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Michael Murphy

Publications and source records attributed to Michael Murphy.

At least 19 recordsLinked to original sources

When Does Continual Learning Require Learning

As large language models (LLMs) become increasingly capable, the next question is how can we enable models to continually learn? Today, the field largely frames this as a problem of context management and mitigating forgetting. We argue this framing is incomplete: continual learning is fundamentally about increasing model competence as the world changes. We disentangle this change along two axes -- space, where the model encounters new domains, and time, where the underlying data drifts under a fixed task. This framing lets us study continual learning under realistic conditions: new domains arrive over time, facts drift past their training cutoff, and agentic interactions accumulate state across episodes. To evaluate methods under this setting, we recast widely used LLM benchmarks as sequential problems and introduce a single mechanism-agnostic protocol that compares prompt-based methods (GEPA, ACE), supervised learning (SFT, SDFT), reinforcement learning (GRPO, SDPO), and context compression (Cartridges, In-place TTT). Prompt-based methods fit each new stage quickly but degrade on future tasks. Distillation-based methods accumulate knowledge stably but struggle to update outdated facts. Context compression improves efficiency without substantially improving the ability to learn new tasks. Online reinforcement learning adapts most effectively to knowledge updates but remains sensitive to noisy reward signals. Overall, our results suggest that continual learning is not a single capability: different patterns of environmental change require fundamentally different update behaviors, determining when adaptation must be learned inside model weights and when it can be achieved through external scaffolding. We hope that understanding where each method succeeds and fails will guide the design of stronger continual learning systems.

cs.LG

Do Generalized-Gamma Scale Mixtures of Normals Fit Large Image Datasets?

A scale mixture of normals is a distribution formed by mixing a collection of normal distributions with fixed mean but different variances. A generalized gamma scale mixture draws the variances from a generalized gamma distribution. Generalized gamma scale mixtures of normals have been proposed as an attractive class of parametric priors for Bayesian inference in inverse imaging problems. Generalized gamma scale mixtures have two shape parameters, one that controls the behavior of the distribution about its mode, and the other that controls its tail decay. In this paper, we provide the first demonstration that the prior model is realistic for multiple large imaging data sets. We draw data from remote sensing, medical imaging, and image classification applications. We study the realism of the prior when applied to Fourier and wavelet (Haar and Gabor) transformations of the images, as well as to the coefficients produced by convolving the images against the filters used in the first layer of AlexNet, a popular convolutional neural network trained for image classification. We discuss data augmentation procedures that improve the fit of the model, procedures for identifying approximately exchangeable coefficients, and characterize the parameter regions that best describe the observed data sets. These regions are significantly broader than the region of primary focus in computational work. We show that this prior family provides a substantially better fit to each data set than any of the standard priors it contains. These include Gaussian, Laplace, $\ell_p$, and Student's $t$ priors. Finally, we identify cases where the prior is unrealistic and highlight characteristic features of images that suggest the model will fit poorly.

stat.AP

Deep-ultraviolet ptychographic pocket-scope (DART): mesoscale lensless molecular imaging with label-free spectroscopic contrast

The mesoscale characterization of biological specimens has traditionally required compromises between resolution, field-of-view, depth-of-field, and molecular specificity, with most approaches relying on external labels. Here we present the Deep-ultrAviolet ptychogRaphic pockeT-scope (DART), a handheld platform that transforms label-free molecular imaging through intrinsic deep-ultraviolet spectroscopic contrast. By leveraging biomolecules' natural absorption fingerprints and combining them with lensless ptychographic microscopy, DART resolves down to 308-nm linewidths across centimeter-scale areas while maintaining millimeter-scale depth-of-field. The system's virtual error-bin methodology effectively eliminates artifacts from limited temporal coherence and other optical imperfections, enabling high-fidelity molecular imaging without lenses. Through differential spectroscopic imaging at deep-ultraviolet wavelengths, DART quantitatively maps nucleic acid and protein distributions with femtogram sensitivity, providing an intrinsic basis for explainable virtual staining. We demonstrate DART's capabilities through molecular imaging of tissue sections, cytopathology specimens, blood cells, and neural populations, revealing detailed molecular contrast without external labels. The combination of high-resolution molecular mapping and broad mesoscale imaging in a portable platform opens new possibilities from rapid clinical diagnostics, tissue analysis, to biological characterization in space exploration.

