Parallel Computation of Vernier Offsets, Curvature and Chevrons in Humans

A vernier offset is detected at once among straight lines, and reaction times are almost independent of the number of simultaneously presented stimuli (distractors), indicating parallel processing of vernier offsets. Reaction times for identifying a vernier offset to one side among verniers offset to the opposite side increase with the number of distractors, indicating serial processing. Even deviations below a photoreceptor diameter can be detected at once. The visual system thus attains positional accuracy below the photoreceptor diameter simultaneously at different positions. I conclude that deviation from straightness, or change of orientation, is detected in parallel over the visual field. Discontinuities or gradients in orientation may represent an elementary feature of vision.

Sequence-Seeking and Counter Streams: A Model for Information Processing in the Cortex

This paper presents a model for the general flow in the neocortex. The basic process, called "sequence-seeking," is a search for a sequence of mappings or transformations, linking source and target representations. The search is bi-directional, "bottom-up" as well as "top-down," and it explores in parallel a large numbe rof alternative sequences. This operation is implemented in a structure termed "counter streams," in which multiple sequences are explored along two separate, complementary pathways which seeking to meet. The first part of the paper discusses the general sequence-seeking scheme and a number of related processes, such as the learning of successful sequences, context effects, and the use of "express lines" and partial matches. The second part discusses biological implications of the model in terms of connections within and between cortical areas. The model is compared with existing data, and a number of new predictions are proposed.

On The Uniqueness of Correspondence Under Orthographic and Perspective Projections

The task of shape recovery from a motion sequence requires the establishment of correspondence between image points. The two processes, the matching process and the shape recovery one, are traditionally viewed as independent. Yet, information obtained during the process of shape recovery can be used to guide the matching process. This paper discusses the mutual relationship between the two processes. The paper is divided into two parts. In the first part we review the constraints imposed on the correspondence by rigid transformations and extend them to objects that undergo general affine (non rigid) transformation (including stretch and shear), as well as to rigid objects with smooth surfaces. In all these cases corresponding points lie along epipolar lines, and these lines can be recovered from a small set of corresponding points. In the second part of the paper we discuss the potential use of epipolar lines in the matching process. We present an algorithm that recovers the correspondence from three contour images. The algorithm was implemented and used to construct object models for recognition. In addition we discuss how epipolar lines can be used to solve the aperture problem.

Computer Recognition of Prismatic Solids

An investigation is made into the problem of constructing a model of the appearance to an optical input device of scenes consisting of plane-faced geometric solids. The goal is to study algorithms which find the real straight edges in the scenes, taking into account smooth variations in intensity over faces of the solids, blurring of edges and noise. A general mathematical analysis is made of optimal methods for identifying the edge lines in figures, given a raster of intensities covering the entire field of view. There is given in addition a suboptimal statistical decision procedure, based on the model, for the identification of a line within a narrow band on the field of view given an array of intensities from within the band. A computer program has been written and extensively tested which implements this procedure and extracts lines from real scenes. Other programs were written which judge the completeness of extracted sets of lines, and propose and test for additional lines which had escaped initial detection. The performance of these programs is discussed in relation to the theory derived from the model, and with regard to their use of global information in detecting and proposing lines.

ADEPT: A Heuristic Program for Proving Theorems of Group Theory

A computer program, named ADEPT (A Distinctly Empirical Prover of Theorems), has been written which proves theorems taken from the abstract theory of groups. Its operation is basically heuristic, incorporating many of the techniques of the human mathematician in a "natural" way. This program has proved almost 100 theorems, as well as serving as a vehicle for testing and evaluating special-purpose heuristics. A detailed description of the program is supplemented by accounts of its performance on a number of theorems, thus providing many insights into the particular problems inherent in the design of a procedure capable of proving a variety of theorems from this domain. Suggestions have been formulated for further efforts along these lines, and comparisons with related work previously reported in the literature have been made.

Selecting Relevant Genes with a Spectral Approach

Array technologies have made it possible to record simultaneously the expression pattern of thousands of genes. A fundamental problem in the analysis of gene expression data is the identification of highly relevant genes that either discriminate between phenotypic labels or are important with respect to the cellular process studied in the experiment: for example cell cycle or heat shock in yeast experiments, chemical or genetic perturbations of mammalian cell lines, and genes involved in class discovery for human tumors. In this paper we focus on the task of unsupervised gene selection. The problem of selecting a small subset of genes is particularly challenging as the datasets involved are typically characterized by a very small sample size ?? the order of few tens of tissue samples ??d by a very large feature space as the number of genes tend to be in the high thousands. We propose a model independent approach which scores candidate gene selections using spectral properties of the candidate affinity matrix. The algorithm is very straightforward to implement yet contains a number of remarkable properties which guarantee consistent sparse selections. To illustrate the value of our approach we applied our algorithm on five different datasets. The first consists of time course data from four well studied Hematopoietic cell lines (HL-60, Jurkat, NB4, and U937). The other four datasets include three well studied treatment outcomes (large cell lymphoma, childhood medulloblastomas, breast tumors) and one unpublished dataset (lymph status). We compared our approach both with other unsupervised methods (SOM,PCA,GS) and with supervised methods (SNR,RMB,RFE). The results clearly show that our approach considerably outperforms all the other unsupervised approaches in our study, is competitive with supervised methods and in some case even outperforms supervised approaches.

Retargeting of pre-set regions on chromosome for high gene expression in mammalian cells

We have developed a system to hunt and reuse special gene integration sites that allow for high and stable gene expression. A vector, named pRGFP8, was constructed. The plasmid pRGFP8 contains a reporter gene, gfp2 and two extraneous DNA fragments. The gene gfp2 makes it possible to screen the high expression regions on the chromosome. The extraneous DNA fragments can help to create the unique loci on the chromosome and increase the gene targeting frequency by increasing the homology. After transfection into Chinese hamster ovary cells (CHO) cells, the linearized pRGFP8 can integrate into the chromosome of the host cells and form the unique sites. With FACS, 90 millions transfected cells were sorted and the cells with strongest GFP expression were isolated, and then 8 stable high expression GFP CHO cell lines were selected as candidates for the new host cell. Taking the unique site created by pRGFP8 on the chromosome in the new host cells as a targeting locus, the gfp2 gene was replaced with the gene of interest, human ifngamma, by transfecting the targeting plasmid pRIH-IFN. Then using FACS, the cells with the dimmest GFP fluorescence were selected. These cells showed they had strong abilities to produce the protein of interest, IFN-gamma. During the gene targeting experiment, we found there is positive correlation between the fluorescence density of the GFP CHO host cells and the specific production rate of IFN-gamma. This result shows that the strategy in our expression system is correct: the production of the interesting protein increases with the increase fluorescence of the GFP host cells. This system, the new host cell lines and the targeting vector, can be utilized for highly expressing the gene of interest. More importantly, by using FACS, we can fully screen all the transfected cells, which can reduce the chances of losing the best cells.