Understanding the source of semantic regularities in word embeddings

Semantic relations are core to how humans understand and express concepts in the real world using language. Recently, there has been a thread of research aimed at modeling these relations by learning vector representations from text corpora. Most of these approaches focus strictly on leveraging the co-occurrences of relationship word pairs within sentences. In this paper, we investigate the hypothesis that examples of a lexical relation in a corpus are fundamental to a neural word embedding’s ability to complete analogies involving the relation. Our experiments, in which we remove all known examples of a relation from training corpora, show only marginal degradation in analogy completion performance involving the removed relation. This finding enhances our understanding of neural word embeddings, showing that co-occurrence information of a particular semantic relation is the not the main source of their structural regularity

Understanding the source of semantic regularities in word embeddings

Semantic relations are core to how humans understand and express concepts in the real world using language. Recently, there has been a thread of research aimed at modeling these relations by learning vector representations from text corpora. Most of these approaches focus strictly on leveraging the co-occurrences of relationship word pairs within sentences. In this paper, we investigate the hypothesis that examples of a lexical relation in a corpus are fundamental to a neural word embedding’s ability to complete analogies involving the relation. Our experiments, in which we remove all known examples of a relation from training corpora, show only marginal degradation in analogy completion performance involving the removed relation. This finding enhances our understanding of neural word embeddings, showing that co-occurrence information of a particular semantic relation is the not the main source of their structural regularity

Bringing "The Moth" to Light: A Planet-Sculpting Scenario for the HD 61005 Debris Disk

The HD 61005 debris disk ("The Moth") stands out from the growing collection of spatially resolved circumstellar disks by virtue of its unusual swept-back morphology, brightness asymmetries, and dust ring offset. Despite several suggestions for the physical mechanisms creating these features, no definitive answer has been found. In this work, we demonstrate the plausibility of a scenario in which the disk material is shaped dynamically by an eccentric, inclined planet. We present new Keck NIRC2 scattered-light angular differential imaging of the disk at 1.2-2.3 microns that further constrains its outer morphology (projected separations of 27-135 AU). We also present complementary Gemini Planet Imager 1.6 micron total intensity and polarized light detections that probe down to projected separations less than 10 AU. To test our planet-sculpting hypothesis, we employed secular perturbation theory to construct parent body and dust distributions that informed scattered-light models. We found that this method produced models with morphological and photometric features similar to those seen in the data, supporting the premise of a planet-perturbed disk. Briefly, our results indicate a disk parent body population with a semimajor axis of 40-52 AU and an interior planet with an eccentricity of at least 0.2. Many permutations of planet mass and semimajor axis are allowed, ranging from an Earth mass at 35 AU to a Jupiter mass at 5 AU.Comment: Accepted to AJ; added Figure 5 and minor text edit

The Gemini Planet Imager View of the HD 32297 Debris Disk

We present new H-band scattered light images of the HD 32297 edge-on debris disk obtained with the Gemini Planet Imager. The disk is detected in total and polarized intensity down to a projected angular separation of 0.?15, or 20 au. On the other hand, the large-scale swept-back halo remains undetected, likely a consequence of its markedly blue color relative to the parent body belt. We analyze the curvature of the disk spine and estimate a radius of ?100 au for the parent body belt, smaller than past scattered light studies but consistent with thermal emission maps of the system. We employ three different flux-preserving post-processing methods to suppress the residual starlight and evaluate the surface brightness and polarization profile along the disk spine. Unlike past studies of the system, our high-fidelity images reveal the disk to be highly symmetric and devoid of morphological and surface brightness perturbations. We find the dust scattering properties of the system to be consistent with those observed in other debris disks, with the exception of HR 4796. Finally, we find no direct evidence for the presence of a planetary-mass object in the system

Debris Disk Results from the Gemini Planet Imager Exoplanet Survey\u27s Polarimetric Imaging Campaign

We report the results of a ∼4 yr direct imaging survey of 104 stars to resolve and characterize circumstellar debris disks in scattered light as part of the Gemini Planet Imager (GPI) Exoplanet Survey. We targeted nearby (≲150 pc), young (≲500 Myr) stars with high infrared (IR) excesses (L IR/L ∗ \u3e 10-5), including 38 with previously resolved disks. Observations were made using the GPI high-contrast integral field spectrograph in H-band (1.6 μm) coronagraphic polarimetry mode to measure both polarized and total intensities. We resolved 26 debris disks and 3 protoplanetary/transitional disks. Seven debris disks were resolved in scattered light for the first time, including newly presented HD 117214 and HD 156623, and we quantified basic morphologies of five of them using radiative transfer models. All of our detected debris disks except HD 156623 have dust-poor inner holes, and their scattered-light radii are generally larger than corresponding radii measured from resolved thermal emission and those inferred from spectral energy distributions. To assess sensitivity, we report contrasts and consider causes of nondetections. Detections were strongly correlated with high IR excess and high inclination, although polarimetry outperformed total intensity angular differential imaging for detecting low-inclination disks (≲70°). Based on postsurvey statistics, we improved upon our presurvey target prioritization metric predicting polarimetric disk detectability. We also examined scattered-light disks in the contexts of gas, far-IR, and millimeter detections. Comparing H-band and ALMA fluxes for two disks revealed tentative evidence for differing grain properties. Finally, we found no preference for debris disks to be detected in scattered light if wide-separation substellar companions were present

