Pairwise Maximum Entropy Models for Studying Large Biological Systems: When They Can Work and When They Can't

Pairwise Maximum Entropy Models for Studying Large Biological Systems: When They Can Work and When They Can't

One of the most critical problems we face in the study of biological systems is building accurate statistical descriptions of them. This problem has been particularly challenging because biological systems typically contain large numbers of interacting elements, which precludes the use of standard brute force approaches. Recently, though, several groups have reported that there may be an altern...

Pbd Systems: When Will They Ever Learn?

We trace the tragicomic courtship between programming by demonstration and machine learning, two fields that seem made for each other but have never quite got together. A long-term historical perspective illuminates the twin roles of interaction and sequence learning in programming by demonstration, and reveals the parallel growth of machine learning as a research area in its own right. A view ...

Local Rules for Global MAP: When Do They Work ?

We consider the question of computing Maximum A Posteriori (MAP) assignmentin an arbitrary pair-wise Markov Random Field (MRF). We present a randomizediterative algorithm based on simple local updates. The algorithm, starting with anarbitrary initial assignment, updates it in each iteration by first, picking a randomnode, then selecting an (appropriately chosen) random local nei...

Formal Methods: The Very Idea Some Thoughts About Why They Work When They Work

The paper de nes formal methods (FMs) and describes economic issues involved in their application. From these considerations and the concepts implicit in \No Silver Bullet", it becomes clear that FMs are best applied during requirements engineering. A explanation of why FMs work when they work is o ered and it is suggested that FMs help the most when the applier is most ignorant about the probl...

When are microcircuits well-modeled by pairwise maximum entropy methods?