FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning

Molecular relational learning (MRL) is crucial for understanding the interaction behaviors between molecular pairs, a critical aspect of drug discovery and development. However, the large feasible model space of MRL poses significant challenges to benchmarking, and existing MRL frameworks face limitations in flexibility and scope. To address these challenges, avoid repetitive coding efforts, and ensure fair comparison of models, we introduce FlexMol, a comprehensive toolkit designed to facilitate the construction and evaluation of diverse model architectures across various datasets and performance metrics. FlexMol offers a robust suite of preset model components, including 16 drug encoders, 13 protein sequence encoders, 9 protein structure encoders, and 7 interaction layers. With its easy-to-use API and flexibility, FlexMol supports the dynamic construction of over 70, 000 distinct combinations of model architectures. Additionally, we provide detailed benchmark results and code examples to demonstrate FlexMol's effectiveness in simplifying and standardizing MRL model development and comparison.

Text-guided Diffusion Model for 3D Molecule Generation

The de novo generation of molecules with targeted properties is crucial in biology, chemistry, and drug discovery. Current generative models are limited to using single property values as conditions, struggling with complex customizations described in detailed human language. To address this, we propose the text guidance instead, and introduce TextSMOG, a new Text-guided Small Molecule Generation Approach via 3D Diffusion Model which integrates language and diffusion models for text-guided small molecule generation. This method uses textual conditions to guide molecule generation, enhancing both stability and diversity. Experimental results show TextSMOG's proficiency in capturing and utilizing information from textual descriptions, making it a powerful tool for generating 3D molecular structures in response to complex textual customizations.

TSI-Bench: Benchmarking Time Series Imputation

Effective imputation is a crucial preprocessing step for time series analysis. Despite the development of numerous deep learning algorithms for time series imputation, the community lacks standardized and comprehensive benchmark platforms to effectively evaluate imputation performance across different settings. Moreover, although many deep learning forecasting algorithms have demonstrated excellent performance, whether their modeling achievements can be transferred to time series imputation tasks remains unexplored. To bridge these gaps, we develop TSI-Bench, the first (to our knowledge) comprehensive benchmark suite for time series imputation utilizing deep learning techniques. The TSI-Bench pipeline standardizes experimental settings to enable fair evaluation of imputation algorithms and identification of meaningful insights into the influence of domain-appropriate missingness ratios and patterns on model performance. Furthermore, TSI-Bench innovatively provides a systematic paradigm to tailor time series forecasting algorithms for imputation purposes. Our extensive study across 34,804 experiments, 28 algorithms, and 8 datasets with diverse missingness scenarios demonstrates TSI-Bench's effectiveness in diverse downstream tasks and potential to unlock future directions in time series imputation research and analysis. The source code and experiment logs are available at https://github.com/WenjieDu/AwesomeImputation.

NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Many deep learning methods have been developed for \emph{de novo} peptide sequencing task, i.e., predicting the peptide sequence for the observed mass spectrum. However, two key challenges seriously hinder the further advancement of this important task. Firstly, since there is no consensus for the evaluation datasets, the empirical results in different research papers are often not comparable, leading to unfair comparison. Secondly, the current methods are usually limited to amino acid-level or peptide-level precision and recall metrics. In this work, we present the first unified benchmark NovoBench for \emph{de novo} peptide sequencing, which comprises diverse mass spectrum data, integrated models, and comprehensive evaluation metrics. Recent impressive methods, including DeepNovo, PointNovo, Casanovo, InstaNovo, AdaNovo and $\pi$-HelixNovo are integrated into our framework. In addition to amino acid-level and peptide-level precision and recall, we evaluate the models' performance in terms of identifying post-tranlational modifications (PTMs), efficiency and robustness to peptide length, noise peaks and missing fragment ratio, which are important influencing factors while seldom be considered. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development. The benchmark will be open-sourced to facilitate future research and application.

Unveiling the Secrets: How Masking Strategies Shape Time Series Imputation

In this study, we explore the impact of different masking strategies on time series imputation models. We evaluate the effects of pre-masking versus in-mini-batch masking, normalization timing, and the choice between augmenting and overlaying artificial missingness. Using three diverse datasets, we benchmark eleven imputation models with different missing rates. Our results demonstrate that masking strategies significantly influence imputation accuracy, revealing that more sophisticated and data-driven masking designs are essential for robust model evaluation. We advocate for refined experimental designs and comprehensive disclosureto better simulate real-world patterns, enhancing the practical applicability of imputation models.

AdaNovo: Adaptive \emph{De Novo} Peptide Sequencing with Conditional Mutual Information

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological samples. Despite the development of various deep learning methods for identifying amino acid sequences (peptides) responsible for observed spectra, challenges persist in \emph{de novo} peptide sequencing. Firstly, prior methods struggle to identify amino acids with post-translational modifications (PTMs) due to their lower frequency in training data compared to canonical amino acids, further resulting in decreased peptide-level identification precision. Secondly, diverse types of noise and missing peaks in mass spectra reduce the reliability of training data (peptide-spectrum matches, PSMs). To address these challenges, we propose AdaNovo, a novel framework that calculates conditional mutual information (CMI) between the spectrum and each amino acid/peptide, using CMI for adaptive model training. Extensive experiments demonstrate AdaNovo's state-of-the-art performance on a 9-species benchmark, where the peptides in the training set are almost completely disjoint from the peptides of the test sets. Moreover, AdaNovo excels in identifying amino acids with PTMs and exhibits robustness against data noise. The supplementary materials contain the official code.

