to incorporate existing labeled datasets of candidates, in addition to a reward function, to speed up learning in GFlowNets. We present empirical results on several biological sequence design tasks, and we find that our method generates more diverse and novel batches with high scoring candidates compared to existing approaches.
Using mel-spectrograms over conventional MFCCs features, we assess the abilities of convolutional neural networks to accurately recognize and classify emotions from speech data. We introduce FSER, a speech emotion recognition model trained on four valid speech databases, achieving a high-classification accuracy of 95,05\%, over 8 different emotion classes: anger, anxiety, calm, disgust, happiness, neutral, sadness, surprise. On each benchmark dataset, FSER outperforms the best models introduced so far, achieving a state-of-the-art performance. We show that FSER stays reliable, independently of the language, sex identity, and any other external factor. Additionally, we describe how FSER could potentially be used to improve mental and emotional health care and how our analysis and findings serve as guidelines and benchmarks for further works in the same direction.
With the success of large-scale pre-training and multilingual modeling in Natural Language Processing (NLP), recent years have seen a proliferation of large, web-mined text datasets covering hundreds of languages. However, to date there has been no systematic analysis of the quality of these publicly available datasets, or whether the datasets actually contain content in the languages they claim to represent. In this work, we manually audit the quality of 205 language-specific corpora released with five major public datasets (CCAligned, ParaCrawl, WikiMatrix, OSCAR, mC4), and audit the correctness of language codes in a sixth (JW300). We find that lower-resource corpora have systematic issues: at least 15 corpora are completely erroneous, and a significant fraction contains less than 50% sentences of acceptable quality. Similarly, we find 82 corpora that are mislabeled or use nonstandard/ambiguous language codes. We demonstrate that these issues are easy to detect even for non-speakers of the languages in question, and supplement the human judgements with automatic analyses. Inspired by our analysis, we recommend techniques to evaluate and improve multilingual corpora and discuss the risks that come with low-quality data releases.
We take a step towards addressing the under-representation of the African continent in NLP research by creating the first large publicly available high-quality dataset for named entity recognition (NER) in ten African languages, bringing together a variety of stakeholders. We detail characteristics of the languages to help researchers understand the challenges that these languages pose for NER. We analyze our datasets and conduct an extensive empirical evaluation of state-of-the-art methods across both supervised and transfer learning settings. We release the data, code, and models in order to inspire future research on African NLP.
From Word2Vec to GloVe, word embedding models have played key roles in the current state-of-the-art results achieved in Natural Language Processing. Designed to give significant and unique vectorized representations of words and entities, those models have proven to efficiently extract similarities and establish relationships reflecting semantic and contextual meaning among words and entities. African Languages, representing more than 31% of the worldwide spoken languages, have recently been subject to lots of research. However, to the best of our knowledge, there are currently very few to none word embedding models for those languages words and entities, and none for the languages under study in this paper. After describing Glove, Word2Vec, and Poincar\'e embeddings functionalities, we build Word2Vec and Poincar\'e word embedding models for Fon and Nobiin, which show promising results. We test the applicability of transfer learning between these models as a landmark for African Languages to jointly involve in mitigating the scarcity of their resources, and attempt to provide linguistic and social interpretations of our results. Our main contribution is to arouse more interest in creating word embedding models proper to African Languages, ready for use, and that can significantly improve the performances of Natural Language Processing downstream tasks on them. The official repository and implementation is at https://github.com/bonaventuredossou/afrivec