Giuseppe Lancia


 
DIMI, Università di Udine
Via delle Scienze 206
33100, Udine, Italia
tel: + 39-0432-55 84 54
fax: + 39-0432-55 84 99
e-mail: lancia@dimi.uniud.it
url: http://www.dimi.uniud.it/lancia



Notizie generali


 



Curriculum Studi


Elenco pubblicazioni

Le pubblicazioni di Giuseppe Lancia sono apparse/accettate sulle seguenti riviste: INFORMS Journal on Computing, Networks, SIAM Journal on Computing, European Journal of Operational Research, Journal of Combinatorial Optimization, Discrete Applied Mathematics, Operations Research Letters, Annals of OR, 4OR, Theoretical Computer Science, Journal of Computer Science and Technology, Computers and Mathematics with Applications, International Journal Of Foundations of Computer Science, IEEE/ACM Transactions on Bioinformatics and Computational Biology, Journal of Computational Biology, Briefings in Bioinformatics, American Journal on Human Genetics, Algorithms for Molecular Biology. Inoltre alcune pubblicazioni sono apparse nei proceedings di conferenze molto selettive quali ACM-SIAM Symposium on Discrete Algorithms (SODA) e ACM REsearch in COMputational Biology (RECOMB) la cui soglia di accettazione è inferiore a un lavoro ogni 4. Altre conferenze con proceedings includono European Symposium on Algorithms (ESA) e Combinatorial Pattern Matching (CPM). Infine ha contribuito con capitoli in volumi quali Springer's Encyclopedia of Algorithms, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Springer's Series in Operations Research and Management Science, Kluwer's Series in Computational Biology e Lecture Notes in Bioinformatics (C.I.M.E. Lecture Notes).


Problemi di Schedulazione

Nell'ambito del noto problema del Job Shop, si è studiata la generalizzazione al caso di deadlines e forbidden times ([I3, A7]) per il minimo makespan e un modello di programmazione intera con generazione colonne per il minimo tempo medio di completamento ([A10]). In ([A5]) si è proposto un metodo efficiente di enumerazione per la soluzione del problema di schedulazione periodica. Infine, in ([I6]) si descrive un branch-and-bound per il problema di min makespan su due macchine parallele indipendenti.

Network Design

Dato un grafo pesato, il routing cost di un albero di supporto è la somma delle lunghezze dei cammini fra ogni coppia di nodi. In ([I5, C2]) viene descritto un Polynomial Time Approximation Scheme per tale problema e in [A9] si illustra un'applicazione all'allineamento di sequenze genomiche. . La soluzione esatta del problema, per via poliedrale, viene studiata in ([A8],[I8]).

Programmazione Matematica

In  ([I9, R6]) viene proposto un metodo per la formulazione compatta di alcuni modelli con un numero esponenziale di vincoli/variabili, di cui un'applicazione e' descritta in [I16,A14]. In ([A12])  viene descritto un metodo automatico per trasformare disuguaglianze valide per l'ATSP in disuguaglianze valide per il STSP. In ([A24])  introduciamo una nuova classe di disuguaglianze generali per modelli ILP che possono essere usate per velocizzare l'esplorazione di un albero di ricerca branch-and-bound.

Applicazioni della Ricerca Operativa in Biologia Molecolare Computazionale

Le applicazioni della Ricerca Operativa alla Biologia Molecolare sono riassunte in [V4], nonche' oggetto di ricerca in [I12,I14]. Tra esse, le seguenti. Sono stati utilizzati metodi tipici dell'ottimizzazione combinatoria per risolvere problemi di analisi dati in biologia molecolare. In particolare, metodi branch-and-price e statistici per il calcolo di distanze evolutive fra genomi ([V2, V1, I7, C4, R4, R2, A6]), metodi euristici e basati su LP Randomized Rounding per l'allineamento di biosequenze ([C3, C1]), branch-and-bound per problema del genotyping ([I4, I2, I1, R3]), branch-and-cut per l'allineamento di strutture proteiche tridimensionali ([C7, R5, A11]) e un approccio Lagrangiano per lo stesso ([C8, C9]). Su tale area un survey e' apparso in [V3]. Sono stati sviluppati algoritmi polinomiali per casi speciali del problema di Haplotyping ([I17, C6, I10, I15, C10, A13, R7]).