physics.optics

Cognition Envelopes for Bounded Decision Making in Autonomous UAS Operations

Cyber-physical systems increasingly rely on foundational models, such as Large Language Models (LLMs) and Vision-Language Models (VLMs) to increase autonomy through enhanced perception, inference, and planning. However, these models also introduce new types of errors, such as hallucinations, over-generalizations, and context misalignments, resulting in incorrect and flawed decisions. To address this, we introduce the concept of Cognition Envelopes, designed to establish reasoning boundaries that constrain AI-generated decisions while complementing the use of meta-cognition and traditional safety envelopes. As with safety envelopes, Cognition Envelopes require practical guidelines and systematic processes for their definition, validation, and assurance. In this paper we describe an LLM/VLM-supported pipeline for dynamic clue analysis within the domain of small autonomous Uncrewed Aerial Systems deployed on Search and Rescue (SAR) missions, and a Cognition Envelope based on probabilistic reasoning and resource analysis. We evaluate the approach through assessing decisions made by our Clue Analysis Pipeline in a series of SAR missions. Finally, we identify key software engineering challenges for systematically designing, implementing, and validating Cognition Envelopes for AI-supported decisions in cyber-physical systems.

cs.AI

Validating Terrain Models in Digital Twins for Trustworthy sUAS Operations

With the increasing deployment of small Unmanned Aircraft Systems (sUAS) in unfamiliar and complex environments, Environmental Digital Twins (EDT) that comprise weather, airspace, and terrain data are critical for safe flight planning and for maintaining appropriate altitudes during search and surveillance operations. With the expansion of sUAS capabilities through edge and cloud computing, accurate EDT are also vital for advanced sUAS capabilities, like geolocation. However, real-world sUAS deployment introduces significant sources of uncertainty, necessitating a robust validation process for EDT components. This paper focuses on the validation of terrain models, one of the key components of an EDT, for real-world sUAS tasks. These models are constructed by fusing U.S. Geological Survey (USGS) datasets and satellite imagery, incorporating high-resolution environmental data to support mission tasks. Validating both the terrain models and their operational use by sUAS under real-world conditions presents significant challenges, including limited data granularity, terrain discontinuities, GPS and sensor inaccuracies, visual detection uncertainties, as well as onboard resources and timing constraints. We propose a 3-Dimensions validation process grounded in software engineering principles, following a workflow across granularity of tests, simulation to real world, and the analysis of simple to edge conditions. We demonstrate our approach using a multi-sUAS platform equipped with a Terrain-Aware Digital Shadow.

cs.SE

Cognitive Guardrails for Open-World Decision Making in Autonomous Drone Swarms

Small Uncrewed Aerial Systems (sUAS) are increasingly deployed as autonomous swarms in search-and-rescue and other disaster-response scenarios. In these settings, they use computer vision (CV) to detect objects of interest and autonomously adapt their missions. However, traditional CV systems often struggle to recognize unfamiliar objects in open-world environments or to infer their relevance for mission planning. To address this, we incorporate large language models (LLMs) to reason about detected objects and their implications. While LLMs can offer valuable insights, they are also prone to hallucinations and may produce incorrect, misleading, or unsafe recommendations. To ensure safe and sensible decision-making under uncertainty, high-level decisions must be governed by cognitive guardrails. This article presents the design, simulation, and real-world integration of these guardrails for sUAS swarms in search-and-rescue missions.

cs.RO

A Security Assessment tool for Quantum Threat Analysis

The rapid advancement of quantum computing poses a significant threat to many current security algorithms used for secure communication, digital authentication, and information encryption. A sufficiently powerful quantum computer could potentially exploit vulnerabilities in these algorithms, rendering data in transit insecure. This threat is expected to materialize within the next 20 years. Immediate transition to quantum-resilient cryptographic schemes is crucial, primarily to mitigate store-now-decrypt-later attacks and to ensure the security of products with decade-long operational lives. This transition requires a systematic approach to identifying and upgrading vulnerable cryptographic implementations. This work developed a quantum assessment tool for organizations, providing tailored recommendations for transitioning their security protocols into a post-quantum world. The work included a systematic evaluation of the proposed solution using qualitative feedback from network administrators and cybersecurity experts. This feedback was used to refine the accuracy and usability of the assessment process. The results demonstrate its effectiveness and usefulness in helping organizations prepare for quantum computing threats. The assessment tool is publicly available at (https://quantum-watch.soton.ac.uk).

