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1. An Automated Model Annotation System (AMAS) for SBML Models

   Woosub Shin, John H. (July 2023, bioRxiv)

   Motivation Annotations of biochemical models provide details of chemical species, documentation of chemical reactions, and other essential information. Unfortunately, the vast majority of biochemical models have few, if any, annotations, or the annotations provide insufficient detail to understand the limitations of the model. The quality and quantity of annotations can be improved by developing tools that recommend annotations. For example, recommender tools have been developed for annotations of genes. Although annotating genes is conceptually similar to annotating biochemical models, there are important technical differences that make it difficult to directly apply this prior work. Results We present AMAS, a system that predicts annotations for elements of models represented in the Systems Biology Markup Language (SBML) community standard. We provide a general framework for predicting model annotations for a query element based on a database of annotated reference elements and a match score function that calculates the similarity between the query element and reference elements. The framework is instantiated to specific element types (e.g., species, reactions) by specifying the reference database (e.g., ChEBI for species) and the match score function (e.g., string similarity). We analyze the computational efficiency and prediction quality of AMAS for species and reactions in BiGG and BioModels and find that it has sub-second response times and accuracy between 80% and 95% depending on specifics of what is predicted. We have incorporated AMAS into an open-source, pip-installable Python package that can run as a command-line tool that predicts and adds annotations to species and reactions to an SBML model. Availability Our project is hosted at https://github.com/sys-bio/AMAS, where we provide examples, documentation, and source code files. Our source code is licensed under the MIT open-source license. 

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2. Learning to Find Usage of Library Functions in Optimized Binaries

   https://doi.org/10.1109/TSE.2021.3106572  

   Ahmed, Toufique; Devanbu, Premkumar; Sawant, Anand Ashok (August 2021, IEEE Transactions on Software Engineering)

   Much software, whether beneficent or malevolent, is distributed only as binaries, sans source code. Absent source code, understanding binaries' behavior can be quite challenging, especially when compiled under higher levels of compiler optimization. These optimizations can transform comprehensible, ``natural" source constructions into something entirely unrecognizable. Reverse engineering binaries, especially those suspected of being malevolent or guilty of intellectual property theft, are important and time-consuming tasks. There is a great deal of interest in tools to ``decompile" binaries back into more natural source code to aid reverse engineering. Decompilation involves several desirable steps, including recreating source-language constructions, variable names, and perhaps even comments. One central step in creating binaries is optimizing function calls, using steps such as inlining. Recovering these (possibly inlined) function calls from optimized binaries is an essential task that most state-of-the-art decompiler tools try to do but do not perform very well. In this paper, we evaluate a supervised learning approach to the problem of recovering optimized function calls. We leverage open-source software and develop an automated labeling scheme to generate a reasonably large dataset of binaries labeled with actual function usages. We augment this large but limited labeled dataset with a pre-training step, which learns the decompiled code statistics from a much larger unlabeled dataset. Thus augmented, our learned labeling model can be combined with an existing decompilation tool, Ghidra, to achieve substantially improved performance in function call recovery, especially at higher levels of optimization. 

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3. Practical Type-Based Taint Checking and Inference

   https://doi.org/10.4230/LIPIcs.ECOOP.2025.18  

   Karimipour, Nima; Das, Kanak; Sridharan, Manu; Hassanshahi, Behnaz (June 2025, Schloss Dagstuhl – Leibniz-Zentrum für Informatik)

   Aldrich, Jonathan; Silva, Alexandra (Ed.)

   Many important security properties can be formulated in terms of flows of tainted data, and improved taint analysis tools to prevent such flows are of critical need. Most existing taint analyses use whole-program static analysis, leading to scalability challenges. Type-based checking is a promising alternative, as it enables modular and incremental checking for fast performance. However, type-based approaches have not been widely adopted in practice, due to challenges with false positives and annotating existing codebases. In this paper, we present a new approach to type-based checking of taint properties that addresses these challenges, based on two key techniques. First, we present a new type-based tainting checker with significantly reduced false positives, via more practical handling of third-party libraries and other language constructs. Second, we present a novel technique to automatically infer tainting type qualifiers for existing code. Our technique supports inference of generic type argument annotations, crucial for tainting properties. We implemented our techniques in a tool TaintTyper and evaluated it on real-world benchmarks. TaintTyper exceeds the recall of a state-of-the-art whole-program taint analyzer, with comparable precision, and 2.93X-22.9X faster checking time. Further, TaintTyper infers annotations comparable to those written by hand, suitable for insertion into source code. TaintTyper is a promising new approach to efficient and practical taint checking. 

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4. VITALSE: visualizing eye tracking and biometric data

   https://doi.org/10.1145/3377812.3382154  

   Roy, Devjeet; Fakhoury, Sarah; Arnaoudova, Venera (June 2020, ICSE '20: Proceedings of the ACM/IEEE 42nd International Conference on Software Engineering: Companion Proceedings)

   null (Ed.)

   Recent research in empirical software engineering is applying techniques from neurocognitive science and breaking new grounds in the ways that researchers can model and analyze the cognitive processes of developers as they interact with software artifacts. However, given the novelty of this line of research, only one tool exists to help researchers represent and analyze this kind of multi-modal biometric data. While this tool does help with visualizing temporal eyetracking and physiological data, it does not allow for the mapping of physiological data to source code elements, instead projecting information over images of code. One drawback of this is that researchers are still unable to meaningfully combine and map physiological and eye tracking data to source code artifacts. The use of images also bars the support of long or multiple code files, which prevents researchers from analyzing data from experiments conducted in realistic settings. To address these drawbacks, we propose VITALSE, a tool for the interactive visualization of combined multi-modal biometric data for software engineering tasks. VITALSE provides interactive and customizable temporal heatmaps created with synchronized eyetracking and biometric data. The tool supports analysis on multiple files, user defined annotations for points of interest over source code elements, and high level customizable metric summaries for the provided dataset. VITALSE, a video demonstration, and sample data to demonstrate its capabilities can be found at http://www.vitalse.app. 

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5. MUNDO: protein function prediction embedded in a multispecies world

   https://doi.org/10.1093/bioadv/vbab025  

   Arsenescu, Victor; Devkota, Kapil; Erden, Mert; Shpilker, Polina; Werenski, Matthew; Cowen, Lenore J (January 2022, Bioinformatics Advances)

   Mulder, Nicola (Ed.)

   Abstract Motivation Leveraging cross-species information in protein function prediction can add significant power to network-based protein function prediction methods, because so much functional information is conserved across at least close scales of evolution. We introduce MUNDO, a new cross-species co-embedding method that combines a single-network embedding method with a co-embedding method to predict functional annotations in a target species, leveraging also functional annotations in a model species network. Results Across a wide range of parameter choices, MUNDO performs best at predicting annotations in the mouse network, when trained on mouse and human protein–protein interaction (PPI) networks, in the human network, when trained on human and mouse PPIs, and in Baker’s yeast, when trained on Fission and Baker’s yeast, as compared to competitor methods. MUNDO also outperforms all the cross-species methods when predicting in Fission yeast when trained on Fission and Baker’s yeast; however, in this single case, discarding the information from the other species and using annotations from the Fission yeast network alone usually performs best. Availability and implementation All code is available and can be accessed here: github.com/v0rtex20k/MUNDO. Supplementary information Supplementary data are available at Bioinformatics Advances online. Additional experimental results are on our github site. 

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