MolTC: Towards Molecular Relational Modeling In Language Models

Molecular Relational Learning (MRL), aiming to understand interactions between molecular pairs, plays a pivotal role in advancing biochemical research. Recently, the adoption of large language models (LLMs), known for their vast knowledge repositories and advanced logical inference capabilities, has emerged as a promising way for efficient and effective MRL. Despite their potential, these methods predominantly rely on the textual data, thus not fully harnessing the wealth of structural information inherent in molecular graphs. Moreover, the absence of a unified framework exacerbates the issue of information underutilization, as it hinders the sharing of interaction mechanism learned across diverse datasets. To address these challenges, this work proposes a novel LLM-based multi-modal framework for Molecular inTeraction prediction following Chain-of-Thought (CoT) theory, termed MolTC, which effectively integrate graphical information of two molecules in pair. For achieving a unified MRL, MolTC innovatively develops a dynamic parameter-sharing strategy for cross-dataset information sharing. Moreover, to train MolTC efficiently, we introduce a Multi-hierarchical CoT concept to refine its training paradigm, and conduct a comprehensive Molecular Interactive Instructions dataset for the development of biochemical LLMs involving MRL. Our experiments, conducted across various datasets involving over 4,000,000 molecular pairs, exhibit the superiority of our method over current GNN and LLM-based baselines. Code is available at https://github.com/MangoKiller/MolTC.

Deep Learning for Multivariate Time Series Imputation: A Survey

The ubiquitous missing values cause the multivariate time series data to be partially observed, destroying the integrity of time series and hindering the effective time series data analysis. Recently deep learning imputation methods have demonstrated remarkable success in elevating the quality of corrupted time series data, subsequently enhancing performance in downstream tasks. In this paper, we conduct a comprehensive survey on the recently proposed deep learning imputation methods. First, we propose a taxonomy for the reviewed methods, and then provide a structured review of these methods by highlighting their strengths and limitations. We also conduct empirical experiments to study different methods and compare their enhancement for downstream tasks. Finally, the open issues for future research on multivariate time series imputation are pointed out. All code and configurations of this work, including a regularly maintained multivariate time series imputation paper list, can be found in the GitHub repository~\url{https://github.com/WenjieDu/Awesome\_Imputation}.

Trusta: Reasoning about Assurance Cases with Formal Methods and Large Language Models

Assurance cases can be used to argue for the safety of products in safety engineering. In safety-critical areas, the construction of assurance cases is indispensable. Trustworthiness Derivation Trees (TDTs) enhance assurance cases by incorporating formal methods, rendering it possible for automatic reasoning about assurance cases. We present Trustworthiness Derivation Tree Analyzer (Trusta), a desktop application designed to automatically construct and verify TDTs. The tool has a built-in Prolog interpreter in its backend, and is supported by the constraint solvers Z3 and MONA. Therefore, it can solve constraints about logical formulas involving arithmetic, sets, Horn clauses etc. Trusta also utilizes large language models to make the creation and evaluation of assurance cases more convenient. It allows for interactive human examination and modification. We evaluated top language models like ChatGPT-3.5, ChatGPT-4, and PaLM 2 for generating assurance cases. Our tests showed a 50%-80% similarity between machine-generated and human-created cases. In addition, Trusta can extract formal constraints from text in natural languages, facilitating an easier interpretation and validation process. This extraction is subject to human review and correction, blending the best of automated efficiency with human insight. To our knowledge, this marks the first integration of large language models in automatic creating and reasoning about assurance cases, bringing a novel approach to a traditional challenge. Through several industrial case studies, Trusta has proven to quickly find some subtle issues that are typically missed in manual inspection, demonstrating its practical value in enhancing the assurance case development process.

PyPOTS: A Python Toolbox for Data Mining on Partially-Observed Time Series

PyPOTS is an open-source Python library dedicated to data mining and analysis on multivariate partially-observed time series, i.e. incomplete time series with missing values, A.K.A. irregularlysampled time series. Particularly, it provides easy access to diverse algorithms categorized into four tasks: imputation, classification, clustering, and forecasting. The included models contain probabilistic approaches as well as neural-network methods, with a well-designed and fully-documented programming interface for both academic researchers and industrial professionals to use. With robustness and scalability in its design philosophy, best practices of software construction, for example, unit testing, continuous integration (CI) and continuous delivery (CD), code coverage, maintainability evaluation, interactive tutorials, and parallelization, are carried out as principles during the development of PyPOTS. The toolkit is available on both Python Package Index (PyPI) and Anaconda. PyPOTS is open-source and publicly available on GitHub https://github.com/WenjieDu/PyPOTS.