William J Ladd

US Patent:

7805437, Sep 28, 2010

Filed:

May 15, 2003

Appl. No.:

10/439411

Inventors:

Tomas Åke Andersson - Göteborg, SE
Leif Fredrik Blom - Frillesås, SE
William M. Ladd - Cambridge MA, US

Assignee:

Spotfire AB - Göteborg

International Classification:

G06F 7/00
G06F 17/30

US Classification:

707722, 707754, 707758, 707769, 703 12

Abstract:

Source data is analyzed and visualized for a user. As the user adjusts graphical query devices, the displayed data is filtered and the visualization is updated accordingly. The invention is particularly useful where the data relates to chemical compounds in that a SAR table is preferably generated, presented in the visualization, and updated according to the query device settings. The displayed SAR table entries may also be clustered as a function of similarity with respect to a chosen property, such as molecular weight or some topological characteristic. A hierarchy of similarity may then be indicated in the SAR table using, for example, a dendrogram.

US Patent:

8082109, Dec 20, 2011

Filed:

Aug 28, 2008

Appl. No.:

12/200568

Inventors:

William M. Ladd - Cambridge MA, US
Keith O. Elliston - Sudbury MA, US
Joseph J. Loureiro - Arlington MA, US

Assignee:

Selventa, Inc. - Cambridge MA

International Classification:

G01N 33/48

US Classification:

702 19, 435 6, 436131, 436501, 514789

Abstract:

The invention relates to computational methods, systems and apparatus useful in the analysis of sets of biomolecules in an accessible body fluid or tissue sample from a patient, which biomolecules collectively or individually are candidates to serve as biomarkers, i. e. , biomolecules which together or individually upon detection or change are indicative that the patient is in some biological state, such as a diseased state. The methods permit one to examine such potential biological markers to determine whether each one is indeed present as a consequence of the biological state, or as an artifact of the biomarker search protocol.

US Patent:

8417661, Apr 9, 2013

Filed:

May 4, 2012

Appl. No.:

13/464104

Inventors:

Ty Matthew Thomson - Arlington MA, US
Dexter Roydon Pratt - Reading MA, US
William M. Ladd - Cambridge MA, US

Assignee:

Selventa, Inc. - Cambridge MA

International Classification:

G06F 9/44
G06N 7/02
G06N 7/06

US Classification:

706 52

Abstract:

One or more measurement signatures are derived from a knowledge base of casual biological facts, where a signature is a collection of measured node entities and their expected directions of change with respect to a reference node. The knowledge base may be a directed network of experimentally-observed casual relationships among biological entities and processes, and a reference node represents a perturbation. A degree of activation of a signature is then assessed by scoring one or more “differential” data sets against the signature to compute an amplitude score. The amplitude score quantifies fold-changes of measurements in the signature. In one particular embodiment, the amplitude score is a weighted average of adjusted log-fold changes of measured node entities in the signature, wherein an adjustment applied to the log-fold changes is based on their expected direction of change. In an alternative embodiment, the amplitude score is based on quantity effects.

US Patent:

20070225956, Sep 27, 2007

Filed:

Mar 27, 2006

Appl. No.:

11/390496

Inventors:

Dexter Roydon Pratt - Reading MA, US
William McClure Ladd - Cambridge MA, US
Suresh Toby Segaran - Somerville MA, US
Jack Pollard - Somerville MA, US

International Classification:

G06G 7/48

US Classification:

703 11

Abstract:

Disclosed are software assisted systems and methods for analyzing biological data sets to generate hypotheses potentially explanatory of the data. Active causative relationships in the biology of complex living systems are discovered by providing a data base of biological assertions comprising a multiplicity of nodes representative of a network of biological entities, actions, functional activities, and concepts, and relationship links between the nodes. Simulating perturbation of individual root nodes in the network initiates a cascade of virtual activity through the relationship links to discern plural branching paths within the data base. Operational data, e.g., experimental data, representative of a real or hypothetical perturbations of one or more nodes are mapped onto the data base. The branching paths then are prioritized as hypotheses on the basis of how well they predict the operational data. Logic based criteria are applied to the graphs to reject graphs as not likely representative of real biology. The result is a set of remaining graphs comprising branching paths potentially explanatory of the molecular biology implied by the data.

US Patent:

20090099784, Apr 16, 2009

Filed:

Sep 25, 2008

Appl. No.:

12/237566

Inventors:

William M. Ladd - Cambridge MA, US
Keith O. Elliston - Sudbury MA, US

International Classification:

G06F 19/00

US Classification:

702 19

Abstract:

The present invention relates to computational methods, systems and apparatus useful in the identification of similarities and/or differences between a plurality of biological states, such as altered biological states in an animal (e.g., a mammal or human). Particularly, the invention relates to comparing two or more causal system models (“CSMs”) which each are indicative of a biological state, such as a disease state, a toxic state, or a drug- or therapy-induced state. The present invention also relates to generating a general CSM from a comparison of two or more other CSMs, and subsequently comparing one or more of the other CSMs to the general CSM. Either of these techniques, or a combination of the two techniques, can be used to identify unique and common features in each CSM.

US Patent:

20120030162, Feb 2, 2012

Filed:

May 31, 2011

Appl. No.:

13/149022

Inventors:

Ty Matthew Thomson - Arlington MA, US
Dexter Roydon Pratt - Reading MA, US
William M. Ladd - Cambridge MA, US

Assignee:

SELVENTA, INC. - Cambridge MA

International Classification:

G06N 5/02

US Classification:

706 52

Abstract:

One or more measurement signatures are derived from a knowledge base of casual biological facts, where a signature is a collection of measured node entities and their expected directions of change with respect to a reference node. The knowledge base may be a directed network of experimentally-observed casual relationships among biological entities and processes, and a reference node represents a perturbation. A degree of activation of a signature is then assessed by scoring one or more “differential” data sets against the signature to compute an amplitude score. The amplitude score quantifies fold-changes of measurements in the signature. In one particular embodiment, the amplitude score is a weighted average of adjusted log-fold changes of measured node entities in the signature, wherein an adjustment applied to the log-fold changes is based on their expected direction of change. In an alternative embodiment, the amplitude score is based on quantity effects.

US Patent:

20140297573, Oct 2, 2014

Filed:

Jun 16, 2014

Appl. No.:

14/305536

Inventors:

- Cambridge MA, US
Dexter Roydon Pratt - Reading MA, US
William M. Ladd - Cambridge MA, US

International Classification:

G06N 3/12

US Classification:

706 13

Abstract:

One or more measurement signatures are derived from a knowledge base of casual biological facts, where a signature is a collection of measured node entities and their expected directions of change with respect to a reference node. The knowledge base may be a directed network of experimentally-observed casual relationships among biological entities and processes, and a reference node represents a perturbation. A degree of activation of a signature is then assessed by scoring one or more “differential” data sets against the signature to compute an amplitude score. The amplitude score quantifies fold-changes of measurements in the signature. In one particular embodiment, the amplitude score is a weighted average of adjusted log-fold changes of measured node entities in the signature, wherein an adjustment applied to the log-fold changes is based on their expected direction of change. In an alternative embodiment, the amplitude score is based on quantity effects.