The Gemini planet imager view of the HD 32297 debris disk

Funding: M.M.B. and J.M. were supported by NASA through Hubble Fellowship grants #51378.01-A and HST-HF2-51414.001, respectively, and I.C. through Hubble Fellowship grant HST-HF2-51405.001-A, awarded by the Space Telescope Science Institute, which is operated by AURA, for NASA, under contract NAS5-26555.We present new H-band scattered light images of the HD 32297 edge-on debris disk obtained with the Gemini Planet Imager. The disk is detected in total and polarized intensity down to a projected angular separation of 0"15, or 20 au. On the other hand, the large-scale swept-back halo remains undetected, likely a consequence of its markedly blue color relative to the parent body belt. We analyze the curvature of the disk spine and estimate a radius of ≍100 au for the parent body belt, smaller than past scattered light studies but consistent with thermal emission maps of the system. We employ three different flux-preserving post-processing methods to suppress the residual starlight and evaluate the surface brightness and polarization profile along the disk spine. Unlike past studies of the system, our high-fidelity images reveal the disk to be highly symmetric and devoid of morphological and surface brightness perturbations. We find the dust scattering properties of the system to be consistent with those observed in other debris disks, with the exception of HR 4796. Finally, we find no direct evidence for the presence of a planetary-mass object in the system.Publisher PDFPeer reviewe

Debris disk results from the Gemini Planet Imager Exoplanet Survey's polarimetric imaging campaign

Funding: Supported by NSF grants AST-1411868 (E.L.N., K.B.F., B.M., and J.P.), AST-141378 (G.D.), and AST-1518332 (T.M.E., R.J.D.R., J.R.G., P.K., G.D.). Supported by NASA grants NNX14AJ80G (E.L.N., B.M., F.M., and M.P.), NNX15AC89G and NNX15AD95G/NExSS (T.M.E., B.M., R.J.D.R., G.D., J.J.W, J.R.G., P.K.), NN15AB52l (D.S.), and NNX16AD44G (K.M.M.). M.R. is supported by the NSF Graduate Research Fellowship Program under grant number DGE-1752134. J.R. and R.D. acknowledge support from the Fonds de Recherche du Quèbec. J. Mazoyer’s work was performed in part under contract with the California Institute of Technology/Jet Propulsion Laboratory funded by NASA through the Sagan Fellowship Program executed by the NASA Exoplanet Science Institute. M.M.B. and J.M. were supported by NASA through Hubble Fellowship grants #51378.01-A and HST-HF2-51414.001, respectively, and I.C. through Hubble Fellowship grant HST-HF2-51405.001-A, awarded by the Space Telescope Science Institute, which is operated by AURA, for NASA, under contract NAS5-26555. K.W.D. is supported by an NRAO Student Observing Support Award SOSPA3-007. J.J.W. is supported by the Heising-Simons Foundation 51 Pegasi b postdoctoral fellowship.We report the results of a ∼4 yr direct imaging survey of 104 stars to resolve and characterize circumstellar debris disks in scattered light as part of the Gemini Planet Imager (GPI) Exoplanet Survey. We targeted nearby (≲150 pc), young (≲500 Myr) stars with high infrared (IR) excesses (LIR/L⋆ > 10-5), including 38 with previously resolved disks. Observations were made using the GPI high-contrast integral field spectrograph in H-band (1.6 μm) coronagraphic polarimetry mode to measure both polarized and total intensities. We resolved 26 debris disks and 3 protoplanetary/transitional disks. Seven debris disks were resolved in scattered light for the first time, including newly presented HD 117214 and HD 156623, and we quantified basic morphologies of five of them using radiative transfer models. All of our detected debris disks except HD 156623 have dust-poor inner holes, and their scattered-light radii are generally larger than corresponding radii measured from resolved thermal emission and those inferred from spectral energy distributions. To assess sensitivity, we report contrasts and consider causes of nondetections. Detections were strongly correlated with high IR excess and high inclination, although polarimetry outperformed total intensity angular differential imaging for detecting low-inclination disks (≲70°). Based on postsurvey statistics, we improved upon our presurvey target prioritization metric predicting polarimetric disk detectability. We also examined scattered-light disks in the contexts of gas, far-IR, and millimeter detections. Comparing H-band and ALMA fluxes for two disks revealed tentative evidence for differing grain properties. Finally, we found no preference for debris disks to be detected in scattered light if wide-separation substellar companions were present.Publisher PDFPeer reviewe

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of diseas

Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer

Background and aims: Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. The study aim was to investigate the association between DNA damage response (DDR), replication stress and novel therapeutic response in PC to develop a biomarker driven therapeutic strategy targeting DDR and replication stress in PC. Methods: We interrogated the transcriptome, genome, proteome and functional characteristics of 61 novel PC patient-derived cell lines to define novel therapeutic strategies targeting DDR and replication stress. Validation was done in patient derived xenografts and human PC organoids. Results: Patient-derived cell lines faithfully recapitulate the epithelial component of pancreatic tumors including previously described molecular subtypes. Biomarkers of DDR deficiency, including a novel signature of homologous recombination deficiency, co-segregates with response to platinum (P < 0.001) and PARP inhibitor therapy (P < 0.001) in vitro and in vivo. We generated a novel signature of replication stress with which predicts response to ATR (P < 0.018) and WEE1 inhibitor (P < 0.029) treatment in both cell lines and human PC organoids. Replication stress was enriched in the squamous subtype of PC (P < 0.001) but not associated with DDR deficiency. Conclusions: Replication stress and DDR deficiency are independent of each other, creating opportunities for therapy in DDR proficient PC, and post-platinum therapy