Applicazioni della Ricerca Operativa in Chimica Molecolare

In ([C5]) è stata studiata la complessità computazionale di alcuni problemi di costruzione di grafi con determinate proprietà topologiche. Ad esempio grafi in cui la somma delle lunghezze dei cammini minimi (Wiener Index) ha un determinato valore. Quando i nodi rappresentano atomi e gli archi legami chimici si hanno applicazioni in chimica combinatorica.
 


 

CITAZIONI (Dati aggiornati ad agosto 2008:) L'articolo piu' citato (fonte Google Scholar) e' [I5] con 111 citazioni. Seguono [I11] con 87 citazioni e [I2] con 73 citazioni. Il mio h-index e' 16 (almeno 16 lavori hanno almeno 16 citazioni ciascuno - fonte Google Scholar).



 

Pubblicazioni su riviste internazionali [I]

[I28] G. Lancia and P. Serafini, ``An effective compact formulation of the max cut problem on sparse graphs'', Electronic Notes in Discrete Mathematics, 37, 111-116, 2011.

[I27] G. Lancia, F. Rinaldi and P. Serafini, ``A time-indexed LP-based approach for min-sum job-shop problems'', Annals of Operations Research, 186, 175--198, 2011.

[I26] L. Tininini, P. Bertolazzi, A. Godi, and G. Lancia, ``CollHaps: a heuristic approach to haplotype inference by parsimony'', IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(3), 511-523, 2010.

[I25] G. Lancia, and P. Serafini, ``A set covering approach with column generation for parsimony haplotyping'', INFORMS Journal on Computing, 21(1), 151-166, 2009.

[I24] G. Lancia, ``Mathematical Programming in Computational Biology: an annotated bibliography'', Algorithms, 1(2), 100-129, 2008.

[I23] G. Lancia, F. Rinaldi and R. Rizzi, ``Flipping letters to minimize the support of a string'', International Journal of Foundations of Computer Science, 19(1), 5-17, 2008.

[I22] G. Lancia, R. Ravi and R. Rizzi, ``Haplotyping for disease association: a combinatorial approach'', IEEE/ACM Transactions on Bioinformatics and Computational Biology, 5(2), 245-251, 2008.

[I21] G. Lancia and R. Rizzi, ``The Approximability of the String Barcoding Problem'', Algorithms for Molecular Biology, 1:12, 2006.

[I20] P. Bertolazzi, P. Festa, G. Felici and G. Lancia, ``Logic Classification and Feature Selection for Biomedical Data'', Computers and Mathematics with Applications, 55(5), 889-899, 2008.

[I19] G. Lancia, ``The phasing of heterozygous traits: algorithms and complexity'', Computers and Mathematics with Applications, 55(5), 960-969, 2008.

[I18] G. Lancia and R. Rizzi, ``A polynomial case of the parsimony haplotyping problem'', Operations Research Letters, 34(3), 289-295, 2006.

[I17] V. Bafna, S. Istrail, G. Lancia, and R. Rizzi, ``Polynomial and APX-hard Cases of the Individual Haplotyping Problem'', Theoretical Computer Science, 335(1):109-125, 2005.

[I16] R. D. Carr and G. Lancia, ``Compact optimization can outperform separation: A case study in structural proteomics'', 4OR, 2(3):221-233, 2005.

[I15] G. Lancia, M. C. Pinotti and R. Rizzi, ``Haplotyping Populations by Pure Parsimony. Complexity, Exact and Approximation Algorithms'', INFORMS Journal on Computing, 16(4):348-359, 2004.

[I14] H. Greenberg, W. Hart, G. Lancia, ``Opportunities for Combinatorial Optimization in Computational Biology'', INFORMS Journal on Computing, 16(3):211-231, 2004.

[I13] A. Caprara, G. Lancia, B. Carr, B. Walenz and S. Istrail, ``1001 optimal PDB structure alignments: Integer Programming methods for finding the maximum contact map overlap'', Journal of Computational Biology, 11(1):27-52, 2004.

