Epitope prediction improved by multitask support vector machines

Motivation: In silico methods for the prediction of antigenic peptides binding to MHC class I molecules play an increasingly important role in the identification of T-cell epitopes. Statistical and machine learning methods, in particular, are widely used to score candidate epitopes based on their similarity with known epitopes and non epitopes. The genes coding for the MHC molecules, however, are highly polymorphic, and statistical methods have difficulties to build models for alleles with few known epitopes. In this case, recent works have demonstrated the utility of leveraging information across alleles to improve the performance of the prediction. Results: We design a support vector machine algorithm that is able to learn epitope models for all alleles simultaneously, by sharing information across similar alleles. The sharing of information across alleles is controlled by a user-defined measure of similarity between alleles. We show that this similarity can be defined in terms of supertypes, or more directly by comparing key residues known to play a role in the peptide-MHC binding. We illustrate the potential of this approach on various benchmark experiments where it outperforms other state-of-the-art methods

Financial deepening and economic growth

The core of Shapley-Shubik games and general equilibrium models with a Venn diagram is applied for a theory on the role of real finance in economic growth among advanced economies. Then the dynamic computable general equilibrium (DCGE) models for Germany, France, UK, Japan and USA are constructed to assess the validity of the over financing hypothesis that reappeared after the financial crisis of 2008. Actual financial deepening ratios observed in the non-consolidated balance sheet of the OECD exceeded by factors of 3.5, 2.4, 5.1, 11.6 and 4.8 to the optimal financial deepening ratios implied by DCGE models respectively in these countries because of excessive leveraging and bubbles up to 19 times of GDP which were responsible for this great recession. Containing such massive fluctuations for macroeconomic stability and growth in these economies is not possible in conventional fiscal and monetary policy models and requires a DCGE analysis like this along with adoption of separating equilibria strategy in line of Miller-Stiglitz-Roth mechanisms to avoid asymmetric information problems in process of financial intermediation so that the gap between actual and optimal ratios of financial deepening remain as small as possible

Leveraging Information Sharing to Increase Supply Chain Configurability

As supply chains evolve beyond the confines of individual organizations, collaboration has become the Holy Grail in supply chain technology. It plays a key role in achieving flexibility and responsiveness. Information sharing between partners is a key determinant of collaboration. This paper investigates information sharing in four different supply chains—3PL, VMI, CPFR, and supply networks—and compares their information sharing structures, shared data objects, and information flow models. The results show how the various parameters of an information flow model constrain the level of collaboration. Further, the modeling exercise provides insights on how to configure a collaborative supply chain by leveraging information sharing

CSI-Free Optimization of Reconfigurable Intelligent Surfaces with Interference by Using Multiport Network Theory

Reconfigurable Intelligent Surfaces (RIS) will play a pivotal role in next-generation wireless systems. Despite efforts to minimize pilot overhead associated with channel estimation, the necessity of configuring the RIS multiple times before obtaining reliable Channel State Information (CSI) may significantly diminish their benefits. Therefore, we propose a CSI-free approach that explores the feasibility of optimizing the RIS for the uplink of a communication system in the presence of interfering users without relying on CSI estimation but leveraging solely some a priori statistical knowledge of the channel. In this context, we consider a multiport network model that accounts for several aspects overlooked by traditional RIS models used in Communication Theory, such as mutual coupling among scattering elements and the presence of structural scattering. The proposed approach targets the maximization of the average achievable rate and is shown to achieve performance that, in some cases, can be very close to the case where the RIS is optimized leveraging perfect CSI.Comment: 12 pages, 8 figure

LLMs as Counterfactual Explanation Modules: Can ChatGPT Explain Black-box Text Classifiers?

Large language models (LLMs) are increasingly being used for tasks beyond text generation, including complex tasks such as data labeling, information extraction, etc. With the recent surge in research efforts to comprehend the full extent of LLM capabilities, in this work, we investigate the role of LLMs as counterfactual explanation modules, to explain decisions of black-box text classifiers. Inspired by causal thinking, we propose a pipeline for using LLMs to generate post-hoc, model-agnostic counterfactual explanations in a principled way via (i) leveraging the textual understanding capabilities of the LLM to identify and extract latent features, and (ii) leveraging the perturbation and generation capabilities of the same LLM to generate a counterfactual explanation by perturbing input features derived from the extracted latent features. We evaluate three variants of our framework, with varying degrees of specificity, on a suite of state-of-the-art LLMs, including ChatGPT and LLaMA 2. We evaluate the effectiveness and quality of the generated counterfactual explanations, over a variety of text classification benchmarks. Our results show varied performance of these models in different settings, with a full two-step feature extraction based variant outperforming others in most cases. Our pipeline can be used in automated explanation systems, potentially reducing human effort

Unveiling the Potential of Probabilistic Embeddings in Self-Supervised Learning

In recent years, self-supervised learning has played a pivotal role in advancing machine learning by allowing models to acquire meaningful representations from unlabeled data. An intriguing research avenue involves developing self-supervised models within an information-theoretic framework, but many studies often deviate from the stochasticity assumptions made when deriving their objectives. To gain deeper insights into this issue, we propose to explicitly model the representation with stochastic embeddings and assess their effects on performance, information compression and potential for out-of-distribution detection. From an information-theoretic perspective, we seek to investigate the impact of probabilistic modeling on the information bottleneck, shedding light on a trade-off between compression and preservation of information in both representation and loss space. Emphasizing the importance of distinguishing between these two spaces, we demonstrate how constraining one can affect the other, potentially leading to performance degradation. Moreover, our findings suggest that introducing an additional bottleneck in the loss space can significantly enhance the ability to detect out-of-distribution examples, only leveraging either representation features or the variance of their underlying distribution.Comment: Under review by AISTATS 202

A Multimodal Learning Framework for Comprehensive 3D Mineral Prospectivity Modeling with Jointly Learned Structure-Fluid Relationships

This study presents a novel multimodal fusion model for three-dimensional mineral prospectivity mapping (3D MPM), effectively integrating structural and fluid information through a deep network architecture. Leveraging Convolutional Neural Networks (CNN) and Multilayer Perceptrons (MLP), the model employs canonical correlation analysis (CCA) to align and fuse multimodal features. Rigorous evaluation on the Jiaojia gold deposit dataset demonstrates the model's superior performance in distinguishing ore-bearing instances and predicting mineral prospectivity, outperforming other models in result analyses. Ablation studies further reveal the benefits of joint feature utilization and CCA incorporation. This research not only advances mineral prospectivity modeling but also highlights the pivotal role of data integration and feature alignment for enhanced exploration decision-making

Video Game Genre Classification Based on Deep Learning

Video games have played a more and more important role in our life. While the genre classification is a deeply explored research subject by leveraging the strength of deep learning, the automatic video game genre classification has drawn little attention in academia. In this study, we compiled a large dataset of 50,000 video games, consisting of the video game covers, game descriptions and the genre information. We explored three approaches for genre classification using deep learning techniques. First, we developed five image-based models utilizing pre-trained computer vision models such as MobileNet, ResNet50 and Inception, based on the game covers. Second, we developed two text-based models, using Long-short Term Memory (LSTM) model and the Universal Sentence Encoder model, based on the game descriptions. For the third approach, we constructed a multi-modal fusion model, which concatenates extracted features from one image-based model and one text-based model. We analysed our results and revealed some challenges that exist in the task of genre classification for video games. Some future works are also proposed