This paper presents a novel clustering algorithm from the SPINEX (Similarity-based Predictions with Explainable Neighbors Exploration) algorithmic family. The newly proposed clustering variant leverages the concept of similarity and higher-order interactions across multiple subspaces to group data into clusters. To showcase the merit of SPINEX, a thorough set of benchmarking experiments was carried out against 13 algorithms, namely, Affinity Propagation, Agglomerative, Birch, DBSCAN, Gaussian Mixture, HDBSCAN, K-Means, KMedoids, Mean Shift, MiniBatch K-Means, OPTICS, Spectral Clustering, and Ward Hierarchical. Then, the performance of all algorithms was examined across 51 synthetic and real datasets from various domains, dimensions, and complexities. Furthermore, we present a companion complexity analysis to compare the complexity of SPINEX to that of the aforementioned algorithms. Our results demonstrate that SPINEX can outperform commonly adopted clustering algorithms by ranking within the top-5 best performing algorithms and has moderate complexity. Finally, a demonstration of the explainability capabilities of SPINEX, along with future research needs, is presented.

The Connectivity Map (CMap) is a large publicly available database of cellular transcriptomic responses to chemical and genetic perturbations built using a standardized acquisition protocol known as the L1000 technique. Databases such as CMap provide an exciting opportunity to enrich drug discovery efforts, providing a 'known' phenotypic landscape to explore and enabling the development of state of the art techniques for enhanced information extraction and better informed decisions. Whilst multiple methods for measuring phenotypic similarity and interrogating profiles have been developed, the field is severely lacking standardized benchmarks using appropriate data splitting for training and unbiased evaluation of machine learning methods. To address this, we have developed 'Leak Proof CMap' and exemplified its application to a set of common transcriptomic and generic phenotypic similarity methods along with an exemplar triplet loss-based method. Benchmarking in three critical performance areas (compactness, distinctness, and uniqueness) is conducted using carefully crafted data splits ensuring no similar cell lines or treatments with shared or closely matching responses or mechanisms of action are present in training, validation, or test sets. This enables testing of models with unseen samples akin to exploring treatments with novel modes of action in novel patient derived cell lines. With a carefully crafted benchmark and data splitting regime in place, the tooling now exists to create performant phenotypic similarity methods for use in personalized medicine (novel cell lines) and to better augment high throughput phenotypic screening technologies with the L1000 transcriptomic technology.

In a number of information retrieval applications (e.g., patent search, literature review, due diligence, etc.), preventing false negatives is more important than preventing false positives. However, approaches designed to reduce review effort (like "technology assisted review") can create false negatives, since they are often based on active learning systems that exclude documents automatically based on user feedback. Therefore, this research proposes a more recall-oriented approach to reducing review effort. More specifically, through iteratively re-ranking the relevance rankings based on user feedback, which is also referred to as relevance feedback. In our proposed method, the relevance rankings are produced by a BERT-based dense-vector search and the relevance feedback is based on cumulatively summing the queried and selected embeddings. Our results show that this method can reduce review effort between 17.85% and 59.04%, compared to a baseline approach (of no feedback), given a fixed recall target.

It explores main concepts from basic to expert level which can help you achieve better grades, develop your academic career, apply your knowledge at work or make business forecasting related decisions. Read data files and perform regression machine learning operations by installing related packages and running code on the Python IDE. Approximate ensemble methods such as random forest regression and gradient boosting machine regression to enhance decision tree regression prediction accuracy. Read data files and perform regression machine learning operations by installing related packages and running code on the Python IDE. Approximate ensemble methods such as random forest regression and gradient boosting machine regression to enhance decision tree regression prediction accuracy.