[I12] G. Lancia, ``Integer Programming Models for Computational Biology Problems'', Journal of Computer Science and Technology, 19(1):60-77, 2004.

[I11] V. Bafna, D. Gusfield, G. Lancia and S. Yooseph, ``Haplotyping as Perfect Phylogeny: A Direct Approach'', Journal of Computational Biology, 10(3-4):323-340, 2003.

[I10] R. Lippert, R. Schwartz, G. Lancia and S. Istrail, ``Algorithmic Strategies for the SNPs Haplotype Assembly Problem'', Briefings in Bioinformatics, 3(1):23-31, 2002.

[I9] R. D. Carr and G. Lancia, ``Compact vs Exponential-Size LP Relaxations'', Operations Research Letters, 30(1):57-65, 2002

[I8] M. Fischetti, G. Lancia and P. Serafini, ``Exact Algorithms for Minimum Routing Cost Trees'', Networks, 39(3):161-173, 2002.

[I7] A. Caprara, G. Lancia, S.K. Ng, ``Sorting Permutations by Reversals through Branch-and-Price'', (ps file), INFORMS Journal on Computing, 13(3):224-244, 2001.

[I6] G. Lancia, ``Scheduling Jobs with Release Dates and Tails on Two Unrelated Parallel Machines to Minimize the Makespan'', (ps file), European Journal of Operational Research, 120(2):55-66, 2000.

[I5] B.Y. Wu, G. Lancia, V. Bafna, K. M. Chao, R. Ravi and C. Y. Tang, ``A Polynomial-time Approximation Scheme for the Minimum Routing Cost Tree Problem'', SIAM Journal on Computing, 29(3):761-778, 1999.

[I4] G. Lancia and M. Perlin, ``Genotyping of Pooled Microsatellite Markers by Combinatorial Optimization Techniques'' (ps file) Discrete Applied Mathematics, 88(1-3):291-314, 1998

[I3] E. Balas, G. Lancia, P. Serafini and A. Vazacopoulos, ``Job Shop Scheduling with Deadlines'' (ps file), Journal of Combinatorial Optimization, 1(4):329-353, 1998

[I2] M. Perlin, G. Lancia and S.K. Ng, ``Toward Fully Automated Genotyping: Genotyping Microsatellite Markers by Deconvolution'' (PubMed abstract), American Journal of Human Genetics, 57(5):1199-1210, 1995

[I1] S. K. Ng, G. Lancia, and M. W. Perlin, ``Fully automated genotyping of microsatellite markers by deconvolution (GMBD)'', American Journal of Human Genetics, 57(4 Supplement): A198, 1995.

Capitoli in volumi con valutazione a diffusione internazionale [V]

[V8] F. Vezzi, G. Lancia and A. Policriti, "Algorithms and Data Structures for Next Generation Sequences'', in Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, (M. Elloumi and Y. Zomaya eds.), Wiley-Blackwell, (to appear), 2012.

[V7] P. Bertolazzi, G. Felici and G. Lancia, ``Application of Feature Selection and Classification to Computational Molecular Biology'', in Biological Data Mining, Chapman \& Hall/CRC Press, 257-293, 2009.

[V6] G. Lancia, ``Perfect Phylogeny Haplotyping'', in Encyclopedia of Algorithms, (Ming-Yang Kao ed.), Springer, 646-650, 2008 (ISBN: 978-0-387-30770-1)

[V5] G. Lancia, ``Mathematical Programming Approaches for Computational Biology Problems'', in Modelli e Algoritmi per l'Ottimizzazione di Sistemi Complessi - Atti della Scuola CIRO 2002, (A. Agnetis and G. Di Pillo eds), 265-310, 2003

[V4] G. Lancia, ``Applications to Computational Molecular Biology'', in ``Handbook on Modeling for Discrete Optimization'', Springer International Series in Operations Research and Management Science, (G. Appa, P. Williams, P. Leonidas and H. Paul eds), Vol. 88, 2006

[V3] G. Lancia and S. Istrail, ``Protein Structure Comparison: Algorithms and Applications'', (ps file) in "Mathematical Methods for Protein Structure Analysis and Design", (C. Guerra and S. Istrail eds), Lecture Notes in Bioinformatics, 2666:1-33, Springer, 2003

