Title
Topic
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‘Keeping in Touch With the Road Not Taken’
Associate professor of biology Javier Apfeld pens an opinion piece on why he’s kept in touch with the field of structural biology, despite having moved on professionally to other fields. “In my case, keeping up with the discoveries others made as they journeyed along paths I didn’t,” he writes, “has allowed me to share in the joy and fulfillment brought by the advancements in knowledge from their journeys.”
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NIH funds Ivanov’s proteome profiling
“Deep proteomic profiling of scarce biological and clinical samples is still a major challenge since no amplification techniques are available for proteins and proteoforms, and current state-of-the-art proteomic techniques based on conventional chromatography columns coupled with mass spectrometry provide suboptimal performance and sensitivity levels. In this study, based on our novel, currently unavailable on the market, chromatographic column technology, we plan to build a reliable, robust, thoroughly evaluated commercialization-ready prototype chromatography platform to enable ultrasensitive proteomic profiling and address the challenges of numerous clinical, academic, and industrial laboratories.”
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‘Persistent Tissue-Specific Resident Microbiota in Oysters Across a Broad Geographical Range’
“Marine animals often harbour complex microbial communities that influence their physiology. However, strong evidence for resident microbiomes in marine bivalves is lacking, despite their contribution to estuarine habitats and coastal economies. We investigated whether marine bivalves harbour stable, resident microorganisms in specific tissues or if their microbiomes primarily consist of transient members reflecting the environmental microbial pool. … [Our] findings underscore the oyster host’s role in selecting its microbiome and highlight the importance of tissue-specific microbial communities in understanding bivalve-associated microbiomes.” Find the paper and full list of authors in Environmental Biology.
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‘Choroid Plexus Volume Only Increases Early after Traumatic Brain Injury’
“Traumatic brain injury (TBI) affects nearly 2.5 million people each year and results in a cascade of neurometabolic effects, including prolonged inflammatory processes. Choroid plexus (ChP) swelling has been postulated to occur following TBI due to neuroinflammation. However, it is unknown if the ChP swells as a consequence of the post-TBI neuroinflammatory cascade, and it is unknown if swelling could be detectable via human volumetric imaging. Therefore, this study aims to test for the effect of TBI on ChP volume using a case–control study design.” Find the paper and full list of authors in Neurotrauma Reports.
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‘Enhanced Proteomic Profiling of Human Plasma-Derived Extracellular Vesicles Through Charge-Based Fractionation’
“The study introduces a charge-based fractionation method for fractionating plasma-derived extracellular vesicles (EVs) into sub-populations aimed at the improved purification from free plasma proteins to enhance the diagnostic potential of EV sub-populations for specific pathophysiological states. Here, we present a novel approach for EV fractionation that leverages EVs’ inherent surface charges, differentiating them from other plasma components and, thus, reducing the sample complexity and increasing the purity of EVs.” Find the paper and full list of authors in the Journal of Extracellular Vesicles.
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‘What I Learned at the White House, or, the Importance of Measurement Researchers Engaging with Policy’
“Computing systems now impact almost every aspect of our daily lives. As these systems evolve and develop, they often raise new challenges to our security and privacy, as well as to our commitments to equity and justice. To identify and mitigate the risks that these new technologies present, it is crucial to have scientific and technological experts participate in the conversation. … In this talk, I’ll reflect on my 18 months serving at the White House Office of Science and Technology Policy (OSTP) as Deputy U.S. Chief Technology Officer for Privacy.”
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DoE funds Feiguin’s quantum materials research
“Our ultimate goal is to accelerate discovery in quantum materials at DOE-supported user facilities. We will meet this goal through three specific aims. Aim 1 — generating and confirming novel low-energy effective many-body models for quantum materials. … Aim 2 — accelerating model solutions for advanced non-perturbative computational methods — is creating new state-of-the-art computational approaches for solving these models. … Finally, aim 3 — creating end-to-end experiment and theory workflows — is laying the foundation for integrating Aims 1 and 2 into new scientific workflows for scattering experiments.”