cs.CR

HIFuzz: Human Interaction Fuzzing for small Unmanned Aerial Vehicles

Small Unmanned Aerial Systems (sUAS) must meet rigorous safety standards when deployed in high-stress emergency response scenarios; however many reported accidents have involved humans in the loop. In this paper, we, therefore, present the HiFuzz testing framework, which uses fuzz testing to identify system vulnerabilities associated with human interactions. HiFuzz includes three distinct levels that progress from a low-cost, limited-fidelity, large-scale, no-hazard environment, using fully simulated Proxy Human Agents, via an intermediate level, where proxy humans are replaced with real humans, to a high-stakes, high-cost, real-world environment. Through applying HiFuzz to an autonomous multi-sUAS system-under-test, we show that each test level serves a unique purpose in revealing vulnerabilities and making the system more robust with respect to human mistakes. While HiFuzz is designed for testing sUAS systems, we further discuss its potential for use in other Cyber-Physical Systems.

cs.HC

Efficiently predicting high resolution mass spectra with graph neural networks

Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a large database of chemical structures. However, current approaches to spectrum prediction model the output space in ways that force a tradeoff between capturing high resolution mass information and tractable learning. We resolve this tradeoff by casting spectrum prediction as a mapping from an input molecular graph to a probability distribution over molecular formulas. We discover that a large corpus of mass spectra can be closely approximated using a fixed vocabulary constituting only 2% of all observed formulas. This enables efficient spectrum prediction using an architecture similar to graph classification - GrAFF-MS - achieving significantly lower prediction error and orders-of-magnitude faster runtime than state-of-the-art methods.

cs.LG

Extending MAPE-K to support Human-Machine Teaming

The MAPE-K feedback loop has been established as the primary reference model for self-adaptive and autonomous systems in domains such as autonomous driving, robotics, and Cyber-Physical Systems. At the same time, the Human Machine Teaming (HMT) paradigm is designed to promote partnerships between humans and autonomous machines. It goes far beyond the degree of collaboration expected in human-on-the-loop and human-in-the-loop systems and emphasizes interactions, partnership, and teamwork between humans and machines. However, while MAPE-K enables fully autonomous behavior, it does not explicitly address the interactions between humans and machines as intended by HMT. In this paper, we present the MAPE-K-HMT framework which augments the traditional MAPE-K loop with support for HMT. We identify critical human-machine teaming factors and describe the infrastructure needed across the various phases of the MAPE-K loop in order to effectively support HMT. This includes runtime models that are constructed and populated dynamically across monitoring, analysis, planning, and execution phases to support human-machine partnerships. We illustrate MAPE-K-HMT using examples from an autonomous multi-UAV emergency response system, and present guidelines for integrating HMT into MAPE-K.

cs.RO

Resolution-enhanced parallel coded ptychography for high-throughput optical imaging

Ptychography is an enabling coherent diffraction imaging technique for both fundamental and applied sciences. Its applications in optical microscopy, however, fall short for its low imaging throughput and limited resolution. Here, we report a resolution-enhanced parallel coded ptychography technique achieving the highest numerical aperture and an imaging throughput orders of magnitude greater than previous demonstrations. In this platform, we translate the samples across the disorder-engineered surfaces for lensless diffraction data acquisition. The engineered surface consists of chemically etched micron-level phase scatters and printed sub-wavelength intensity absorbers. It is designed to unlock an optical space with spatial extent (x, y) and frequency content (kx, ky) that is inaccessible using conventional lens-based optics. To achieve the best resolution performance, we also report a new coherent diffraction imaging model by considering both the spatial and angular responses of the pixel readouts. Our low-cost prototype can directly resolve 308-nm linewidth on the resolution target without aperture synthesizing. Gigapixel high-resolution microscopic images with a 240-mm^2 effective field of view can be acquired in 15 seconds. For demonstrations, we recover slow-varying 3D phase objects with many 2{\pi} wraps, including optical prism and convex lens. The low-frequency phase contents of these objects are challenging to obtain using other existing lensless techniques. For digital pathology applications, we perform accurate virtual staining by using the recovered phase as attention guidance in a deep neural network. Parallel optical processing using the reported technique enables novel optical instruments with inherent quantitative nature and metrological versatility.

