Making Automatic Differentiation Truly Automatic: Coupling PETSc with ADIC

Despite its name, automatic differentiation (AD) is often far from an automatic process. often one must specify independent and dependent variables, indicate the derivative quantities to be computed, and perhaps even provide information about the structure of the Jacobians or Hessians being computed. However, when AD is used in conjunction with a toolkit with well-defined interfaces, many of these issues do not arise. They describe recent research into coupling the ADIC automatic differentiation tool with PETSc, a toolkit for the parallel numerical solution of PDEs. This research leverages the interfaces and objects of PETSc to make the AD process very nearly transparent

Exploiting separability in large-scale linear support vector machine training

Linear support vector machine training can be represented as a large quadratic program. We present an efficient and numerically stable algorithm for this problem using interior point methods, which requires only O(n) operations per iteration. Through exploiting the separability of the Hessian, we provide a unified approach, from an optimization perspective, to 1-norm classification, 2-norm classification, universum classification, ordinal regression and ɛ-insensitive regression. Our approach has the added advantage of obtaining the hyperplane weights and bias directly from the solver. Numerical experiments indicate that, in contrast to existing methods, the algorithm is largely unaffected by noisy data, and they show training times for our implementation are consistent and highly competitive. We discuss the effect of using multiple correctors, and monitoring the angle of the normal to the hyperplane to determine termination

Update on treatment recommendations from the fourth international workshop on Waldenström's macroglobulinemia

Waldenström macroglobulinemia (WM) is a distinct B-cell lymphoproliferative disorder characterized by lymphoplasmacytic bone marrow infiltration along with an immunoglobulin M (lgM) monoclonal gammopathy. Patients with disease-related cytopenias, bulky adenopathy or organomegaly, symptomatic hyperviscosity, severe neuropathy, amyloidosis, cryoglobulinemia, cold agglutinin disease, or evidence of disease transformation should be considered for immediate therapy. Initiation of therapy should not be based on serum lgM levels alone, and asymptomatic patients should be observed. Individual patient considerations should be considered when deciding on a first-line agent including the presence of cytopenias, need for rapid disease control, age, and candidacy for autologous transplantation. Therapeutic outcomes should be evaluated using updated criteria. As part of the Fourth International Workshop on Waldenström's Macroglobulinemia, a consensus panel updated its recommendations on both first-line and salvage therapy in view of recently published and ongoing clinical trials. The panel considered encouraging results from recent studies of first-line combinations such as rituximab with nucleoside analogs with or without alkylating agents or with cyclophosphamide-based therapies (eg, cyclophosphamide, doxorubicin, vincristine, and prednisone or cyclophosphamide and dexamethasone) or the combination of rituximab with thalidomide. Such therapeutic approaches are likely to yield responses at least as good as, if not better than, monotherapy with any of the alkylating agents, nucleoside analogs, or rituximab. In the salvage setting, reuse of a first-line regimen or use of a different regimen should be considered along with bortezomib, alemtuzumab, autologous transplantation, and, in selected circumstances, allogeneic transplantation. Finally, the panel reaffirmed its encouragement of the active enrollment of patients with WM onto innovative clinical trials whenever possible. © 2008 by American Society of Clinical Oncology

Using an iterative linear solver in an interior-point method for generating support vector machines

Machine learning, Support vector machines, Quadratic programming, Interior-point methods, Krylov-space methods, Matrix-free preconditioning,

Response assessment in Waldenström macroglobulinaemia: Update from the VIth International Workshop

This report represents a further update of the consensus panel criteria for the assessment of clinical response in patients with Waldenström macroglobulinaemia (WM). These criteria have been updated in light of further data demonstrating an improvement in categorical responses with new drug regimens as well as acknowledgement of the fact that such responses are predictive of overall outcome. A number of key changes are proposed but challenges do however remain and these include the variability in kinetics of immunoglobulin M (IgM) reduction with different treatment modalities and the apparent discrepancy between IgM and bone marrow/tissue response noted with some regimens. Planned sequential bone marrow assessments are encouraged in clinical trials. © 2012 Blackwell Publishing Ltd