[V2] A. Caprara and G. Lancia, ``Experimental and Statistical Analysis of Sorting by Reversals'', (ps file) in "Comparative Genomics: Empirical and Analyitical Approaches to Gene Order Dynamics, Map Alignment and Evolution of Gene Families", (D. Sankoff and J. H. Nadeau eds), Kluwer Series in Computational Biology, 1:171-183, 2000

[V1] A. Caprara, G. Lancia and S. K. Ng, ``A branch-and-bound Algorithm for Sorting By Reversals'' (ps file) in "Mathematical Support for Molecular Biology", (M. Farach, S. Roberts, M. Vingron and M. Waterman eds), DIMACS series in Discrete Mathematics and Theoretical Computer Science, The American Mathematical Society, 47:213-226, 1999

Convegni internazionali con valutazione (quelli estremamente selettivi sono evidenziati con (*) ) [C]

[C15] G. Lancia, R. Rizzi and R. Schwartz, ``Tiling binary matrices in haplotyping: Complexity, algorithms and models'', in Proceedings of The Prague Stringology Conference, PSC10, 22-31, 2010

[C14] G. Lancia, P. Serafini and F. Rinaldi, ``A compact optimization approach for job-shop problems'', in Multidisciplinary Internbational Scheduling conference: Theory and Application (MISTA07), 293--300, 2007

[C13] G. Lancia, F. Rinaldi and R. Rizzi, ``Flipping letters to minimize the support of a string'', in The Prague Stringology Conference, PSC06, Lecture Notes in Computer Science, 2006

[C12] M. Dalpasso, G. Lancia and R. Rizzi, ``The String Barcoding Problem is NP-Hard'', in RECOMB Satellite on Comparative Genomics, (A. Mc Lyshag and D. Huson eds), Lecture Notes in Bioinformatics, Springer, 85--93, 2005

[C11] G. Lancia, ``Combinatorial optimization problems in the study of human diversities'', 9th International Conference on Operational Research (KOI), ISBN 953-6931-08-7, 35-36, Grafika ed., 2002.

(*) [C10] R. Rizzi, V. Bafna, S. Istrail, and G. Lancia, ``Practical Algorithms and Fixed-parameter Tractability of the Single Individual SNP Haplotyping Problem'', 2nd Workshop on Algorithms in Bioinformatics (WABI), Lecture Notes in Computer Science, 2452:29-43, Springer, 2002 (33 lavori accettati / 89 sottomessi).

[C9] A. Caprara and G. Lancia, ``Optimal and Near-Optimal solutions for 3D Structure Comparisons'', 1st IEEE Conference on 3D Data Processing, Visualization and Transmision (3DPVT), 737-744, IEEE press, 2002.

(*) [C8] A. Caprara and G. Lancia, ``Structural Alignment of Large-Size Proteins via Lagrangian Relaxation'', 6th ACM Conference on Computational Molecular Biology (RECOMB), 100-109, ACM press, 2002 (35 lavori accettati / 118 sottomessi).

(*) [C7] G. Lancia, B. Carr, B. Walenz and S. Istrail, ``101 Optimal PDB Structure Alignments: A Branch-and-Cut Algorithm for the Maximum Contact Map Overlap Problem'', 5th ACM Conference on Computational Molecular Biology (RECOMB), 193-202, ACM press, 2001 (35 lavori accettati / 128 sottomessi).

(*) [C6] G. Lancia, V. Bafna, S. Istrail, R. Lippert and R. Schwartz, ``SNPs Problems, Algorithms and Complexity'', European Symposium on Algorithms (ESA), (ps file) Lecture Notes in Computer Science, 2161:182-193, Springer-Verlag eds., 2001 (41 lavori accettati / 102 sottomessi).

(*) [C5] D. Goldman, S. Istrail, G. Lancia, A. Piccolboni, and B. Walentz, ``Algorithmic Strategies in Combinatorial Chemistry'' (ps file), XI ACM-SIAM Symposium On Discrete Algorithms (SODA), 275-284, 2000 (123 lavori accettati / 335 sottomessi).

