The prediction of protein stability changes following single-point mutations plays a pivotal role in computational biology, particularly in areas like drug discovery, enzyme reengineering, and genetic disease analysis. Although deep-learning strategies have pushed the field forward, their use in standard workflows remains limited due to resource demands. Conversely, potential-like methods are fast, intuitive, and efficient. Yet, these typically estimate Gibbs free energy shifts without considering the free-energy variations in the unfolded protein state, an omission that may breach mass balance and diminish accuracy. This study shows that incorporating a mass-balance correction (MBC) to account for the unfolded state significantly enhances these methods. While many machine learning models partially model this balance, our analysis suggests that a refined representation of the unfolded state may improve the predictive performance.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a gene editing technology that has revolutionized the fields of biology and medicine. However, one of the challenges of using CRISPR is predicting the on-target efficacy and off-target sensitivity of single-guide RNAs (sgRNAs). This is because most existing methods are trained on separate datasets with different genes and cells, which limits their generalizability. In this paper, we propose a novel ensemble learning method for sgRNA design that is accurate and generalizable. Our method combines the predictions of multiple machine learning models to produce a single, more robust prediction. This approach allows us to learn from a wider range of data, which improves the generalizability of our model. We evaluated our method on a benchmark dataset of sgRNA designs and found that it outperformed existing methods in terms of both accuracy and generalizability. Our results suggest that our method can be used to design sgRNAs with high sensitivity and specificity, even for new genes or cells. This could have important implications for the clinical use of CRISPR, as it would allow researchers to design more effective and safer treatments for a variety of diseases.

CRISPR-based genome editing has revolutionized biotechnology, yet optimizing guide RNA (gRNA) design for efficiency and safety remains a critical challenge. Recent advances (2020--2025, updated to reflect current year if needed) demonstrate that artificial intelligence (AI), especially deep learning, can markedly improve the prediction of gRNA on-target activity and identify off-target risks. In parallel, emerging explainable AI (XAI) techniques are beginning to illuminate the black-box nature of these models, offering insights into sequence features and genomic contexts that drive Cas enzyme performance. Here we review how state-of-the-art machine learning models are enhancing gRNA design for CRISPR systems, highlight strategies for interpreting model predictions, and discuss new developments in off-target prediction and safety assessment. We emphasize breakthroughs from top-tier journals that underscore an interdisciplinary convergence of AI and genome editing to enable more efficient, specific, and clinically viable CRISPR applications.

The NLLG (Natural Language Learning & Generation) arXiv reports assist in navigating the rapidly evolving landscape of NLP and AI research across cs.CL, cs.CV, cs.AI, and cs.LG categories. This fourth installment captures a transformative period in AI history - from January 1, 2023, following ChatGPT's debut, through September 30, 2024. Our analysis reveals substantial new developments in the field - with 45% of the top 40 most-cited papers being new entries since our last report eight months ago and offers insights into emerging trends and major breakthroughs, such as novel multimodal architectures, including diffusion and state space models. Natural Language Processing (NLP; cs.CL) remains the dominant main category in the list of our top-40 papers but its dominance is on the decline in favor of Computer vision (cs.CV) and general machine learning (cs.LG). This report also presents novel findings on the integration of generative AI in academic writing, documenting its increasing adoption since 2022 while revealing an intriguing pattern: top-cited papers show notably fewer markers of AI-generated content compared to random samples. Furthermore, we track the evolution of AI-associated language, identifying declining trends in previously common indicators such as "delve".

