Planning in partially-observable switching-mode continuous domains

Continuous-state POMDPs provide a natural representation for a variety of tasks, including many in robotics. However, most existing parametric continuous-state POMDP approaches are limited by their reliance on a single linear model to represent the world dynamics. We introduce a new switching-state dynamics model that can represent multi-modal state-dependent dynamics. We present the Switching Mode POMDP (SM-POMDP) planning algorithm for solving continuous-state POMDPs using this dynamics model. We also consider several procedures to approximate the value function as a mixture of a bounded number of Gaussians. Unlike the majority of prior work on approximate continuous-state POMDP planners, we provide a formal analysis of our SM-POMDP algorithm, providing bounds, where possible, on the quality of the resulting solution. We also analyze the computational complexity of SM-POMDP. Empirical results on an unmanned aerial vehicle collisions avoidance simulation, and a robot navigation simulation where the robot has faulty actuators, demonstrate the benefit of SM-POMDP over a prior parametric approach.National Science Foundation (U.S.). Division of Information and Intelligent Systems (Grant 0546467

Computability, inference and modeling in probabilistic programming

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011.Cataloged from PDF version of thesis.Includes bibliographical references (p. 135-144).We investigate the class of computable probability distributions and explore the fundamental limitations of using this class to describe and compute conditional distributions. In addition to proving the existence of noncomputable conditional distributions, and thus ruling out the possibility of generic probabilistic inference algorithms (even inefficient ones), we highlight some positive results showing that posterior inference is possible in the presence of additional structure like exchangeability and noise, both of which are common in Bayesian hierarchical modeling. This theoretical work bears on the development of probabilistic programming languages (which enable the specification of complex probabilistic models) and their implementations (which can be used to perform Bayesian reasoning). The probabilistic programming approach is particularly well suited for defining infinite-dimensional, recursively-defined stochastic processes of the sort used in nonparametric Bayesian statistics. We present a new construction of the Mondrian process as a partition-valued Markov process in continuous time, which can be viewed as placing a distribution on an infinite kd-tree data structure.by Daniel M. Roy.Ph.D

A Cautionary Tale: MARVELS Brown Dwarf Candidate Reveals Itself To Be A Very Long Period, Highly Eccentric Spectroscopic Stellar Binary

We report the discovery of a highly eccentric, double-lined spectroscopic binary star system (TYC 3010-1494-1), comprising two solar-type stars that we had initially identified as a single star with a brown dwarf companion. At the moderate resolving power of the MARVELS spectrograph and the spectrographs used for subsequent radial-velocity (RV) measurements (R ~ <30,000), this particular stellar binary mimics a single-lined binary with an RV signal that would be induced by a brown dwarf companion (Msin(i)~50 M_Jup) to a solar-type primary. At least three properties of this system allow it to masquerade as a single star with a very low-mass companion: its large eccentricity (e~0.8), its relatively long period (P~238 days), and the approximately perpendicular orientation of the semi-major axis with respect to the line of sight (omega~189 degrees). As a result of these properties, for ~95% of the orbit the two sets of stellar spectral lines are completely blended, and the RV measurements based on centroiding on the apparently single-lined spectrum is very well fit by an orbit solution indicative of a brown dwarf companion on a more circular orbit (e~0.3). Only during the ~5% of the orbit near periastron passage does the true, double-lined nature and large RV amplitude of ~15 km/s reveal itself. The discovery of this binary system is an important lesson for RV surveys searching for substellar companions; at a given resolution and observing cadence, a survey will be susceptible to these kinds of astrophysical false positives for a range of orbital parameters. Finally, for surveys like MARVELS that lack the resolution for a useful line bisector analysis, it is imperative to monitor the peak of the cross-correlation function for suspicious changes in width or shape, so that such false positives can be flagged during the candidate vetting process.Comment: 16 pages, 11 figures, 6 table

Detection of metastases using circulating tumour DNA in uveal melanoma

Background: Approximately 50% of uveal melanoma (UM) patients will develop metastatic disease depending on the genetic features of the primary tumour. Patients need 3–12 monthly scans, depending on their prognosis, which is costly and often non-specific. Circulating tumour DNA (ctDNA) quantification could serve as a test to detect and monitor patients for early signs of metastasis and therapeutic response. Methods: We assessed ctDNA as a biomarker in three distinct UM cohorts using droplet-digital PCR: (A) a retrospective analysis of primary UM patients to predict metastases; (B) a prospective analysis of UM patients after resolution of their primary tumour for early detection of metastases; and (C) monitoring treatment response in metastatic UM patients. Results: Cohort A: ctDNA levels were not associated with the development of metastases. Cohort B: ctDNA was detected in 17/25 (68%) with radiological diagnosis of metastases. ctDNA was the strongest predictor of overall survival in a multivariate analysis (HR = 15.8, 95% CI 1.7–151.2, p = 0.017). Cohort C: ctDNA monitoring of patients undergoing immunotherapy revealed a reduction in the levels of ctDNA in patients with combination immunotherapy. Conclusions: Our proof-of-concept study shows the biomarker feasibility potential of ctDNA monitoring in for the clinical management of uveal melanoma patients