(*) [C4] A. Caprara, G. Lancia and S. K. Ng, ``Fast Practical Solution of Sorting by Reversals'' (ps file), XI ACM-SIAM Symposium On Discrete Algorithms (SODA), 12-21, 2000 (123 lavori accettati / 335 sottomessi).

[C3] G. Lancia and R. Ravi, ``GESTALT: GEnomic STeiner ALigmenTs'' (ps file) Combinatorial Pattern Matching (CPM), Lecture Notes in Computer Science, 1645:101-114, Springer-Verlag eds., 1999 (19 lavori accettati / 26 sottomessi).

(*) [C2] B.Y. Wu, G. Lancia, V. Bafna, K. M. Chao, R. Ravi and C. Y. Tang, ``A PTAS for the Minimum Routing Cost Tree Problem'' (ps file), IX ACM-SIAM Symposium On Discrete Algorithms (SODA), 21-32, 1998 (78 lavori accettati / 238 sottomessi).

[C1] A. Ben Dor, G. Lancia, J. Perone and R. Ravi, ``Banishing Bias from Consensus Sequences'' (ps file) Combinatorial Pattern Matching (CPM), Lecture Notes in Computer Science, 1264:247-261, Springer-Verlag eds, 1997 (21 lavori accettati / 32 sottomessi).

Rapporti tecnici [R]

[R7] V. Bafna, D. Gusfield, G. Lancia and S. Yooseph, ``Haplotyping as Perfect Phylogeny: a Direct Approach'',  (ps file)  Technical Report CSE-2002-21, UC Davis, 2002

[R6] R. Carr and G. Lancia, ``Compact vs Exponential-size LP Relaxations'',  (online pdf)  Technical Report SAND2000-2170, Sandia National Labs, Albuquerque, 2000

[R5] R. Carr, G. Lancia and S. Istrail, ``Branch-and Cut Algorithms for Independent Set Problems: Integrality Gap and an Application to Protein Structure Alignment'',  (online pdf) Technical Report SAND2000-2171, Sandia National Labs, Albuquerque, 2000

[R4] A. Caprara, G. Lancia, S.K. Ng, ``Sorting Permutations by Reversals through Branch-and-Price'', (ps file) Research Report OR/99/1 DEIS, Università di Bologna, 1999

[R3] G. Lancia and M. Perlin, ``Genotyping of Pooled Microsatellite Markers by Combinatorial Optimization Techniques'', WP 1995-30 G.S.I.A., Carnegie Mellon University, 1995

[R2] A. Caprara, G. Lancia, S.K. Ng, ``A Column-Generation based Branch-and-Bound Algorithm for Sorting by Reversals'', Research Report OR/95/7 DEIS, Università di Bologna, 1995

[R1] G. Lancia, ``The 2-Machine Loading-Scheduling Problem'', WP1992-27 G.S.I.A., Carnegie-Mellon University, 1992

Altri lavori scientifici [A]

[A25] G. Lancia, F. Rinaldi and P. Serafini, ``Local Search Inequalities'', AIRO2008, Ischia, 2008.

[A24] P. Bertolazzi, G. Felici and G. Lancia, ``Barcode analysis with optimized logic formulas'', AIRO2007, Genova, 2007.

[A23] G. Lancia, F. Rinaldi and P. Serafini, ``A compact optimization approach for job-shop problems'', AIRO2007, Genova, 2007.

[A22] P. Bertolazzi, A. Godi, G. Lancia, and L. Tininini, ``CollHaps: a heuristic approach to haplotype inference by parsimony'', EURO XXII, Praga, CZ, 2007.

[A21] G. Lancia, P. Serafini, ``A branch-and-price-and-cut approach to the parsimony haplotyping problem'', AIRO2006, Cesena, 2006.

[A20] G. Lancia, ``The phasing of heterozygous traits: algorithms and complexity'', 1st FIMA Intl conference, Champoluc, 2006.

[A19] P. Bertolazzi, C. Gentili and G. Lancia, ``Feature Selection and Logic Classification to identify Thrombin-binding Compounds'', 1st FIMA Intl conference, Champoluc, 2006.