physics.optics

A Catalog of High-Velocity CIV Mini-BALs in the VLT-UVES and Keck-HIRES Archives

We present a catalog of high-velocity CIV $\lambda$ 1548,1551 mini-Broad Absorption Lines (mini-BALs) in the archives of the VLT-UVES and Keck-HIRES spectrographs. We identify high-velocity CIV mini-BALs based on smooth rounded BAL-like profiles with velocity blueshifts $<$ $-$4000 km/s and widths in the range 70 $\lesssim$ FWHM(1548) $\lesssim$ 2000 km/s (for $\lambda$1548 alone). We find 105 mini-BALs in 44 quasars from a total sample of 638 quasars. The fraction of quasars with at least one mini-BAL meeting our criteria is roughly $\sim9$% after correcting for incomplete velocity coverage. However, the numbers of systems rise sharply at lower velocities and narrower FWHMs, suggesting that many outflow lines are missed by our study. All of the systems are highly ionized based on the strong presence of NV and OVI and/or the absence of SiII and CII when within the wavelength coverage. Two of the mini-BAL systems in our catalog, plus three others at smaller velocity shifts, have PV $\lambda$1118,1128 absorption indicating highly saturated CIV absorption and total hydrogen column densities $\gtrsim 10^{22}$ cm$^{-3}$. Most of the mini-BALs are confirmed to have optical depths $\gtrsim$1 with partial covering of the quasar continuum source. The covering fractions are as small as 0.06 in CIV and 0.03 in SiIV , corresponding to outflow absorbing structures $<0.002$ pc across. When multiple lines are measured, the lines of less abundant ions tend to have narrower profiles and smaller covering fractions indicative of inhomogeneous absorbers where higher column densities occur in smaller clumps. This picture might extend to BAL outflows if the broader and generally deeper BALs form in either the largest clumps or collections of many mini-BAL-like clumps that blend together in observed quasar spectra.

astro-ph.GA

Super-resolved multispectral lensless microscopy via angle-tilted, wavelength-multiplexed ptychographic modulation

We report an angle-tilted, wavelength-multiplexed ptychographic modulation approach for multispectral lensless on-chip microscopy. In this approach, we illuminate the specimen with lights at 5 wavelengths simultaneously. A prism is added at the illumination path for spectral dispersion. Lightwaves at different wavelengths, thus, hit the specimen at slightly different incident angles, breaking the ambiguities in mixed state ptychographic reconstruction. At the detection path, we place a thin diffuser in-between the specimen and the monochromatic image sensor for encoding the spectral information into 2D intensity measurements. By scanning the sample to different x-y positions, we acquire a sequence of monochromatic images for reconstructing the 5 complex object profiles at the 5 wavelengths. An up-sampling procedure is integrated into the recovery process to bypass the resolution limit imposed by the imager pixel size. We demonstrate a half-pitch resolution of 0.55 microns using an image sensor with 1.85-micron pixel size. We also demonstrate quantitative and high-quality multispectral reconstructions of stained tissue sections for digital pathology applications.

physics.optics

OpenWSI: a low-cost, high-throughput whole slide imaging system via single-frame autofocusing and open-source hardware

Recent advancements in whole slide imaging (WSI) have moved pathology closer to digital practice. Existing systems require precise mechanical control and the cost is prohibitive for most individual pathologists. Here we report a low-cost and high-throughput WSI system termed OpenWSI. The reported system is built using off-the-shelf components including a programmable LED array, a photographic lens, and a low-cost computer numerical control (CNC) router. Different from conventional WSI platforms, our system performs real-time single-frame autofocusing using color-multiplexed illumination. For axial positioning control, we perform coarse adjustment using the CNC router and precise adjustment using the ultrasonic motor ring in the photographic lens. By using a 20X objective lens, we show that the OpenWSI system has a resolution of ~0.7 microns. It can acquire whole slide images of a 225-mm^2 region in ~2 mins, with throughput comparable to existing high-end platforms. The reported system offers a turnkey solution to transform the high-end WSI platforms into one that can be made broadly available and utilizable without loss of capacity.

eess.IV

Which Cubic Graphs have Quadrangulated Spherical Immersions?

