Algorithmic Program Debugging (ACM Distinguished Dissertation)|Ehud Y, Gordion Seals and Sealings: Individuals and Society (University Museum Monograph)|Elspeth Dusinberre, From Deluge to Discourse: Myth, History, and the Generation of Chinese Fiction (SUNY Series in Chinese Philosophy and Culture) (Suny Series, Chinese Philosophy & Culture)|Deborah Lynn Porter, Lost Tribe: A Algorithmic Program Debugging (ACM Distinguished Dissertation)|Ehud Y, Xango Music|Geoffrey Philp, Apollo and Marsyas, and Other Poems: |Eugene Lee-Hamilton, Just for Two Easy (Part(s)) (Eighth Note Publications)|David Marlatt Algorithmic Program Debugging ACM Distinguished Dissertation|Ehud Y Shapiro, The poor mans evening portion being a selection of a verse of Scripture with short observations for every day in the year intended for the use of are rich in faith and heirs of the kingdom|Robert Hawker, The New Educational Music Course Third Music Reader|W W Gilchrist, Elyot Four Plays|Kevin Elyot
Algorithmic Program Debugging (ACM Distinguished Dissertation)|Ehud Y. Shapiro.
Ehud is the founder of the Ba Rock Band and conceived its original artistic program. He is a winner of two ERC European Research Council Advanced Grants.
Born in Jerusalem inthe guiding light for Ehud Shapiro's scientific endeavors was the philosophy of science of Karl Popperwith which he became acquainted through a high-school project supervised by Moshe Kroy from the Department of Philosophy, Tel Aviv University.
In Shaprio completed his undergraduate studies in Tel Aviv University in Mathematics and Philosophy with distinction. Shapiro's PhD work with Dana Angluin in Computer Science at Yale university attempted to provide an algorithmic interpretation to Popper's philosophical approach to scientific discoveryresulting in both a computer system for the inference of logical theories from facts and a methodology for acm algorithmic debugging dissertation distinguished program debuggingdeveloped using the programming language Prolog.
His thesis, " Algorithmic Program Debugging ", acm algorithmic debugging dissertation distinguished program, [5] was published by MIT Press as a ACM Distinguished Dissertation, followed in by "The Art of Prolog", acm algorithmic debugging dissertation distinguished program, a textbook co-authored with Leon Sterling.
Coming to the Department of Computer Science and Applied Mathematics at the Weizmann Institute of Science in as a post-doctoral fellow, Shapiro was inspired by the Japanese Fifth Generation Computer Systems project to invent a high-level programming language for parallel and distributed computer systems, named Concurrent Prolog, acm algorithmic debugging dissertation distinguished program.
A two-volume book on Concurrent Prolog and related work was published by MIT Press in Shapiro's work had a decisive influence on the strategic direction of the Japanese national project, and he cooperated closely with the project throughout its years duration. InShapiro took leave of absence from his tenured position at Weizmann to found Ubique Ltd. and serve as its CEOacm algorithmic debugging dissertation distinguished program, an Israeli Internet software pioneer.
Building on Concurrent Prolog, Ubique developed "Virtual Places", a precursor to today's broadly-used Instant Messaging systems. Ubique was sold to America Online inand following a management acm algorithmic debugging dissertation distinguished program out in was sold again to IBM inwhere it continues to develop SameTime, IBM's leading Instant Messaging product based on Ubique's technology.
Preparing for return to academia, Shapiro ventured into self-study of molecular biology. Shapiro attempted to build a computer from biological molecules, guided by a vision of "A Doctor in a Cell": A biomolecular computer that operates inside the living body, programmed with medical knowledge to diagnose diseases and produce the requisite drugs. Lacking experience in molecular biology, Shapiro realized his first design for a molecular computer as a LEGO-like mechanical device built using 3D stereolithographywhich was patented upon his return to Weizmann in InProf.
Shapiro also designed an effective method of synthesizing error-free DNA molecules from error-prone building blocks. Shapiro founded the CADMAD consortium: The CADMAD technological platform aims to deliver a revolution in DNA processing analogous to the revolution text editing underwent with the introduction of electronic text editors.
Shapiro presented a vision of the next grand challenge in Human biology: To uncover the Human cell lineage tree. Inside all of us is a cell lineage tree — the history of how our body grows from a single cell the fertilized egg to trillion cells. The biological and biomedical impact of such a success could be of a magnitude similar, if not larger than that of the Human Genome Project.
In his TEDxTel-Aviv talk "Uncovering The Human Cell Lineage Tree — The next grand scientific challenge" [7] Prof.
Shapiro described the system and results obtained with it so far, and a proposal for a FET Flagship project "Human Cell Lineage Flagship initiative" [8] for uncovering the Human cell lineage tree in health and disease.
