Publications

Collective communication systems such as MPI offer high performance group communication primitives at the cost of application flexibility. Today, an increasing number of distributed applications (e.g, reinforcement learning) require flexibility in expressing dynamic and asynchronous communication patterns. To accommodate these applications, task-based distributed computing frameworks (e.g., Ray, Dask, Hydro) have become popular as they allow applications to dynamically specify communication by invoking tasks, or functions, at runtime. This design makes efficient collective communication challenging because (1) the group of communicating processes is chosen at runtime, and (2) processes may not all be ready at the same time. We design and implement Hoplite, a communication layer for task-based distributed systems that achieves high performance collective communication without compromising application flexibility. The key idea of Hoplite is to use distributed protocols to compute a data transfer schedule on the fly. This enables the same optimizations used in traditional collective communication, but for applications that specify the communication incrementally. We show that Hoplite can achieve similar performance compared with a traditional collective communication library, MPICH. We port a popular distributed computing framework, Ray, on atop of Hoplite. We show that Hoplite can speed up asynchronous parameter server and distributed reinforcement learning workloads that are difficult to execute efficiently with traditional collective communication by up to 8.1x and 3.9x, respectively.

Recognition algorithms based on convolutional networks (CNNs) typically use the output of the last layer as feature representation. However, the information in this layer may be too coarse to allow precise localization. On the contrary, earlier layers may be precise in localization but will not capture semantics. To get the best of both worlds, we define the hypercolumn at a pixel as the vector of activations of all CNN units above that pixel. Using hypercolumns as pixel descriptors, we show results on three fine-grained localization tasks: simultaneous detection and segmentation[22], where we improve state-of-the-art from 49.7[22] mean AP^r to 60.0, keypoint localization, where we get a 3.3 point boost over[20] and part labeling, where we show a 6.6 point gain over a strong baseline.

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

We propose a segmentation system based on the normalized cut framework proposed by Shi and Malik (see Proc. IEEE Conf. Computer Vision and Pattern Recognition, San Juan, Puerto Rico, p.731-7, 1997). The goal is to partition the image from a big picture point of view. Perceptually significant groups are detected first while small variations and details are treated later. Different image features-intensity, color, texture, contour continuity, motion and stereo disparity are treated in one uniform framework.

Activity-based protein profiling (ABPP) is a versatile strategy for identifying and characterizing functional protein sites and compounds for therapeutic development. However, the vast majority of ABPP methods for covalent drug discovery target highly nucleophilic amino acids such as cysteine or lysine. Here, we report a methionine-directed ABPP platform using Redox-Activated Chemical Tagging (ReACT), which leverages a biomimetic oxidative ligation strategy for selective methionine modification. Application of ReACT to oncoprotein cyclin-dependent kinase 4 (CDK4) as a representative high-value drug target identified three new ligandable methionine sites. We then synthesized a methionine-targeting covalent ligand library bearing a diverse array of heterocyclic, heteroatom, and stereochemically rich substituents. ABPP screening of this focused library identified 1oxF11 as a covalent modifier of CDK4 at an allosteric M169 site. This compound inhibited kinase activity in a dose-dependent manner on purified protein and in breast cancer cells. Further investigation of 1oxF11 found prominent cation-π and H-bonding interactions stabilizing the binding of this fragment at the M169 site. Quantitative mass-spectrometry studies validated 1oxF11 ligation of CDK4 in breast cancer cell lysates. Further biochemical analyses revealed cross-talk between M169 oxidation and T172 phosphorylation, where M169 oxidation prevented phosphorylation of the activating T172 site on CDK4 and blocked cell cycle progression. By identifying a new mechanism for allosteric methionine redox regulation on CDK4 and developing a unique modality for its therapeutic intervention, this work showcases a generalizable platform that provides a starting point for engaging in broader chemoproteomics and protein ligand discovery efforts to find and target previously undruggable methionine sites.

It has been previously demonstrated that nanovessels can be highly competent catalysts providing high rate accelerations and unique selectivity to the organic transformations which they mediate. However, for supramolecular assemblies to be considered a standard reagent in organic synthesis they must first demonstrate the ability to catalyze increasingly complex transformations. Herein, we report a three-component Aza-Darzens reaction that generates <i>N</i>-phenylaziridines, catalyzed by a supramolecular host, that provides the stereoisomer opposite to the one generated in bulk solution (<i>trans</i> vs <i>cis</i>). This transformation constitutes a rare catalytic three-component coupling within a supramolecular assembly, providing a supramolecular solution to a synthetically challenging transformation.

The SENSE study provides evidence that a multicomponent group sleep intervention that includes cognitive-behavioral and mindfulness-based therapies can reduce sleep initiation problems and related daytime dysfunction, along with concomitant anxiety symptoms, among at-risk adolescents. (PsycINFO Database Record

HP-STM is an efficient method to study structural changes of the catalyst under different gas mixtures. The particles have to be homogeneously distributed over the region of analysis. Colloidal synthesis is a reliable way to produce monodisperse NP’s with narrow size distribution, but the disadvantages of this synthesis are:• the capping agent has to be removed without damaging the substrate by avoiding aggregation of the nanoparticles• the deposition process (dip coating or Langmuir-Blodgett deposition) induces unavoidable dirt on surfaceWe were able to image PtCo nanoparticles with good resolution.

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.