This paper presents a real-time modular defense system named Sentra-Guard. The system detects and mitigates jailbreak and prompt injection attacks targeting large language models (LLMs). The framework uses a hybrid architecture with FAISS-indexed SBERT embedding representations that capture the semantic meaning of prompts, combined with fine-tuned transformer classifiers, which are machine learning models specialized for distinguishing between benign and adversarial language inputs. It identifies adversarial prompts in both direct and obfuscated attack vectors. A core innovation is the classifier-retriever fusion module, which dynamically computes context-aware risk scores that estimate how likely a prompt is to be adversarial based on its content and context. The framework ensures multilingual resilience with a language-agnostic preprocessing layer. This component automatically translates non-English prompts into English for semantic evaluation, enabling consistent detection across over 100 languages. The system includes a HITL feedback loop, where decisions made by the automated system are reviewed by human experts for continual learning and rapid adaptation under adversarial pressure. Sentra-Guard maintains an evolving dual-labeled knowledge base of benign and malicious prompts, enhancing detection reliability and reducing false positives. Evaluation results show a 99.96% detection rate (AUC = 1.00, F1 = 1.00) and an attack success rate (ASR) of only 0.004%. This outperforms leading baselines such as LlamaGuard-2 (1.3%) and OpenAI Moderation (3.7%). Unlike black-box approaches, Sentra-Guard is transparent, fine-tunable, and compatible with diverse LLM backends. Its modular design supports scalable deployment in both commercial and open-source environments. The system establishes a new state-of-the-art in adversarial LLM defense.

We perform trend detection on two datasets of Arxiv papers, derived from its machine learning (cs.LG) and natural language processing (cs.CL) categories. Our approach is bottom-up: we first rank papers by their normalized citation counts, then group top-ranked papers into different categories based on the tasks that they pursue and the methods they use. We then analyze these resulting topics. We find that the dominating paradigm in cs.CL revolves around natural language generation problems and those in cs.LG revolve around reinforcement learning and adversarial principles. By extrapolation, we predict that these topics will remain lead problems/approaches in their fields in the short- and mid-term.

Mathematical models, calibrated to data, have become ubiquitous to make key decision processes in modern quantitative finance. In this work, we propose a novel framework for data-driven model selection by integrating a classical quantitative setup with a generative modelling approach. Leveraging the properties of the signature, a well-known path-transform from stochastic analysis that recently emerged as leading machine learning technology for learning time-series data, we develop the Sig-SDE model. Sig-SDE provides a new perspective on neural SDEs and can be calibrated to exotic financial products that depend, in a non-linear way, on the whole trajectory of asset prices. Furthermore, we our approach enables to consistently calibrate under the pricing measure $\mathbb Q$ and real-world measure $\mathbb P$. Finally, we demonstrate the ability of Sig-SDE to simulate future possible market scenarios needed for computing risk profiles or hedging strategies. Importantly, this new model is underpinned by rigorous mathematical analysis, that under appropriate conditions provides theoretical guarantees for convergence of the presented algorithms.

Techniques of machine learning for automatic text categorization are applied and adapted for the problem of inventory catalog data attribution, with different approaches explored and optimal solution addressing the tradeoff between accuracy and performance is selected.

Determination of binding affinity of proteins in the formation of protein complexes requires sophisticated, expensive and time-consuming experimentation which can be replaced with computational methods. Most computational prediction techniques require protein structures which limit their applicability to protein complexes with known structures. In this work, we explore sequence based protein binding affinity prediction using machine learning. Our paper highlights the fact that the generalization performance of even the state of the art sequence-only predictor of binding affinity is far from satisfactory and that the development of effective and practical methods in this domain is still an open problem. We also propose a novel sequence-only predictor of binding affinity called ISLAND which gives better accuracy than existing methods over the same validation set as well as on external independent test dataset. A cloud-based webserver implementation of ISLAND and its Python code are available at the URL: http://faculty.pieas.edu.pk/fayyaz/software.html#island.

In this paper we present the Women in Computer Vision Workshop - WiCV 2019, organized in conjunction with CVPR 2019. This event is meant for increasing the visibility and inclusion of women researchers in the computer vision field. Computer vision and machine learning have made incredible progress over the past years, but the number of female researchers is still low both in academia and in industry. WiCV is organized especially for the following reason: to raise visibility of female researchers, to increase collaborations between them, and to provide mentorship to female junior researchers in the field. In this paper, we present a report of trends over the past years, along with a summary of statistics regarding presenters, attendees, and sponsorship for the current workshop.