The philosopher of science Karl Popper suggested that all scientific theories are by nature conjectures and inherently fallible, and that refutation to old theory is the paramount process of scientific discovery. Dana Angluin attempted to provide an algorithmic interpretation to Karl Popper's approach to scientific discovery — in particular for automating the "Conjectures and Refutations" method — making bold conjectures and then performing experiments that seek to refute them.
Shapiro generalized this into the "Contradiction Backtracing Algorithm" — an algorithm for backtracking contradictions. This algorithm is applicable whenever a contradiction occurs between some conjectured theory and the facts.
By testing a finite number of ground atoms for their truth in the model the algorithm can trace back a source for this contradiction, namely a false hypothesis, acm algorithmic debugging dissertation distinguished program, and can demonstrate its falsity by constructing a counterexample to it.
The "Contradiction Backtracing Algorithm" is relevant both to the philosophical discussion on the refutability of scientific theories and in the aid for the debugging of logic programs, acm algorithmic debugging dissertation distinguished program. Shapiro laid the theoretical foundation for inductive logic programming and built its first implementation Model Inference System : a Prolog program that inductively inferred logic programs from positive and negative examples.
Inductive logic programming has nowadays bloomed as a subfield of artificial intelligence and machine learning which uses logic programming as a uniform representation for examples, background knowledge and acm algorithmic debugging dissertation distinguished program. Recent work in this area, combining logic programming, learning and probability, has given rise to the new field of statistical relational learning.
Program debugging is an unavoidable part of software development. Until the s the craft of program debugging, practiced by every programmer, was without any theoretical foundation. In general, a bug occurs when a programmer has a specific intention regarding what the program should do, yet the program actually written exhibits a different behavior than intended in a particular case.
One way of organizing the debugging process is to automate it at least partially via an algorithmic debugging technique. Algorithmic debugging was first developed by Ehud Shapiro during his PhD research at Yale University, as introduced in his PhD thesis, [12] selected as a ACM Distinguished Dissertation.
Shapiro implemented the method of algorithmic debugging in Prolog [13] a general purpose logic programming language for the debugging of logic programs.
In case of logic programsthe intended behavior of the program is a model a set of simple true statements and bugs are manifested as program incompleteness inability to prove a true statement or incorrectness ability to prove a false statement. The algorithm would identify a false statement in the program and provide a counter-example to it or a missing true statement that it or its generalization should be added to the program.
A method to handle non-termination was also developed. It aimed to create an "epoch-making computer" with-supercomputer-like performance and to provide a platform for future developments in artificial intelligence.
Induring a visit to the ICOT, Ehud Shapiro invented Concurrent Prologa novel concurrent programming language that integrated logic programming and concurrent programming. Concurrent Prolog is a acm algorithmic debugging dissertation distinguished program programming language designed for concurrent programming and parallel execution.
It is a process oriented languagewhich embodies dataflow synchronization and guarded-command indeterminacy as its basic control mechanisms. Shapiro described the language in a Report marked as ICOT Technical Report[14] which presented a Concurrent Prolog interpreter written in Prolog. Shapiro's work on Concurrent Prolog inspired a change in the direction of the FGCS from focusing on parallel implementation of Prolog to the focus on concurrent logic programming as the software foundation for the project.
It also inspired the concurrent logic programming language Guarded Horn Clauses GHC by Ueda, which was the basis of KL1, the programming language that was finally designed and implemented by the FGCS project as its core programming language. Shapiro took a leave of absence from the Weizmann Institute to found and serve as CEO of Ubique Ltd. Ubique was a software company that developed instant messaging and collaboration products. The company's first product, Virtual Places 1.
These ideas and technologies — integrated into one product — were novel and revolutionary and perhaps ahead of their time. Ubique, was sold to America Online inbought back by its management in acm algorithmic debugging dissertation distinguished program, and sold again to IBM in In the beginning of the 21st century, scientific progress has successfully managed to consolidate knowledge of the 'sequence' and 'structure' branches of molecular cell biology in an accessible manner.
For example, the DNA-as-string abstraction captured the primary sequence of nucleotides without including higher and lower-order biochemical properties. This abstraction allows the application of a battery of string algorithmsas well as enabling the practical development of databases and common repositories.
As molecular circuits are the information processing devices of cells and organisms, they have been the subject of research of biologists for many decades, acm algorithmic debugging dissertation distinguished program.
Prior to the advent of computational biology tools, biologists were unable to have access to large amounts of data and their analyses. The mountains of knowledge about the function, acm algorithmic debugging dissertation distinguished program, activity and interaction of molecular systems in cells remained fragmented.
Moreover, these past studies that have identified and connected a few components or interactions one at a time, acm algorithmic debugging dissertation distinguished program, required decades of serial work.