Species Specificity in Major Urinary Proteins by Parallel Evolution

Species-specific chemosignals, pheromones, regulate social behaviors such as aggression, mating, pup-suckling, territory establishment, and dominance. The identity of these cues remains mostly undetermined and few mammalian pheromones have been identified. Genetically-encoded pheromones are expected to exhibit several different mechanisms for coding 1) diversity, to enable the signaling of multiple behaviors, 2) dynamic regulation, to indicate age and dominance, and 3) species-specificity. Recently, the major urinary proteins (Mups) have been shown to function themselves as genetically-encoded pheromones to regulate species-specific behavior. Mups are multiple highly related proteins expressed in combinatorial patterns that differ between individuals, gender, and age; which are sufficient to fulfill the first two criteria. We have now characterized and fully annotated the mouse Mup gene content in detail. This has enabled us to further analyze the extent of Mup coding diversity and determine their potential to encode species-specific cues

TOI-1728b: The Habitable-zone Planet Finder confirms a warm super Neptune orbiting an M dwarf host

We confirm the planetary nature of TOI-1728b using a combination of ground-based photometry, near-infrared Doppler velocimetry and spectroscopy with the Habitable-zone Planet Finder.TOI-1728 is an old, inactive M0 star with \teff{} $= 3980^{+31}_{-32}$ K, which hosts a transiting super Neptune at an orbital period of $\sim$ 3.49 days. Joint fitting of the radial velocities and TESS and ground-based transits yields a planetary radius of $5.05_{-0.17}^{+0.16}$ R$_{\oplus}$, mass $26.78_{-5.13}^{+5.43}$ M$_{\oplus}$ and eccentricity $0.057_{-0.039}^{+0.054}$. We estimate the stellar properties, and perform a search for He 10830 \AA absorption during the transit of this planet and claim a null detection with an upper limit of 1.1$\%$ with 90\% confidence. A deeper level of He 10830 \AA ~ absorption has been detected in the planet atmosphere of GJ 3470b, a comparable gaseous planet. TOI-1728b is the largest super Neptune -- the intermediate subclass of planets between Neptune and the more massive gas-giant planets -- discovered around an M dwarf. With its relatively large mass and radius, TOI-1728 represents a valuable datapoint in the M-dwarf exoplanet mass-radius diagram, bridging the gap between the lighter Neptune-sized planets and the heavier Jovian planets known to orbit M-dwarfs. With a low bulk density of $1.14_{-0.24}^{+0.26}$ g/cm$^3$, and orbiting a bright host star (J $\sim 9.6$, V $\sim 12.4$), TOI-1728b is also a promising candidate for transmission spectroscopy both from the ground and from space, which can be used to constrain planet formation and evolutionary models.Comment: 21 pages, 12 figures, 4 tables: Accepted for publicatio

The Habitable Zone Planet Finder Reveals a High Mass and Low Obliquity for the Young Neptune K2-25b

Using radial velocity data from the Habitable Zone Planet Finder, we have measured the mass of the Neptune-sized planet K2-25b, as well as the obliquity of its M4.5 dwarf host star in the 600–800 Myr Hyades cluster. This is one of the youngest planetary systems for which both of these quantities have been measured and one of the very few M dwarfs with a measured obliquity. Based on a joint analysis of the radial velocity data, time-series photometry from the K2 mission, and new transit light curves obtained with diffuser-assisted photometry, the planet's radius and mass are 3.44 ± 0.12 R_⊕ and 24.5_(-5.2)^(+5.7) M_⊕. These properties are compatible with a rocky core enshrouded by a thin hydrogen–helium atmosphere (5% by mass). We measure an orbital eccentricity of e = 0.43 ± 0.05. The sky-projected stellar obliquity is λ = 3° ± 16°, compatible with spin–orbit alignment, in contrast to other "hot Neptunes" that have been studied around older stars

The Habitable-zone Planet Finder Reveals A High Mass and a Low Obliquity for the Young Neptune K2-25b

Using radial-velocity data from the Habitable-zone Planet Finder, we have measured the mass of the Neptune-sized planet K2-25b, as well as the obliquity of its M4.5-dwarf host star in the 600-800MYr Hyades cluster. This is one of the youngest planetary systems for which both of these quantities have been measured, and one of the very few M dwarfs with a measured obliquity. Based on a joint analysis of the radial velocity data, time-series photometry from the K2 mission, and new transit light curves obtained with diffuser-assisted photometry, the planet's radius and mass are $3.44\pm 0.12 \mathrm{R_\oplus}$ and $24.5_{-5.2}^{+5.7} \mathrm{M_\oplus}$. These properties are compatible with a rocky core enshrouded by a thin hydrogen-helium atmosphere (5% by mass). We measure an orbital eccentricity of $e=0.43 \pm 0.05$. The sky-projected stellar obliquity is $\lambda=3 \pm 16^{\circ}$, compatible with spin-orbit alignment, in contrast to other "hot Neptunes" that have been studied around older stars.Comment: Accepted for publication in AJ, 31 pages, 14 figure