[A18] L. Tininini, P. Bertolazzi, A. Godi, G. Lancia, ``CollHaps: Haplotype Inference by Collapse Rules'', Poster Session, RECOMB, Venezia, 2006.

[A17] G. Lancia, R. Rizzi, ``Combinatorial Problems Arising in the Analysis of Human Polymorphisms'', AIRO2005, Camerino, 2005.

[A16] G. Lancia, ``Optimization Problems in Polymorphism Analysis'', INFORMS Annual Meeting, Denver, USA, 2004.

[A15] G. Lancia, F. Rinaldi, R. Rizzi, ``Reducing the k-mer diversity of a string'', AIRO2004, Lecce, 2004.

[A14,5] R. Carr, G. Lancia, S. Istrail, A. Johnston, B.Walenz, "Innovative Branching Strategies with Applications to Computational Biology'', INROMS Annual Meeting, Hawaii, USA, 2001.

[A14] B. Carr, G. Lancia, ``A successful application of Compact Optimization: the Protein Folding Comparison problem'', Proc. of XVI A.I.R.O. Annual Conference, 134, CUEC ed., 2001

[A13] G. Lancia, ``Easy and Hard Cases of SNP Haplotyping Problems'', The European Operational Research conference, EURO2001, Rotterdam, 2001

[A12] E. Balas, R. Carr, and G. Lancia, ``On the Connections Between the Symmetric and Asymmetric Traveling Salesman Problems'', Working Paper, Sandia Natl. Labs, 2000

[A11] B. Carr, G. Lancia and S. Istrail, ``The Maximum Independent Set Problem with Applications to Protein Structure Alignment'', International Symposium on Mathematical Programming, Atlanta, USA, 2000

[A10] G. Lancia, F. Rinaldi and P. Serafini, ``A Column Generation Approach to Solve Job Shop Problems'', XV Triennial IFORS Conference, Pechino, Cina, 1999

[A9] B.Y. Wu, G. Lancia, V. Bafna, K. M. Chao, R. Ravi and C. Y. Tang, ``Minimum Routing Cost Spanning Trees and Multiple Sequence Alignments'', IX SIAM Conference on Discrete Mathematics, Toronto, Canada, 1998.

[A8] G. Lancia and P. Serafini, ``A branch-and-price algorithm for minimum routing cost trees'', IX SIAM Conference on Discrete Mathematics, Toronto, Canada, 1998.

[A7] E. Balas, G. Lancia, P. Serafini and A. Vazacopoulos, ``Job Shop Scheduling with Deadlines'', AIRO97, St. Vincent e ISMP97, Losanna, 1997

[A6] A. Caprara, G. Lancia and S. K. Ng, ``A column-generation based branch-and-price Algorithm for Sorting By Reversals'', ISMP97, Losanna, Svizzera, 1997

[A5] G. Lancia, F. Rinaldi, P. Serafini, ``Improving Algorithms for Periodic Scheduling'', in Workshop on Models and Algorithms for Planning and Scheduling Problems, Cambridge, 1997

[A4] G. Lancia, ``Combinatorial Problems in Computational Molecular Biology'', (ps file) PhD thesis, Graduate School of Industrial Administration, Carnegie Mellon University, 1997

[A3] E. Balas, G. Lancia, P. Serafini and A. Vazacopoulos, ``Scheduling with Deadlines and Forbidden Times'', INFORMS96, Washington DC, 1996

[A2] G. Lancia, ``Biologia Computazionale: Problemi Combinatoriali in Biologia Molecolare'', AIRO news, n.2, 1996 (link)

[A1] G. Lancia, ``Combinatorial and Network-Flow Algorithms for Project Scheduling Problems'', Tesi di Laurea, Università di Udine, 1990

Dispense Didattiche  [D]

[D3] G. Lancia, `'Matematica Discreta'', Corso di Matematica Discreta per Biotecnologie, Udine, 2003

[D2] G. Lancia, `'Appunti di teoria della complessita' computazionale'',  (ps file) Corso di Ricerca Operativa, Padova, 2001

[D1] G. Lancia, `'Programmazione Lineare Intera'',  (ps file) Corso di Ricerca Operativa, Padova, 1997
 
 


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