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Shansky receives National Institute of Mental Health support to study brain development post-pregnancy
“Pregnancy is characterized by marked changes in circulating hormones that can induce long-lasting changes in the brain. The goal of this project is to determine how the hormone allopregnanolone may induce a robust neural inhibition in the medial prefrontal cortex during pregnancy, resulting in over-compensatory actions that persist well after birth. Our work will provide much-needed insight into the development of the brain post-pregnancy.”
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‘Understanding Cognitive Aging Through White Matter: A Fixel-Based Analysis’
“Diffusion-weighted imaging (DWI) has been frequently used to examine age-related deterioration of white matter microstructure and its relationship to cognitive decline. However, typical tensor-based analytical approaches are often difficult to interpret due to the challenge of decomposing and (mis)interpreting the impact of crossing fibers within a voxel. We hypothesized that a novel analytical approach capable of resolving fiber-specific changes within each voxel (i.e., fixel-based analysis [FBA])—would show greater sensitivity relative to the traditional tensor-based approach for assessing relationships between white matter microstructure, age, and cognitive performance.” Find the paper and full list of authors in Human Brain Mapping.
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‘Epibiosis by Florida Crown Conch on Green Sea Turtles in a Northern Florida Estuary’
“We report the first observations of Melongena corona (Florida Crown Conch) as an epibiont attached to the carapace of juvenile Chelonia mydas (Green Sea Turtle). The Florida Crown Conch is a carnivorous marine gastropod found in benthic intertidal communities along the coast of Florida, southeastern Alabama, and parts of the Caribbean. … [W]e propose that Green Turtles may be facilitating the northern expansion of the Florida Crown Conch, which would be an important dynamic to account for when designing and implementing conservation, restoration, and aquaculture programs for shellfish areas.” Find the paper and authors list in Southeastern Naturalist.
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‘Ethics and Transparency in Game Data’
“While existing work has discussed ethics and fairness in relation to data generally, and a small number of papers have raised the same issues within games specifically, work on addressing fairness and ethical issues with game data collection and usage is still rare. … Our goal for this workshop is, thus, to bring together researchers and professionals working in the spaces of game human–computer interaction (HCI), game data and AI, and ethics in both games and AI to discuss and identify interdisciplinary research opportunities and devise potential solutions.” Find the paper and list of authors in the CHI PLAY Companion…
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‘A Nominal Approach to Probabilistic Separation Logic’
“Currently, there is a gap between the tools used by probability theorists and those used in formal reasoning about probabilistic programs. On the one hand, a probability theorist decomposes probabilistic state along the simple and natural product of probability spaces. On the other hand, recently developed probabilistic separation logics decompose state via relatively unfamiliar measure-theoretic constructions for computing unions of sigma-algebras and probability measures. We bridge the gap between these two perspectives by showing that these two methods of decomposition are equivalent up to a suitable equivalence of categories.” Find the paper and full list of authors in ArXiv.
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‘Knowledge Transfer from High-Resource to Low-Resource Programming Languages for Code LLMs’
“Over the past few years, Large Language Models of Code (Code LLMs) have started to have a significant impact on programming practice. …Code LLMs produce impressive results on high-resource programming languages that are well represented in their training data (e.g., Java, Python, or JavaScript), but struggle with low-resource languages that have limited training data available (e.g., OCaml, Racket, and several others). This paper presents an effective approach for boosting the performance of Code LLMs on low-resource languages using semi-synthetic data.” Find the paper and full list of authors in ArXiv.
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‘Finding Linear Explanations for a Given Ranking’
“Given a relation and a ranking of its tuples, but no information about the ranking function, we propose RankExplain to solve 2 types of problems: SAT asks if any linear scoring function can exactly reproduce the given ranking. OPT identifies the linear scoring function that minimizes position-based error, i.e., the total of the ranking-position differences over all tuples in the top-k. Our solution consists of linear programs that solve the problems exactly and can be implemented using MILP solvers.” Find the paper and full list of authors in ArXiv.