We consider spherical quadrangulations -- spherical embeddings of multigraphs, possibly with loops, so that every face has boundary walk of length 4 -- in which all vertices have degree 3 or 4. Interpreting each degree 4 vertex as a crossing, these embeddings can also be thought of as transversal immersions of cubic graphs which we refer to as the {\it extracted graphs}. We also consider quadrangulations of the disk in which interior vertices have degree 3 or 4 and boundary vertices have degree 2 or 3. First, we classify all such quadrangulations of the disk. Then, we provide four methods for constructing spherical quadrangulations, two of which use quadrangulations of the disk as input. Two of these methods provide one-parameter families of quadrangulations, for which we prove that the sequence of isomorphism types of extracted graphs is periodic. We close with a description of computer computations which yielded spherical quadrangulations for all but three cubic multigraphs on eight vertices.

math.CO

Discovery of the Transition of a Mini-Broad Absorption Line into Broad Absorption in the SDSS Quasar J115122.14+020426.3

We present the detection of a rare case of dramatic strengthening in the UV absorption profiles in the spectrum of the quasar J115122.14+020426.3 between observations ~2.86 years apart in the quasar rest-frame. A 2001 spectrum from the Sloan Digital Sky Survey (SDSS) shows a CIV "mini-broad" absorption line (FWHM=1,220 km/s) with a maximum blueshift velocity ~9,520 km/s, while a later spectrum from the Very Large Telescope (VLT) shows significantly broader and stronger absorption line, with a maximum blueshift velocity of ~12,240 km/s, that qualifies as a broad absorption line. A similar variability pattern is observed in two additional systems at lower blueshifted velocities and in the Lya and NV transitions as well. One of the absorption systems appears to be resolved and shows evidence for partial covering of the quasar continuum source (Cf~0.65), indicating a transverse absorber size of, at least, ~6 x 10^(16) cm. In contrast, a cluster of narrower CIV lines appears to originate in gas that fully covers the continuum and broad emission line sources. There is no evidence for changes in the centroid velocity of the absorption troughs. This case suggests that, at least some of the absorbers that produce "mini-broad" and broad absorption lines in quasar spectra do not belong to intrinsically separate classes. Here, the "mini-broad" absorption line is most likely interpreted as an intermediate phase before the appearance of a broad absorption line due to their similar velocity. While the current observations do not provide enough constraints to discern among the possible causes for this variability, future monitoring of multiple transitions at high resolution will help achieve this goal.

astro-ph.CO

A new candidate for probing Population III nucleosynthesis with carbon-enhanced damped Lyman-alpha systems

We report the identification of a very metal-poor damped Lyman-alpha system (DLA) at z_abs = 3.067295 that is modestly carbon-enhanced, with an iron abundance of ~1/700 solar ([Fe/H] = -2.84) and [C,O/Fe] ~ +0.6. Such an abundance pattern is likely to be the result of nucleosynthesis by massive stars. On the basis of 17 metal absorption lines, we derive a 2 sigma upper limit on the DLA's kinetic temperature of T_DLA <= 4700 K, which is broadly consistent with the range of spin temperature estimates for DLAs at this redshift and metallicity. While the best-fitting abundance pattern shows the expected hallmarks of Population III nucleosynthesis, models of high-mass Population II stars can match the abundance pattern almost as well. We discuss current limitations in distinguishing between these two scenarios and the marked improvement in identifying the remnants of Population III stars expected from the forthcoming generation of 30-metre class telescopes.

astro-ph.CO

Towards an experimentally feasible controlled-phase gate on two blockaded Rydberg atoms

We investigate the implementation of a controlled-Z gate on a pair of Rydberg atoms in spatially separated dipole traps where the joint excitation of both atoms into the Rydberg level is strongly suppressed (the Rydberg blockade). We follow the adiabatic gate scheme of Jaksch et al. [1], where the pair of atoms are coherently excited using lasers, and apply it to the experimental setup outlined in Ga\"etan et al. [2]. We apply optimisation to the experimental parameters to improve gate fidelity, and consider the impact of several experimental constraints on the gate success.

quant-ph