Here we present the training and evaluation of NanoNER, a Named Entity Recognition (NER) model for Nanobiology. NER consists in the identification of specific entities in spans of unstructured texts and is often a primary task in Natural Language Processing (NLP) and Information Extraction. The aim of our model is to recognise entities previously identified by domain experts as constituting the essential knowledge of the domain. Relying on ontologies, which provide us with a domain vocabulary and taxonomy, we implemented an iterative process enabling experts to determine the entities relevant to the domain at hand. We then delve into the potential of distant supervision learning in NER, supporting how this method can increase the quantity of annotated data with minimal additional manpower. On our full corpus of 728 full-text nanobiology articles, containing more than 120k entity occurrences, NanoNER obtained a F1-score of 0.98 on the recognition of previously known entities. Our model also demonstrated its ability to discover new entities in the text, with precision scores ranging from 0.77 to 0.81. Ablation experiments further confirmed this and allowed us to assess the dependency of our approach on the external resources. It highlighted the dependency of the approach to the resource, while also confirming its ability to rediscover up to 30% of the ablated terms. This paper details the methodology employed, experimental design, and key findings, providing valuable insights and directions for future related researches on NER in specialized domain. Furthermore, since our approach require minimal manpower , we believe that it can be generalized to other specialized fields.

Information retrieval systems retrieves relevant documents based on a query submitted by the user. The documents are initially indexed and the words in the documents are assigned weights using a weighting technique called TFIDF which is the product of Term Frequency (TF) and Inverse Document Frequency (IDF). TF represents the number of occurrences of a term in a document. IDF measures whether the term is common or rare across all documents. It is computed by dividing the total number of documents in the system by the number of documents containing the term and then computing the logarithm of the quotient. By default, we use base 10 to calculate the logarithm. In this paper, we are going to test this weighting technique by using a range of log bases from 0.1 to 100.0 to calculate the IDF. Testing different log bases for vector model weighting technique is to highlight the importance of understanding the performance of the system at different weighting values. We use the documents of MED, CRAN, NPL, LISA, and CISI test collections that scientists assembled explicitly for experiments in data information retrieval systems.

ABSTRACT Starches are important energy sources found in plants with many uses in the pharmaceutical industry such as binders, disintegrants, bulking agents in drugs and thus require very careful physicochemical analysis for proper identification and verification which includes microscopy. In this work, we applied artificial intelligence techniques (using transfer learning and deep convolution neural network CNNs to microscopical images obtained from 9 starch samples of different botanical sources. Our approach obtained an accuracy of 61% when the machine learning model was pretrained on microscopic images from MicroNet dataset. However the accuracy jumped to 81% for model pretrained on random day to day images obtained from Imagenet dataset. The model pretrained on the imagenet dataset also showed a better precision, recall and f1 score than that pretrained on the imagenet dataset.

Originally published on Towards AI the World's Leading AI and Technology News and Media Company. If you are building an AI-related product or service, we invite you to consider...

Large Neural Networks are difficult to use in production environments as they are memory intensive and are slow during inference. Most successful Deep Learning Models such as Transformers are being followed by their Lite Versions which dramatically speed up inference trading off accuracy. In this article, let's explore Least Squares Quantization, an algorithm to speed up large neural networks by quantizing them while reducing the accuracy gap from the non-quantized model. Hadi Pouransari, Zhucheng Tu, Oncel Tuzel, researchers at Apple, introduced this approach in a paper- Least Squares Binary Quantization of Neural Networks, on 23rd March 2020. We all agree that smaller models are better for practical purposes in memory usage and inference time.

AP (Average precision) is a popular metric in measuring the accuracy of object detectors like Faster R-CNN, SSD, etc. Average precision computes the average precision value for recall value over 0 to 1. It sounds complicated but actually pretty simple as we illustrate it with an example. But before that, we will do a quick recap on precision, recall, and IoU first. Precision measures how accurate is your predictions. Recall measures how good you find all the positives.

New proposed models are often compared to state-of-the-art using statistical significance testing. Literature is scarce for classifier comparison using metrics other than accuracy. We present a survey of statistical methods that can be used for classifier comparison using precision, accounting for inter-precision correlation arising from use of same dataset. Comparisons are made using per-class precision and methods presented to test global null hypothesis of an overall model comparison. Comparisons are extended to multiple multi-class classifiers and to models using cross validation or its variants. Partial Bayesian update to precision is introduced when population prevalence of a class is known. Applications to compare deep architectures are studied.

According to Cobanoglu et al and Murphy, it is now widely acknowledged that the single target paradigm (one protein or target, one disease, one drug) that has been the dominant premise in drug development in the recent past is untenable. More often than not, a drug-like compound (ligand) can be promiscuous - that is, it can interact with more than one target protein. In recent years, in in silico target prediction methods the promiscuity issue has been approached computationally in different ways. In this study we confine attention to the so-called ligand-based target prediction machine learning approaches, commonly referred to as target-fishing. With a few exceptions, the target-fishing approaches that are currently ubiquitous in cheminformatics literature can be essentially viewed as single-label multi-classification schemes; these approaches inherently bank on the single target paradigm assumption that a ligand can home in on one specific target. In order to address the ligand promiscuity issue, one might be able to cast target-fishing as a multi-label multi-class classification problem. For illustrative and comparison purposes, single-label and multi-label Naive Bayes classification models (denoted here by SMM and MMM, respectively) for target-fishing were implemented. The models were constructed and tested on 65,587 compounds and 308 targets retrieved from the ChEMBL17 database. SMM and MMM performed differently: for 16,344 test compounds, the MMM model returned recall and precision values of 0.8058 and 0.6622, respectively; the corresponding recall and precision values yielded by the SMM model were 0.7805 and 0.7596, respectively. However, at a significance level of 0.05 and one degree of freedom McNemar test performed on the target prediction results returned by SMM and MMM for the 16,344 test ligands gave a chi-squared value of 15.656, in favour of the MMM approach.

Clustering is often formulated as the maximum likelihood estimation of a mixture model that explains the data. The EM algorithm widely used to solve the resulting optimization problem is inherently a gradient-descent method and is sensitive to initialization. The resulting solution is a local optimum in the neighborhood of the initial guess. This sensitivity to initialization presents a significant challenge in clustering large data sets into many clusters. In this paper, we present a different approach to approximate mixture fitting for clustering. We introduce an exemplar-based likelihood function that approximates the exact likelihood. This formulation leads to a convex minimization problem and an efficient algorithm with guaranteed convergence to the globally optimal solution. The resulting clustering can be thought of as a probabilistic mapping of the data points to the set of exemplars that minimizes the average distance and the information-theoretic cost of mapping.

Clustering is often formulated as the maximum likelihood estimation of a mixture model that explains the data. The EM algorithm widely used to solve the resulting optimization problem is inherently a gradient-descent method and is sensitive to initialization. The resulting solution is a local optimum in the neighborhood of the initial guess. This sensitivity to initialization presents a significant challenge in clustering large data sets into many clusters. In this paper, we present a different approach to approximate mixture fitting for clustering. We introduce an exemplar-based likelihood function that approximates the exact likelihood. This formulation leads to a convex minimization problem and an efficient algorithm with guaranteed convergence to the globally optimal solution. The resulting clustering can be thought of as a probabilistic mapping of the data points to the set of exemplars that minimizes the average distance and the information-theoretic cost of mapping.