Characterizing the differential excision of mRNA is critical for understanding the functional complexity of a cell or tissue, from normal developmental processes to disease pathogenesis. Most transcript reconstruction methods infer full-length transcripts from high-throughput sequencing data. However, this is a challenging task due to incomplete annotations and the differential expression of transcripts across cell-types, tissues, and experimental conditions. Several recent methods circumvent these difficulties by considering local splicing events, but these methods lose transcript-level splicing information and may conflate transcripts. We develop the first probabilistic model that reconciles the transcript and local splicing perspectives. First, we formalize the sequence of mRNA excisions (SME) reconstruction problem, which aims to assemble variable-length sequences of mRNA excisions from RNA-sequencing data. We then present a novel hierarchical Bayesian admixture model for the Reconstruction of Excised mRNA (BREM). BREM interpolates between local splicing events and full-length transcripts and thus focuses only on SMEs that have high posterior probability. We develop posterior inference algorithms based on Gibbs sampling and local search of independent sets and characterize differential SME usage using generalized linear models based on converged BREM model parameters. We show that BREM achieves higher F1 score for reconstruction tasks and improved accuracy and sensitivity in differential splicing when compared with four state-of-the-art transcript and local splicing methods on simulated data. Lastly, we evaluate BREM on both bulk and scRNA sequencing data based on transcript reconstruction, novelty of transcripts produced, model sensitivity to hyperparameters, and a functional analysis of differentially expressed SMEs, demonstrating that BREM captures relevant biological signal.

The subject of conversational mining has become of great interest recently due to the explosion of social and other online media. Supplementing this explosion of text is the advancement in pre-trained language models which have helped us to leverage these sources of information. An interesting domain to analyse is conversations in terms of complexity and value. Complexity arises due to the fact that a conversation can be asynchronous and can involve multiple parties. It is also computationally intensive to process. We use unsupervised methods in our work in order to develop a conversational pattern mining technique which does not require time consuming, knowledge demanding and resource intensive labelling exercises. The task of identifying repeating patterns in sequences is well researched in the Bioinformatics field. In our work, we adapt this to the field of Natural Language Processing and make several extensions to a motif detection algorithm. In order to demonstrate the application of the algorithm on a dynamic, real world data set; we extract motifs from an open-source film script data source. We run an exploratory investigation into the types of motifs we are able to mine.

Noname manuscript No. (will be inserted by the editor) Abstract This paper proposes a distributed weighted regularized lea st squares algorithm (DWRLS) with radial basis functions to tackle spherical data that are stored acr oss numerous local servers and cannot be shared with each other. Via developing a novel integral operator approa ch based on spherical quadrature rules, we succeed in deriving optimal approximation rates for DWRLS and theor etically demonstrate that DWRLS performs similarly as running a weighted regularized least squares algo rithm on the whole data stored on a large enough machine. This interesting finding implies that distributed learning is capable of sufficiently exploiting potential values of distributively stored spherical data, even thoug h local servers cannot access the whole data. Keywords Distributed learning Scattered data approximation Sphere Integral operator 1 Introduction In geophysics, solar system, climate prediction, environm ent governance and meteorology, and image rendering, samples formed as input-output pairs are collected over spheres [13, 15, 49], such as the surface of the earth and the direction of radiance. Due to the storage bo ttleneck and data privacy, these spherical data are often distributively stored across numerous computati onal servers.

Online continual learning (OCL) aims to train neural networks incrementally from a non-stationary data stream with a single pass through data. Rehearsal-based methods attempt to approximate the observed input distributions over time with a small memory and revisit them later to avoid forgetting. Despite their strong empirical performance, rehearsal methods still suffer from a poor approximation of past data's loss landscape with memory samples. This paper revisits the rehearsal dynamics in online settings. We provide theoretical insights on the inherent memory overfitting risk from the viewpoint of biased and dynamic empirical risk minimization, and examine the merits and limits of repeated rehearsal. Inspired by our analysis, a simple and intuitive baseline, repeated augmented rehearsal (RAR), is designed to address the underfitting-overfitting dilemma of online rehearsal. Surprisingly, across four rather different OCL benchmarks, this simple baseline outperforms vanilla rehearsal by 9%-17% and also significantly improves the state-of-the-art rehearsal-based methods MIR, ASER, and SCR. We also demonstrate that RAR successfully achieves an accurate approximation of the loss landscape of past data and high-loss ridge aversion in its learning trajectory. Extensive ablation studies are conducted to study the interplay between repeated and augmented rehearsal, and reinforcement learning (RL) is applied to dynamically adjust the hyperparameters of RAR to balance the stability-plasticity trade-off online.

End-to-end speech recognition models trained using joint Connectionist Temporal Classification (CTC)-Attention loss have gained popularity recently. In these models, a non-autoregressive CTC decoder is often used at inference time due to its speed and simplicity. However, such models are hard to personalize because of their conditional independence assumption that prevents output tokens from previous time steps to influence future predictions. To tackle this, we propose a novel two-way approach that first biases the encoder with attention over a predefined list of rare long-tail and out-of-vocabulary (OOV) words and then uses dynamic boosting and phone alignment network during decoding to further bias the subword predictions. We evaluate our approach on open-source VoxPopuli and in-house medical datasets to showcase a 60% improvement in F1 score on domain-specific rare words over a strong CTC baseline.