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‘Formal Model-Driven Analysis of Resilience of GossipSub to Attacks From Misbehaving Peers’
“GossipSub is a new peer-to-peer communication protocol designed to counter attacks from misbehaving peers by controlling what information is sent and to whom, via a score function computed by each peer that captures positive and negative behaviors of its neighbors. The score function depends on several parameters (weights, caps, thresholds) that can be configured by applications using GossipSub. … In this work we take a foundational approach to understanding the resilience of GossipSub to attacks from misbehaving peers.” Find the paper and full list of authors in the IEEE Symposium on Security and Privacy.
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‘Gradually Typed Languages Should Be Vigilant!’
“In gradual typing, different languages perform different dynamic type checks for the same program. … This raises the question of whether, given a gradually typed language, the combination of the translation that injects checks in well-typed terms and the dynamic semantics that determines their behavior sufficiently enforce the static type system of the language. … In response, we present vigilance, a semantic analytical instrument that defines when the check-injecting translation and dynamic semantics of a gradually typed language are adequate for its static type system.” Find the paper and authors list inthe ACM Programming Languages proceedings.
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‘Dragonfly Algorithm Application for Solving the Nurse Scheduling Problem’
“Scheduling plays a crucial role in allocating re-sources to tasks in various domains, including healthcare. Nurse scheduling, in particular, presents significant challenges due to the limited number of nurses. This paper illustrates how a novel meta-heuristic model known as Dragonfly Algorithm (DA) is used to efficiently solve the nurse scheduling problem faced by a major hospital in Belgium. The DA, inspired by the swarming behaviours of dragonflies, offers a new approach to solving this problem.” Find the paper and full list of authors in the proceedings of the International Conference on Computing, Networking and Communications.
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‘Cloud Load Balancing Algorithms Performance Evaluation Using a Unified Testing Platform’
“Due to its improved response time, availability, and efficiency, load balancing emerged as an essential framework for designing high-performance distributed computing systems. This paper introduces a unified testing platform that objectively compares load balancing algorithms and measures their performance. It employs various request patterns and load types to simulate real-world conditions. We evaluate a selection of static and dynamic algorithms on throughput, response time, and failure rate metrics. The results show that most, but not all, dynamic algorithms perform better than static ones.” Find the paper and list of authors in the International Conference on Computing, Networking and Communications proceedings.
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‘Visual Exploration of Machine Learning Model Behavior With Hierarchical Surrogate Rule Sets’
“One of the potential solutions for model interpretation is to train a surrogate model: a more transparent model that approximates the behavior of the model to be explained. Typically, classification rules or decision trees are used due to their logic-based expressions. However, decision trees can grow too deep, and rule sets can become too large to approximate a complex model. … In this paper, we focus on tabular data and present novel algorithmic and interactive solutions to address these issues.” Find the paper and full list of authors in IEEE Transactions on Visualization and Computer Graphics
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‘RePresent: Enabling Access to Justice for Pro Se Litigants via Co-Authored Serious Games’
“Increasing numbers of people represent themselves in legal disputes—known as pro se litigants. Many lack the skills, experience, or knowledge to navigate legal proceedings without a lawyer. … Serious games may provide an effective, interactive, and engaging way of educating pro se litigants about the law and enabling their access to justice. Through participatory design with legal experts and an authoring tool, we co-designed RePresent, a serious game that helps individuals with limited access to legal support prepare for pro se litigation.” Find the paper and list of authors in the 2024 ACM Designing Interactive Systems Conference proceedings.
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‘Robo-Instruct: Simulator-Augmented Instruction Alignment For Finetuning CodeLLMs’
“Open-weight LLMs are particularly appealing choices to generate training data for fine-tuning Code LLMs on domain-specific service robot applications because they are cost-effective, customizable, and offer better privacy protection. However, unlike proprietary LLMs, open-weight models are more error-prone and often produce programs that violate domain-specific constraints. … In this work, we introduce ROBO-INSTRUCT that preserves the diversity of programs generated by an LLM while providing the correctness of simulator-based checking.” Find the paper and full list of authors at ArXiv.