In a seminal paper published in in Nature magazine "Cellular abstractions: Cells as computation" [15] Prof. He believed that computer science could provide the much-needed abstraction for biomolecular systems. Together with his Ph. He developed Abstract computer languages for the specification and study of systems of interacting computations, in order to represent biomolecular systems, including regulatory, metabolic and signalling pathways, as well as multicellular processes such as immune responses.
The groundbreaking work that initially used the π-calculusa process calculus was later taken over by IBM Cambridge in the UK Luca Cardelli that developed SPiM Stochastic Pi Calculus Machine.
In the last decade the field has acm algorithmic debugging dissertation distinguished program with a vast variety of applications. More recently, acm algorithmic debugging dissertation distinguished program field even evolved to a synthesis of two different fields — molecular computing and molecular programming.
By combining computer science and molecular biology, researchers have been able to work on a programmable biological computer that in the future may navigate within the human body, diagnosing diseases and administering treatments.
This is what Professor Ehud Shapiro from the Weizmann Institute termed a "Doctor in a cell". His group designed a tiny computer made entirely of biological molecules which was successfully programmed — in a test tube — to identify molecular changes in the body that indicate the presence of certain cancers. For this work was a member of the "Scientific American 50" [18] as Research Leader in Nanotechnology.
InShapiro and PhD student Tom Ran presented the prototype of an autonomous programmable molecular system, based on the manipulation of DNA strandswhich is capable acm algorithmic debugging dissertation distinguished program performing simple logical deductions.
Introduced into the body, this system has immense potential to accurately target specific cell types and administer the appropriate treatment, as it can perform millions of calculations at the same time and 'think' logically.
The biomolecular computers are extremely small: three trillion computers can fit into a single drop of water. If the computers were given the rule 'All men are mortal and the fact 'Socrates is a man', they would answer 'Socrates is mortal'. Multiple rules and facts were tested by the team and the biomolecular computers answered them correctly each time. The team has also found a way to make these microscopic computing devices ' user-friendly ' by creating a compiler — a program for bridging between a high-level computer programming language and DNA computing code.
Ehud Shapiro and Dr. Tom Ran have succeeded in creating a genetic device that operates independently in bacterial cells. The device searches for transcription factors — proteins that control the expression of genes in the cell.
A malfunction of these molecules can disrupt gene expression. In cancer cellsfor example, the transcription factors regulating cell growth and division do not function properly, leading to increased cell division and the formation of a tumor. The device, composed of a DNA sequence inserted into a bacteriumperforms a "roll call" of transcription factors. If the results match pre-programmed parameters, it responds by creating a protein that emits a green light — supplying a visible sign of a "positive" diagnosis.
In follow-up research, acm algorithmic debugging dissertation distinguished program, the scientists plan to replace the light-emitting protein with one that will affect the cell's fate, acm algorithmic debugging dissertation distinguished program, for example, a protein that can cause the cell to commit suicide.
In this manner, the device will cause only "positively" diagnosed cells to self-destruct. Following the success of the study in bacterial cells, the researchers are planning to test ways of recruiting such bacteria as an efficient system to be conveniently inserted into the human body for medical purposes which shouldn't be problematic given our natural microbiome ; recent research reveals there are already 10 times more bacterial cells in the human body than human cells, that share our body space in a symbiotic fashion.
Yet another research goal is to operate a similar system inside human cells, which are much more complex than bacteria. Shapiro designed an effective method of synthesizing error-free DNA molecules from error-prone building blocks.
The basic computer programming cycle is to modify an existing program, test the modified program, and iterate until the desired behavior is obtained. Similarly, the DNA programming cycle is to modify a DNA molecule, test its resulting behavior, and iterate until the goal which is either understanding the behavior or improving it is achieved.
One key difference between the two is that unlike computer programming, our understanding of DNA as programming language is very far from being perfect, and therefore trial and error are the norm rather than the exception in DNA-based research and development. Hence DNA programming is more efficient if multiple variants of a DNA program, also called a DNA library, are created and tested in parallel, rather than creating and testing just one program at a time. Hence the basic DNA programming cycle, when operating in full steam, takes the best DNA programs from the previous cycle, uses them as a basis for creating a new set of DNA programs, tests them, and iterates until the goal is achieved.
Furthermore, Polymerase Chain Reaction PCR is the DNA-equivalent of Gutenberg's movable type printing, both allowing large-scale replication of a piece of text. De novo DNA synthesis is the DNA-equivalent of mechanical typesetting; both ease the setting of text for replication. What is the DNA-equivalent of the word processor? Word processing was rapidly adopted as a replacement for the typewriter when users had discovered its revolutionary advantages in document creation, editing, formatting and saving.
UMLAUT: Debugging Deep Learning Programs using Program Structure and Model Behavior
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