Matrix multiplication is a fundamental operation in machine learning and is commonly distributed into multiple parallel tasks for large datasets. Stragglers and other failures can severely impact the overall completion time. Recent works in coded computing provide a novel strategy to mitigate stragglers with coded tasks, with an objective of minimizing the number of tasks needed to recover the overall result, known as the recovery threshold. However, we demonstrate that this combinatorial definition does not directly optimize the probability of failure. In this paper, we introduce a novel analytical metric, which focuses on the most likely event and measures the optimality of a coding scheme by its probability of decoding. Our general framework encompasses many other computational schemes and metrics as a special case. Far from being a purely theoretical construction, these definitions lead us to a practical construction of random codes for matrix multiplication, i.e., locally random alloy codes, which are optimal with respect to the measures. We present experimental results on Amazon EC2 which empirically demonstrate the improvement in terms of running time and numerical stability relative to well-established benchmarks.

Ransomware has appeared as one of the major global threats in recent days. The alarming increasing rate of ransomware attacks and new ransomware variants intrigue the researchers to constantly examine the distinguishing traits of ransomware and refine their detection strategies. Application Programming Interface (API) is a way for one program to collaborate with another; API calls are the medium by which they communicate. Ransomware uses this strategy to interact with the OS and makes a significantly higher number of calls in different sequences to ask for taking action. This research work utilizes the frequencies of different API calls to detect and classify ransomware families. First, a Web-Crawler is developed to automate collecting the Windows Portable Executable (PE) files of 15 different ransomware families. By extracting different frequencies of 68 API calls, we develop our dataset in the first phase of the two-phase feature engineering process. After selecting the most significant features in the second phase of the feature engineering process, we deploy six Supervised Machine Learning models: Na"ive Bayes, Logistic Regression, Random Forest, Stochastic Gradient Descent, K-Nearest Neighbor, and Support Vector Machine. Then, the performances of all the classifiers are compared to select the best model. The results reveal that Logistic Regression can efficiently classify ransomware into their corresponding families securing 99.15% overall accuracy. Finally, instead of relying on the 'Black box' characteristic of the Machine Learning models, we present the post-hoc analysis of our best-performing model using 'SHapley Additive exPlanations' or SHAP values to ascertain the transparency and trustworthiness of the model's prediction.

We are pleased to announce, thanks to the acquisition of Latham BioPharm Group, we are accelerating in the Life Sciences sector with the creation of a Life Science Consulting division. Latham BioPharm Group founded in 1996 by Peter Latham, is one of the top Life Science Consulting specialty firms supporting Non-Dilutive Funding, Product Development, and Strategic decision-making for a wide range of sectors and clients. "Pete and I have agreed on a global goal, supported by significant financial resources, that will allow us to grow organically at more than 20% per year...." says Matthieu Courtecuisse, Founder and CEO of Sia Partners.

The anti-interference capability of wireless links is a physical layer problem for edge computing. Although convolutional codes have inherent error correction potential due to the redundancy introduced in the data, the performance of the convolutional code is drastically degraded due to multipath effects on the channel. In this paper, we propose the use of a Hidden Markov Model (HMM) for the reconstruction of convolutional codes and decoding by the Viterbi algorithm. Furthermore, to implement soft-decision decoding, the observation of HMM is replaced by Gaussian mixture models (GMM). Our method provides superior error correction potential than the standard method because the model parameters contain channel state information (CSI). We evaluated the performance of the method compared to standard Viterbi decoding by numerical simulation. In the multipath channel, the hybrid HMM decoder can achieve a performance gain of 4.7 dB and 2 dB when using hard-decision and soft-decision decoding, respectively. The HMM decoder also achieves significant performance gains for the RSC code, suggesting that the method could be extended to turbo codes.

We introduce a method to successively locate equilibria (steady states) of dynamical systems on Riemannian manifolds. The manifolds need not be characterized by an a priori known atlas or by the zeros of a smooth map. Instead, they can be defined by point-clouds and sampled as needed through an iterative process. If the manifold is an Euclidean space, our method follows isoclines, curves along which the direction of the vector field $X$ is constant. For a generic vector field $X$, isoclines are smooth curves and every equilibrium lies on isoclines. We generalize the definition of isoclines to Riemannian manifolds through the use of parallel transport: generalized isoclines are curves along which the directions of $X$ are parallel transports of each other. As in the Euclidean case, generalized isoclines of generic vector fields $X$ are smooth curves that connect equilibria of $X$. Our algorithm can be regarded as an extension of the method of Newton trajectories to the manifold setting when the manifold is unknown. This work is motivated by computational statistical mechanics, specifically high dimensional (stochastic) differential equations that model the dynamics of molecular systems. Often, these dynamics concentrate near low-dimensional manifolds and have transitions (saddle points with a single unstable direction) between metastable equilibria. We employ iteratively sampled data and isoclines to locate these saddle points. Coupling a black-box sampling scheme (e.g., Markov chain Monte Carlo) with manifold learning techniques (diffusion maps in the case presented here), we show that our method reliably locates equilibria of $X$.