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‘StudentEval: A Benchmark of Student-Written Prompts for Large Language Models of Code’
“Code LLMs have the potential to make it easier for non-experts to understand and write code. However, current CodeLLM benchmarks rely on a single expert-written prompt per problem, making it hard to generalize their success to non-expert users. In this paper, we present a new natural-language-to-code benchmark of prompts written by a key population of non-experts: beginning programmers. … We use StudentEval to evaluate 12 Code LLMs and find that StudentEval is a better discriminator of model performance than existing benchmarks.” Find the paper and full list of authors in ACL Anthology.
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‘NL2Code-Reasoning and Planning With LLMs for Code Development’
“There is huge value in making software development more productive with AI. An important component of this vision is the capability to translate natural language to a programming language (“NL2Code”) and thus to significantly accelerate the speed at which code is written. This workshop gathers researchers, practitioners, and users from industry and academia that are working on NL2Code, specifically on the problem of using large language models to convert statements posed in a human language to a formal programming language.” Find the paper and authors list in the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining proceedings.
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‘E(2)-Equivariant Graph Planning for Navigation’
“Learning for robot navigation presents a critical and challenging task. The scarcity and costliness of real-world datasets necessitate efficient learning approaches. In this letter, we exploit Euclidean symmetry in planning for 2D navigation, which originates from Euclidean transformations between reference frames and enables parameter sharing. To address the challenges of unstructured environments, we formulate the navigation problem as planning on a geometric graph and develop an equivariant message passing network to perform value iteration.” Find the paper and full list of authors in IEEE Robotics and Automation Letters.
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‘Privacy Norms of Transformative Fandom: A Case Study of an Activity-Defined Community’
“Transformative media fandom is a remarkably coherent, long-lived, and diverse community united primarily by shared engagement in the varied activities of fandom. Its social norms are highly-developed and frequently debated, and have been studied by the CSCW and Media Studies communities in the past, but rarely using the tools and theories of privacy, despite fannish norms often bearing strongly on privacy. We use privacy scholarship and existing theories thereof to examine these norms and bring an additional perspective to understanding fandom communities.” Find the paper and full list of authors in the Proceedings of the ACM on Human-Computer Interaction.
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‘Seamlessly Insecure: Uncovering Outsider Access Risks in AiDot-Controlled Matter Devices’
“Matter is the recently proclaimed standard for seamless interoperability among connected Internet of Things (IoT) devices, seeking to unify the fragmented IoT landscape. In this paper, we analyze a range of Matter-enabled devices, uncovering a critical security flaw within the manufacturer’s implementation of the device commissioning process. This flaw allows the adversary to exploit an unenrolled manufacturer channel on an operational Matter device to enable unauthorized access, without notifying the user or compromising the existing Matter connection.” Find the paper and full list of authors in the IEEE Symposium on Security and Privacy Workshops.
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‘Envisioning New Futures of Positive Social Technology: Beyond Paradigms of Fixing, Protecting and Preventing’
“Social technology research today largely focuses on mitigating the negative impacts of technology and, therefore, often misses the potential of technology to enhance human connections and well-being. However, we see a potential to shift towards a holistic view of social technology’s impact on human flourishing. We introduce Positive Social Technology (Positech), a framework that shifts emphasis toward leveraging social technologies to support and augment human flourishing.” Find the paper and full list of authors in ArXiv.
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‘GenAudit: Fixing Factual Errors in Language Model Outputs With Evidence’
“LLMs can generate factually incorrect statements even when provided access to reference documents. Such errors can be dangerous in high-stakes applications (e.g., document-grounded QA for healthcare or finance). We present GenAudit — a tool intended to assist fact-checking LLM responses for document-grounded tasks. GenAudit suggests edits to the LLM response by revising or removing claims that are not supported by the reference document, and also presents evidence from the reference for facts that do appear to have support.” Find the paper and full list of authors in ArXiv.
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‘Unveiling AI-Driven Collective Action for a Worker-Centric Future’
“Collective action by gig knowledge workers is a potent method for enhancing labor conditions on platforms like Upwork, Amazon Mechanical Turk, and Toloka. However, this type of collective action is still rare today. Existing systems for supporting collective action are inadequate for workers to identify and understand their different workplace problems, plan effective solutions, and put the solutions into action. This talk will discuss how with my research lab we are creating worker-centric AI enhanced technologies that enable collective action among gig knowledge workers.”